Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Deleterious alleles in the context of domestication, inbreeding, and selection
Bosse, Mirte ; Megens, Hendrik-Jan ; Derks, Martijn F.L. ; Cara, Ángeles M.R. de; Groenen, Martien A.M. - \ 2018
Evolutionary Applications (2018). - ISSN 1752-4563
deleterious alleles - domestication - genetic load - inbreeding - selection

Each individual has a certain number of harmful mutations in its genome. These mutations can lower the fitness of the individual carrying them, dependent on their dominance and selection coefficient. Effective population size, selection, and admixture are known to affect the occurrence of such mutations in a population. The relative roles of demography and selection are a key in understanding the process of adaptation. These are factors that are potentially influenced and confounded in domestic animals. Here, we hypothesize that the series of events of bottlenecks, introgression, and strong artificial selection associated with domestication increased mutational load in domestic species. Yet, mutational load is hard to quantify, so there are very few studies available revealing the relevance of evolutionary processes. The precise role of artificial selection, bottlenecks, and introgression in further increasing the load of deleterious variants in animals in breeding and conservation programmes remains unclear. In this paper, we review the effects of domestication and selection on mutational load in domestic species. Moreover, we test some hypotheses on higher mutational load due to domestication and selective sweeps using sequence data from commercial pig and chicken lines. Overall, we argue that domestication by itself is not a prerequisite for genetic erosion, indicating that fitness potential does not need to decline. Rather, mutational load in domestic species can be influenced by many factors, but consistent or strong trends are not yet clear. However, methods emerging from molecular genetics allow discrimination of hypotheses about the determinants of mutational load, such as effective population size, inbreeding, and selection, in domestic systems. These findings make us rethink the effect of our current breeding schemes on fitness of populations.

Data from: Genome-wide SNP data unveils the globalization of domesticated pigs
Yang, Bin ; Cui, Leilei ; Pérez-Enciso, M. ; Traspov, Aleksei ; Crooijmans, R.P.M.A. ; Zinovieva, Natalia ; Schook, Lawrence B. ; Gatphayak, Kesinee ; Knorr, Christophe ; Triantafyllidis, Alex ; Alexandri, Panoraia ; Semiadi, Gono ; Hanotte, Olivier ; Dias, Deodália ; Dovč, Peter ; Uimari, Pekka ; Iacolina, Laura ; Scandura, Massimo ; Groenen, M. ; Huang, L. ; Megens, H.J.W.C. - \ 2017
pig - domestication - genome - selection
Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Results: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Conclusions: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.
Smaakfestijn Slowfood 2016
Bas, Noortje - \ 2016
grain legumes - vegetable legumes - gene banks - legumes - agro-biodiversity - domestication - habitats - food supply - climatic change
Diversiteit in peulvruchten : op je bord en in de vriezer
Ontwikkeling pluimveehouderij met focus op dierenwelzijn - Dierenwelzijn in beeld
Ruis, M.A.W. - \ 2016
You Tube
pluimvee - dierlijke productie - dierenwelzijn - diergedrag - huisvesting, dieren - diervoeding - diergezondheid - dierethiek - domesticatie - kippen - pluimveehouderij - lesmaterialen - poultry - animal production - animal welfare - animal behaviour - animal housing - animal nutrition - animal health - animal ethics - domestication - fowls - poultry farming - teaching materials
De hedendaagse kip is ontstaan uit vier wilde rassen. Het Bankivahoen uit Zuid-Oost Azie is hiervan de belangrijkste. Vanaf 1.500 vóór Christus verspreidde het hoen zich door heel Zuid-Oost Azië, China en Japan. In Noordwest Europa is de kip vermoedelijk rond 200 voor Christus geïntroduceerd door de Grieken en Romeinen. In de jaren ’50 van de vorige eeuw werd in Nederland op grote schaal geïnvesteerd in innovaties en verschenen de grote broedmachines en de eerste volautomatische legbatterijen. Ook kwamen begin jaren ’50 verschillende ‘merken’ hybride kippen - kruisingen van zuivere lijnen of rassen - op de markt. Hieruit ontstonden de hoogproductieve leghennen en vleeskuikens.

Halverwege de jaren ’60 dringt in de maatschappij het besef door dat er weinig oog is voor het welzijn van kippen. Decennia later heeft dit geleid tot een aantal veranderingen en verboden. Vanaf 2012 is het in heel Europa verboden om leghennen in legbatterijen te houden, en het aantal vleeskuikens per vierkante meter is in Europa aan banden gelegd. Een ander voorbeeld is de aankomende plicht om leghennen, en vermeerderingsdieren voor de vleessector, met hele snavels te houden. De pluimveesector is de uitdaging aangegaan om vlees en eieren duurzamer te produceren.
Ontwikkeling varkenshouderij met focus op dierenwelzijn - Dierenwelzijn in beeld
Ruis, M.A.W. - \ 2016
Wageningen UR Livestock Research
pigs - animal production - animal welfare - animal housing - animal nutrition - animal health - animal ethics - domestication - pig farming - teaching materials - varkens - dierlijke productie - dierenwelzijn - huisvesting, dieren - diervoeding - diergezondheid - dierethiek - domesticatie - varkenshouderij - lesmaterialen
De geschiedenis van het varken gaat terug naar de eerste boeren die wilde zwijnen gingen houden. Ongeveer 6.000 jaar vóór Christus zouden in Iran en Irak de eerste varkens uit zwijnen zijn gedomesticeerd. De eerste landbouwers met tamme varkens vestigden zich ongeveer 5.000 jaar vóór Christus in Nederland. Het varken is altijd een vaste bewoner van boerenbedrijven geweest. Varkens waren natuurlijk leveranciers van spek en vlees, maar ze ploegden ook de akkers om, zorgden voor bemesting en ze verwerkten ook afval van de boerderij. Na de Tweede Wereldoorlog werd de varkenshouderij enorm geïndustrialiseerd: schaalvergroting, mechanisatie, en specialisatie werden gestimuleerd. Men keek in de jaren vijftig tot zeventig van de vorige eeuw met een zakelijke blik naar het dier; de economische voordelen waren het belangrijkst. Vanaf halverwege de jaren zestig nam de aandacht voor dierenwelzijn toe, en dit heeft geleid tot een aantal verboden en verplichtingen. Voorbeelden zijn een verbod op de volledige roostervloeren en het aanbinden van de zeugen, en verplichte groepshuisvesting voor drachtige zeugen. De varkenshouderij is de uitdaging aangegaan om varkensvlees duurzamer te produceren.
Genetic diversity and evolution in Lactuca L. (Asteraceae) : from phylogeny to molecular breeding
Wei, Z. - \ 2016
University. Promotor(en): Eric Schranz. - Wageningen : Wageningen University - ISBN 9789462576148 - 210 p.
lactuca sativa - leafy vegetables - phylogeny - genetic diversity - domestication - molecular breeding - genomes - dna - quantitative trait loci - evolution - bladgroenten - fylogenie - genetische diversiteit - domesticatie - moleculaire veredeling - genomen - loci voor kwantitatief kenmerk - evolutie

Cultivated lettuce (Lactuca sativa L.) is an important leafy vegetable worldwide. However, the phylogenetic relationships between domesticated lettuce and its wild relatives are still not clear. In this thesis, I focus on the phylogenetic relationships within Lactuca L., including an analysis of the wild Lactuca species that are endemic to Africa for the first time. The genetic variation of responses to salinity in a recombinant inbred line population, derived from a cross between the lettuce crop (L. sativa ‘Salinas’) and wild species (L. serriola), was investigated and the candidate gene in the identified QTL regions was further studied.

In Chapter 1, I introduce and discuss topics related to genetic diversity and evolution in Lactuca, including an overview of lettuce cultivars and uses, its hypothesized domestication history, the taxonomic position of Lactuca, current status of molecular breeding in lettuce and mechanisms of salinity tolerance in plants, especially the High-affinity K+ Transporter (HKT) gene family.

In Chapter 2, the most extensive molecular phylogenetic analysis of Lactuca was constructed based on two chloroplast genes (ndhF and trnL-F), including endemic African species for the first time. This taxon sampling covers nearly 40% of the total Lactuca species endemic to Africa and 34% of all Lactuca species. DNA sequences from all the subfamilies of Asteraceae in Genbank and those generated from Lactuca herbarium samples were used to elucidate the monophyly of Lactuca and the affiliation of Lactuca within Asteracaeae. Based on the subfamily tree, 33 ndhF sequences from 30 species and 79 trnL-F sequences from 48 species were selected to infer phylogenetic relationships within Lactuca using Randomized Axelerated Maximum Likelihood (RAxML) and Bayesian Inference (BI) analyses. In addition, biogeographical, chromosomal and morphological character states were analysed based on the Bayesian tree topology. The results showed that Lactuca contains two distinct phylogenetic clades - the crop clade and the Pterocypsela clade. Other North American, Asian and widespread species either form smaller clades or mix with the Melanoseris species in an unresolved polytomy. The newly sampled African endemic species probably should be excluded from Lactuca and treated as a new genus.

In Chapter 3, twenty-seven wild Lactuca species and four outgroup species were sequenced using next generation sequencing (NGS) technology. The sampling covers 36% of total Lactuca species and all the important geographical groups in the genus. Thirty chloroplast genomes, including one complete (partial) large single copy region (LSC), one small single copy region (SSC), one inverted repeat (IR) region, and twenty-nine nuclear ribosomal DNA sequences (containing the internal transcribed spacer region ) were successfully assembled and analysed. A methodology paper for which I am co-author, but is not included in this thesis, of the sequencing pipeline was published: ‘Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly (IOGA) pipeline’. These NGS data helped resolve deeper nodes in the phylogeny within Lactuca and resolved the polytomy from Chapter 2. The results showed that there are at least four main groups within Lactuca: the crop group, the Pterocypsela group, the North American group and the group containing widely-distributed species. I also confirmed that the endemic African species should be removed and treated as a new genus.

In Chapter 4, quantitative trait loci (QTLs) related to salt-induced changes in Root System Architecture (RSA) and ion accumulation were determined using a recombinant inbred line population derived from a cross between cultivated lettuce and wild lettuce. I measured the components of RSA by replicated lettuce seedlings grown on vertical agar plates with different NaCl concentrations in a controlled growth chamber environment. I also quantified the concentration of sodium and potassium in replicates of greenhouse-grown plants watered with 100 mM NaCl. The results identified a total of fourteen QTLs using multi-trait linkage analysis, including three major QTLs associated with general root development (qRC9.1), root growth in salt stress condition (qRS2.1), and ion accumulation (qLS7.2).

In Chapter 5, one of the identified QTL regions (qLS7.2) reported in Chapter 4 was found to contain a homolog of the HKT1 from Arabidopsis thaliana. I did a phylogenetic analysis of Lactuca HKT1-like protein sequences with other published HKT protein sequences and determined transmembrane and pore segments of lettuce HKT1;1 alleles, according to the model proposed for AtHKT1;1. Gene expression pattern and level of LsaHKT1;1 (L. sativa ‘Salinas’) and LseHKT1;1 (L. serriola) in root and shoot were investigated in plants growing hydroponically over a time-course. The measurements of Na+ and K+ contents were sampled at the same time as the samples used for gene expression test. In addition, I examined the 5’ promoter regions of the two genotypes. The results showed low expression levels of both HKT1;1 alleles in Lactuca root and relatively higher expression in shoot, probably due to the negative cis-regulatory elements of HKT1 alleles found in Lactuca promoter regions. Significant allelic differences were found in HKT1;1 expression in early stage (0-24 hours) shoots in and in late stage (2-6 days) roots. shoot HKT1;1 expression/root HKT1;1 expression was generally consistent with the ratios of Na+/K+ balance in the relevant tissues (shoot Na+/K+ divided by root Na+/K+).

In Chapter 6, I summarize and discuss the results from previous chapters briefly. The implications of Chapter 2 and 3 for Lactuca phylogenetics are discussed, including some key characters for the diagnosis of species within Lactuca, the use of herbarium DNA for NGS technology, and perspectives into Lactuca phylogeny. Future perspectives of genome-wide association mapping for lettuce breeding were also discussed. Lastly, I propose to integrate phylogenetic approaches into investigations of allelic differences in lettuce, not just associated with salinity stress but also with other stressed and beneficial characters, both within and between species.

Plantenveredeling Domesticatie en voedselzekerheid
Jacobsen, Evert - \ 2015
plant breeding - varieties - domestication - plant breeding methods - genetic variation - food crops - genetic resources - resistance breeding - food security
Speciation and domestication in Suiformes: a genomic perspective
Frantz, L.A.F. - \ 2015
University. Promotor(en): Martien Groenen, co-promotor(en): Ole Madsen; Hendrik-Jan Megens. - Wageningen : Wageningen University - ISBN 9789462572546 - 227
domesticatie - suiformes - soortvorming - dierveredeling - genomica - evolutie - genenstroom - dna-sequencing - moleculaire fylogenetica - domestication - speciation - animal breeding - genomics - evolution - gene flow - dna sequencing - molecular phylogenetics

Abstract

Frantz, L.A.F. (2015). Speciation and Domestication in Suiformes: a genomic perspective. PhD thesis, Wageningen University, the Netherlands

The diversity of life on earth owes its existence to the process of speciation. The concept of speciation is primordial for evolutionary biologists because it provides a framework to understand how contemporary biodiversity came to be. Moreover, not only natural phenomena can result in the differentiation of life forms. Indeed, biodiversity can also be the result of direct and indirect human influence such as domestication. In this thesis, I investigate these evolutionary processes (speciation and domestication) in the Suiformes superfamily (pigs and related species). I use complete genome sequences to illuminate many specific aspects of the speciation and domestication in Suiformes as well as to draw general conclusions on these crucial processes. In chapter 2 I show how genomes provide an essential source of information to retrieve deep taxonomic relationships among Suiformes. This allows me to describe multiple novel aspects of their early evolutionary history such as the fact that Suiformes colonised North America at least twice. In this chapter, I further highlight and discuss novel methodological limitations that are inherent to phylogenomics. In chapters 3, 4 and 5 I use genome sequences to resolve the evolutionary history of the genus Sus (domestic pigs and wild boars species). More precisely, I show that, contrary to the expectation of simple models of speciation, the evolutionary history of these species involved alternating periods of gene-flow and genetic differentiation that are tightly linked to past climatic fluctuations that took place over the last 4 million years. In addition, these chapters also provide novel insights into the process of speciation by demonstrating that genetic differentiation between species can be achieved, even when gene-flow is strong. Lastly, in chapter 6 I tested multiple models of domestication for S. scrofa. In this chapter I show that models involving reproductive isolation between wild and domestic forms are incompatible with genomic data. Moreover, this chapter demonstrates that, while domestic pigs are morphologically homogenous, they are not genetically homogenous. Together, these findings have important implications for our understanding of the process of domestication because it shows that this process was not solely the result of captivity. Together, the results of this work not only provide a comprehensive evolutionary history for the Suiformes, but also novel insights into the complex processes (speciation and domestication) that are responsible for the diversity of life on earth.

Data from: Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations
Bosse, M. ; Megens, H.J.W.C. ; Madsen, O. ; Frantz, L.A.F. ; Paudel, Y. ; Crooijmans, R.P.M.A. ; Groenen, M. - \ 2014
pigs - phylogenetic tree - domestication - hybridization
The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine-scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.
Does phenology distinguish bitter and sweet African bush mango trees (Irvingia spp., Irvingiaceae)?
Vihotogbe, R. ; Berg, R.G. van den; Bongers, F. ; Sinsin, B. ; Sosef, M.S.M. - \ 2014
Trees-Structure and Function 28 (2014)6. - ISSN 0931-1890 - p. 1777 - 1791.
genetic diversity - dahomey gap - west-africa - phenotypic variation - conservation status - gabonensis - domestication - forest - cameroon - fruits
Key message This phenological analysis of bitter and sweet bush mango trees is part of their biosystematics. It supports the species distinction hypothesis postulated by Harris (Bull J Bot Nat Belg 65(1-2):143-196, 1996 ) and Lowe et al. (Mol Ecol 9:831-841, 2000 ). African Bush Mango trees are priority food trees in Sub-Saharan Africa. The unclear distinction between bitter and sweet fruited trees is still subject to taxonomic debate. This hinders their effective use and conservation programmes. This study investigates differences in phenological behaviour between bitter and sweet fruited populations and their taxonomic implications. Monthly phenological description data on seven populations of bitter or sweet bush mangos across Benin and Togo were used to assess within and between mango type phenological diversity, to discriminate bitter and sweet trees and to evaluate their responses to environmental factors. The phenological states differentiating bitter and sweet trees were identified and individual trees were classified based on the discriminating phenological characters. Finally, phenological variation was analyzed with time of the year, soil type, type of bush mango tree, and climatic zone. Phenological diversity varies significantly among populations. Bitter and sweet trees have consistently different phenological states. Bitter trees have a lower phenological diversity for all phenological phases throughout the year compared to sweet trees, possibly due to their limited distribution range in the study area. The tree types also differ in their reproductive responses to environmental factors, but did not respond differently to soils. These results support the hypothesis that bitter and sweet trees represent different taxa and we suggest for efficient conservation purpose to consider them as different species.
Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations
Frantz, L.A.F. ; Madsen, O. ; Megens, H.J.W.C. ; Groenen, M. ; Lohse, H. - \ 2014
Molecular Ecology 23 (2014)22. - ISSN 0962-1083 - p. 5566 - 5574.
last glacial period - pig genomes - quaternary - evolution - reveals - domestication - demography - inference - sundaland - history
In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island South-East Asia (ISEA). A previous study revealed signatures of interspecific admixture between these Sus species (Genome biology, 14, 2013, R107). However, the timing, directionality and extent of this admixture remain unknown. Here, we use a likelihood-based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that interspecific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture.
Reappraising the Concept of Biocultural Diversity: a Perspective from South Africa
Cocks, M.L. ; Wiersum, K.F. - \ 2014
Human Ecology 42 (2014)5. - ISSN 0300-7839 - p. 727 - 737.
eastern-cape - ecological knowledge - medicinal-plants - biodiversity - conservation - landscapes - forests - domestication - people - communities
Biocultural diversity has been conceptualised as the sum of the world’s differences regarding biological diversity at all levels and cultural diversity in all its manifestations, and their interactions. The concept is often framed in the context ofconservation as a retention versus loss model by emphasizing the religious and spiritual values of the natural environment and the positive interactions between traditional indigenous people and conservation of natural ecosystems and indigenous species. On the basis of our research amongst the ‘non-traditional’ amaXhosa in South Africa, we argue that this interpretation is too narrow and that the concept needs to be reappraised in order to capture the dynamic, complex and relational nature of biocultural diversity relations. We conclude that the concept involves a complex of human values and practices related to the three main dimensions of biodiversity at landscapes, species and genetic levels. It is not only related to the conservation of wild species in culturally venerated natural ecosystems, but also to human creativity in creating hybrid nature-culture systems, including the incorporation of biodiversity in the human domain through the creation of human-modified landscape elements and agro-biodiversity. The biocultural values and practices are subject to various dynamics in relation to socioeconomic change. Some lose their importance as a result of modernization, but others endure even in urban conditions.
Impacts of the diversity of traditional uses and potential economic value on food tree species conservation status: case study of African bush mango trees (Irvingiaceae) in the Dahomey Gap (West Africa).
Vihotogbé, R. ; Kakai, R.G. ; Bongers, F. ; Andel, T. van; Berg, R.G. van den; Sinsin, B. ; Sosef, M.S.M. - \ 2014
Plant Ecology and Evolution 147 (2014)1. - ISSN 2032-3913 - p. 109 - 125.
timber forest products - domestication - gabonensis
Background and aims – Bitter and sweet African bush mango trees belong to the family Irvingiaceae and produce valuable non-timber forest products in humid lowland areas of West and Central Africa. The bitter and sweet types are treated as distinct taxa at the variety or species level. They have not been studied in the western part of their distribution range, and many aspects of their large-scale utilization remain unknown. In this study, we link differences in socio-cultural groups to the agroforestry status of bush mango trees in order to identify the key factors influencing their abundance and conservation in the study area. Methods – First, we gathered uses and local management strategies from nine main socio-cultural areas in Benin and Togo, part of the Dahomey Gap. Second, occurrence data were obtained throughout the Gap and imported into DIVA-GIS and MATLAB to calculate the spatial pattern of the density and analyse its structure and variation relative to three factors: the country, the phytogeographical zone and the dominant soil category. Third, agroforestry system characteristics and farmers' social status relative to 841 trees were used in a multinomial logistic regression to identify anthropogenic factors driving the intensive cultivation of bush mango trees. Finally, the impact of socio-cultural activities on extent and density of bush mango tree populations was analysed. Key results – In the entire study zone, the sweet mesocarp is consumed and the endocarp of bush mangoes is commercialized. The application of endocarp-based diets and socio-therapeutic uses are common to communities in Benin. Sweet bush mango trees are generally found either in home gardens or cultivation fields where they may occur at high densities (up to 1020 trees per 25 ha). Bitter trees, however, are confined to the Volta forest region in Togo and occur at low densities (<462 trees per 25 ha) in the wild, sometimes in protected areas, in forest gardens and in fields. This indicates a clear difference in cultivation methods between the bitter and sweet trees. Farmland status, farmer socio-cultural group and type of bush mango trees determined the cultivation intensity. Conclusion – The fact that small farmlands are converted into sweet bush mango tree orchards indicates that farmers actively cultivate bush mango trees in the study area. Diversity of indigenous knowledge, however, is not correlated either to intensive cultivation or domestication efforts and local genetic conservation program. Where slash and burn agriculture and intensive collection of fruits jeopardize bitter trees, traditional fishing systems (using bush mango twigs), a traditional selection strategy, and intensive land commercialization severely threaten sweet bush mango tree genetic resources.
Boekbespreking: Het oerrund, een levende legende
Oldenbroek, J.K. - \ 2014
Zeldzaam huisdier 39 (2014)3. - ISSN 0929-905X - p. 20 - 21.
rundvee - rundveerassen - bos primigenius - domesticatie - rassen (dieren) - begrazing - cattle - cattle breeds - domestication - breeds - grazing
Uitgeverij Roodbont heeft een interessant boek uitgegeven over de achtergronden van een project waarin het uitgestorven oerrund teruggefokt wordt. Het is een initiatief van de stichting Taurus samen met Rewilding Europe en ARK Natuurontwikkeling. Het is een boek geworden met veel informatie over de geschiedenis van het (oer)rund, de rol die het speelde bij begrazing, de domesticatie en over de rassen van nu die het meest op het oerrund lijken. Het boek is geïllustreerd met schitterende tekeningen en foto’s.
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing
Aflitos, S.A. ; Schijlen, E.G.W.M. ; Jong, J.H.S.G.M. de; Ridder, D. de; Smit, S. ; Finkers, H.J. ; Bakker, F.T. ; Geest, H.C. van de; Lintel Hekkert, B. te; Haarst, J.C. van; Smits, L.W.M. ; Koops, A.J. ; Sanchez-Perez, M.J. ; Heusden, A.W. van; Visser, R.G.F. ; Schranz, M.E. ; Peters, S.A. - \ 2014
The Plant Journal 80 (2014)1. - ISSN 0960-7412 - p. 136 - 148.
single-nucleotide polymorphisms - burrows-wheeler transform - wild tomatoes - genus lycopersicon - read alignment - fruit size - evolution - domestication - solanaceae - plant
We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon, and Neolycopersicon groups which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment reveals group-, species-, and accession-specific polymorphisms, which explains characteristic fruit traits and growth habits in the different cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences dN/dS ratio in fruit and growth diversification genes compared to a random set of genes, pointing to positive selection and to differences in selection pressure between crop accessions and wild species. In wild species SNPs are found in excess of 10 million, i.e. 20 fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, highest levels of heterozygosity were found for allogamous SI wild species, while facultative and autogamous SC species display a lower heterozygosity level. Using whole genome SNP information for Maximum Likelihood analysis we achieved complete tree resolution, whereas ML trees based on SNPs from 10 fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat pointing at the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.
On the relationship between an Asian haplotype on chromosome 6 that reduces androstenone levels in boars and the differential expression of SULT2A1 in the testis
Hidalgo, A.M. ; Bastiaansen, J.W.M. ; Harlizius, B. ; Megens, H.J.W.C. ; Madsen, O. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. - \ 2014
BMC Genetics 15 (2014). - ISSN 1471-2156
genome-wide association - quantitative trait loci - 16-androstene steroids - pig genomes - taint - gene - domestication - reveals - sulfoconjugation - visualization
Background Androstenone is one of the major compounds responsible for boar taint, a pronounced urine-like odor produced when cooking boar meat. Several studies have identified quantitative trait loci (QTL) for androstenone level on Sus scrofa chromosome (SSC) 6. For one of the candidate genes in the region SULT2A1, a difference in expression levels in the testis has been shown at the protein and RNA level. Results Haplotypes were predicted for the QTL region and their effects were estimated showing that haplotype 1 was consistently related with a lower level, and haplotype 2 with a higher level of androstenone. A recombinant haplotype allowed us to narrow down the QTL region from 3.75 Mbp to 1.94 Mbp. An RNA-seq analysis of the liver and testis revealed six genes that were differentially expressed between homozygotes of haplotypes 1 and 2. Genomic sequences of these differentially expressed genes were checked for variations within potential regulatory regions. We identified one variant located within a CpG island that could affect expression of SULT2A1 gene. An allele-specific expression analysis in the testis did not show differential expression between the alleles of SULT2A1 located on the different haplotypes in heterozygous animals. However a synonymous mutation C166T (SSC6: 49,117,861 bp in Sscrofa 10.2; C/T) was identified within the exon 2 of SULT2A1 for which the haplotype 2 only had the C allele which was higher expressed than the T allele, indicating haplotype-independent allelic-imbalanced expression between the two alleles. A phylogenetic analysis for the 1.94 Mbp region revealed that haplotype 1, associated with low androstenone level, originated from Asia. Conclusions Differential expression could be observed for six genes by RNA-seq analysis. No difference in the ratio of C:T expression of SULT2A1 for the haplotypes was found by the allele-specific expression analysis, however, a difference in expression between the C over T allele was found for a variation within SULT2A1, showing that the difference in androstenone levels between the haplotypes is not caused by the SNP in exon 2.
Signatures of Diversifying Selection in European Pig Breeds
Wilkinson, S. ; Lu, Z.H. ; Megens, H.J.W.C. ; Archibald, A.L. ; Haley, C. ; Jackson, I.J. ; Groenen, M. ; Crooijmans, R.P.M.A. ; Ogden, R. ; Wiener, P. - \ 2013
pig - porcine - selection - domestication - introgression - breed development
Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition.
Porcine colonization of the Americas: a 60k SNP story
Burgos-Paz, W. ; Souza, C. ; Megens, H.J.W.C. ; Ramayo-Caldas, Y. ; Crooijmans, R.P.M.A. ; Groenen, M. - \ 2013
Heredity 110 (2013)4. - ISSN 0018-067X - p. 321 - 330.
high-altitude - pig breeds - r-package - selection - genome - adaptation - footprints - domestication - association - expression
The pig, Sus scrofa, is a foreign species to the American continent. Although pigs originally introduced in the Americas should be related to those from the Iberian Peninsula and Canary islands, the phylogeny of current creole pigs that now populate the continent is likely to be very complex. Because of the extreme climates that America harbors, these populations also provide a unique example of a fast evolutionary phenomenon of adaptation. Here, we provide a genome wide study of these issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across 14 countries and 183 pigs from outgroup breeds that are potential founders of the American populations, including wild boar, Iberian, international and Chinese breeds. Results show that American village pigs are primarily of European ancestry, although the observed genetic landscape is that of a complex conglomerate. There was no correlation between genetic and geographical distances, neither continent wide nor when analyzing specific areas. Most populations showed a clear admixed structure where the Iberian pig was not necessarily the main component, illustrating how international breeds, but also Chinese pigs, have contributed to extant genetic composition of American village pigs. We also observe that many genes related to the cardiovascular system show an increased differentiation between altiplano and genetically related pigs living near sea level.
Morphological Characterization of African Bush Mango trees (Irvingia species) in the Dahomey Gap (West Africa)
Vihotogbe, R. ; Berg, R.G. van den; Sosef, M.S.M. - \ 2013
Genetic Resources and Crop Evolution 60 (2013)4. - ISSN 0925-9864 - p. 1597 - 1614.
phenotypic variation - indigenous fruits - domestication - gabonensis - cameroon - selection - nigeria - accessions - kernels - farmers
The variation of the morphological characters of bitter and sweet African bush mango trees (Irvingia species) was investigated in the Dahomey Gap which is the West African savannah woodland area separating the Upper and the Lower Guinean rain forest blocks. African bush mangoes have been rated as the highest priority multi-purpose food trees species that need improvement research in West and Central Africa. A total of 128 trees from seven populations were characterized for their bark, fruits, mesocarp and seeds to assess the morphological differences between bitter and sweet trees and among populations. Multivariate analysis revealed that none of the variables: type of bark, mature fruit exocarp colour, fruit roughness and fresh mesocarp colour, could consistently distinguish bitter from sweet trees in the field. The analysis of the measurements of fruits, mesocarps and seeds demonstrated that bitter fruits have the heaviest seeds and this consistently distinguishes them from sweet fruits. However, the measurements of the fruit, mesocarp and seed did not have a joint effect in grouping types and populations of ABMTs. This indicates high diversity with a potential for selection existing across all phytogeographical regions investigated. The sweet trees of Couffo and those of Dassa in Benin are clearly different from all other populations. This can be attributed to traditional domestication (bringing into cultivation) and climate, respectively. The large fruits and the heavy seeds of the cultivated populations are evidence of successful on-going traditional selection of sweet trees in the Dahomey Gap.
Farm-by-farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed
Herrero-Medrano, J. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. - \ 2013
Animal Genetics 44 (2013)3. - ISSN 0268-9146 - p. 259 - 266.
population-structure - phylogenetic-relationships - genetic diversity - dna - program - domestication - inference - software
The Chato Murciano (CM), a pig breed from the Murcia region in the southeastern region of Spain, is a good model for endangered livestock populations. The remaining populations are bred on approximately 15 small farms, and no herdbook exists. To assess the genetic threats to the integrity and survival of the CM breed, and to aid in designing a conservation program, three genetic marker systems – microsatellites, SNPs and mtDNA – were applied across the majority of the total breeding stock. In addition, mtDNA and SNPs were genotyped in breeds that likely contributed genetically to the current CM gene pool. The analyses revealed the levels of genetic diversity within the range of other European local breeds (He = 0.53). However, when the eight farms that rear at least 10 CM pigs were independently analyzed, high levels of inbreeding were found in some. Despite the evidence for recent crossbreeding with commercial breeds on a few farms, the entire breeding stock remains readily identifiable as CM, facilitating the design of traceability assays. The genetic management of the breed is consistent with farm size, farm owner and presence of other pig breeds on the farm, demonstrating the highly ad hoc nature of current CM breeding. The results of genetic diversity and substructure of the entire breed, as well as admixture and crossbreeding obtained in the present study, provide a benchmark to develop future conservation strategies. Furthermore, this study demonstrates that identifying farm-based practices and farm-based breeding stocks can aid in the design of a sustainable breeding program for minority breeds.
Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape
Bosse, M. ; Megens, H.J.W.C. ; Madsen, O. ; Paudel, Y. ; Frantz, L.A.F. ; Schook, L.B. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. - \ 2012
Plos Genetics 8 (2012)11. - ISSN 1553-7404
human-populations - pig breeds - evolutionary history - genetic diversity - wild boar - domestication - conservation - runs - snp - map
Inbreeding has long been recognized as a primary cause of fitness reduction in both wild and domesticated populations. Consanguineous matings cause inheritance of haplotypes that are identical by descent (IBD) and result in homozygous stretches along the genome of the offspring. Size and position of regions of homozygosity (ROHs) are expected to correlate with genomic features such as GC content and recombination rate, but also direction of selection. Thus, ROHs should be non-randomly distributed across the genome. Therefore, demographic history may not fully predict the effects of inbreeding. The porcine genome has a relatively heterogeneous distribution of recombination rate, making Sus scrofa an excellent model to study the influence of both recombination landscape and demography on genomic variation. This study utilizes next-generation sequencing data for the analysis of genomic ROH patterns, using a comparative sliding window approach. We present an in-depth study of genomic variation based on three different parameters: nucleotide diversity outside ROHs, the number of ROHs in the genome, and the average ROH size. We identified an abundance of ROHs in all genomes of multiple pigs from commercial breeds and wild populations from Eurasia. Size and number of ROHs are in agreement with known demography of the populations, with population bottlenecks highly increasing ROH occurrence. Nucleotide diversity outside ROHs is high in populations derived from a large ancient population, regardless of current population size. In addition, we show an unequal genomic ROH distribution, with strong correlations of ROH size and abundance with recombination rate and GC content. Global gene content does not correlate with ROH frequency, but some ROH hotspots do contain positive selected genes in commercial lines and wild populations. This study highlights the importance of the influence of demography and recombination on homozygosity in the genome to understand the effects of inbreeding.
New Genes in Traditional Seed Systems: Diffusion, Detectability and Persistence of Transgenes in a Maize Metapopulation
Heerwaarden, J. van; Vecchyo, D.O. Del; Alvarez-Buylla, E.R. ; Bellon, M.R. - \ 2012
PLoS One 7 (2012)10. - ISSN 1932-6203
population-genetics - mexico - landraces - oaxaca - flow - domestication - introgression - conservation - management - diversity
Gene flow of transgenes into non-target populations is an important biosafety concern. The case of genetically modified (GM) maize in Mexico has been of particular interest because of the country’s status as center of origin and landrace diversity. In contrast to maize in the U.S. and Europe, Mexican landraces form part of an evolving metapopulation in which new genes are subject to evolutionary processes of drift, gene flow and selection. Although these processes are affected by seed management and particularly seed flow, there has been little study into the population genetics of transgenes under traditional seed management. Here, we combine recently compiled data on seed management practices with a spatially explicit population genetic model to evaluate the importance of seed flow as a determinant of the long-term fate of transgenes in traditional seed systems. Seed flow between farmers leads to a much wider diffusion of transgenes than expected by pollen movement alone, but a predominance of seed replacement over seed mixing lowers the probability of detection due to a relative lack of homogenization in spatial frequencies. We find that in spite of the spatial complexities of the modeled system, persistence probabilities under positive selection are estimated quite well by existing theory. Our results have important implications concerning the feasibility of long term transgene monitoring and control in traditional seed systems.
Signatures of selection in the genomes of commercial and non-commercial chicken breeds
Elferink, M.G. ; Megens, H.J.W.C. ; Vereijken, A. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. - \ 2012
PLoS One 7 (2012). - ISSN 1932-6203
quantitative trait loci - single-nucleotide polymorphisms - pulmonary-hypertension syndrome - genetic diversity - ascites syndrome - body-composition - growth-factor - layer cross - dna pools - domestication
Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations.
Characterization of African Bush Mango trees with emphasis on the differences between sweet and bitter trees in the Dahomey Gap (West Africa)
Vihotogbe, R. - \ 2012
University. Promotor(en): Marc Sosef; B. Sinsin, co-promotor(en): Ronald van den Berg. - [S.l. : S.n. - ISBN 9789461734129 - 189
irvingia - domesticatie - bomen - plantenmorfologie - plantengeografie - genetische diversiteit - taxonomie - smaken - benin - west-afrika - domestication - trees - plant morphology - phytogeography - genetic diversity - taxonomy - tastes - west africa
New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties
Cornille, A. ; Gladieux, P. ; Smulders, M.J.M. ; Roldán-Ruiz, I. ; Laurens, F. ; Cam, B. le; Nersesyan, A. ; Clavel, J. ; Olonova, M. ; Feugey, L. ; Gabrielyan, I. ; Zhang, Xiu-Guo ; Tenaillon, M.I. ; Giraud, T. - \ 2012
Plos Genetics 8 (2012)5. - ISSN 1553-7404
appels - malus domestica - domesticatie - voorouders - wilde verwanten - genetische bronnen van plantensoorten - genetische diversiteit - apples - domestication - ancestors - wild relatives - plant genetic resources - genetic diversity - approximate bayesian computation - multilocus genotype data - allele frequency data - sylvestris l. mill. - population-structure - microsatellite markers - molecular-genetics - spondias-purpurea - genus malus - fruit tree
The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species.
Wild Animals in Our Backyard. A Contextual Approach to the Intrinsic Value of Animals
Swart, J.A.A. ; Keulartz, F.W.J. - \ 2011
Acta Biotheoretica 59 (2011)2. - ISSN 0001-5342 - p. 185 - 200.
international guidelines - netherlands - welfare - ethics - reintroduction - domestication - otter
As a reflection on recent debates on the value of wild animals we examine the question of the intrinsic value of wild animals in both natural and man-made surroundings. We examine the concepts being wild and domesticated. In our approach we consider animals as dependent on their environment, whether it is a human or a natural environment. Stressing this dependence we argue that a distinction can be made between three different interpretations of a wild animal’s intrinsic value: a species-specific, a naturalistic, and an individualistic interpretation. According to the species-specific approach, the animal is primarily considered as a member of its species; according to the naturalistic interpretation, the animal is seen as dependent on the natural environment; and according to the individualistic approach, the animal is seen in terms of its relationship to humans. In our opinion, the species-specific interpretation, which is the current dominant view, should be supplemented—but not replaced by—naturalistic and individualistic interpretations, which focus attention on the relationship of the animal to the natural and human environments, respectively. Which of these three interpretations is the most suitable in a given case depends on the circumstances and the opportunity for the animal to grow and develop according to its nature and capabilities.
Het wilde dier in onze samenleving. Een contextuele benadering van intrinsieke waarde
Keulartz, J. ; Swart, J.A.A. - \ 2010
Filosofie en Praktijk 31 (2010)2. - ISSN 0167-2444 - p. 12 - 27.
wilde dieren - waarden - domesticatie - filosofie - habitats - natuurwaarde - wild animals - values - domestication - philosophy - natural value
In deze bijdrage gaan de auteurs in op de vraag naar de intrinsieke waarde van wilde dieren in natuurlijke én menselijke omgevingen. Na eerst enkele bestaande benaderingen te schetsen, gaan zij in op het onderscheid tussen wild en gedomesticeerd als opmaat naar een meer genuanceerd beeld van het begrip intrinsieke waarde. De auteurs stellen dat er een drietal interpretaties van intrinsieke waarde van het wilde dier onderscheiden kunnen worden: een naturalistische, een soortspecifieke en een individualistische interpretatie. De omstandigheden en de mogelijkheden van het dier zich te kunnen ontplooien volgens zijn aard en capaciteiten horen te bepalen welke interpretatie de meest geëigende is.
As you weed, so shall you reap: on the origin of algaculture in damselfish
Aanen, D.K. - \ 2010
BMC Biology 8 (2010). - ISSN 1741-7007
domestication - evolution
Within their territories, damselfish cultivate particular algae for consumption. A recent study in BMC Evolutionary Biology shows extensive variation among and within fish species in the composition of these algal 'gardens', varying from monocultures to cultures of mixed species, and in the mode of cultivation. This fish-algal agriculture may provide insight into the early stages of domestication
Domesticeren, fokken, winnen en verliezen : natuurlijke en kunstmatige selectie
Oldenbroek, Kor - \ 2010
domestication - animal breeding - genetic diversity - selection - inbreeding - rare breeds - conservation
In search of tetraploid wheat accessions reduced in celiac disease-related gluten epitopes
Broeck, H.C. van den; Hongbing, C. ; Lacaze, X. ; Dusautoir, J.C. ; Gilissen, L.J.W.J. ; Smulders, J.M. ; Meer, I.M. van der - \ 2010
Molecular BioSystems 6 (2010)11. - ISSN 1742-206X - p. 2206 - 2213.
durum-wheat - storage proteins - polyploid wheat - bread wheat - subunit genes - domestication - gliadin - peptides - triticum - complex
Tetraploid wheat (durum wheat) is mainly used for the preparation of pasta. As a result of breeding, thousands of tetraploid wheat varieties exist, but also tetraploid landraces are still maintained and used for local food preparations. Gluten proteins present in wheat can induce celiac disease, a T-cell mediated auto-immune disorder, in genetically predisposed individuals after ingestion. Compared to hexaploid wheat, tetraploid wheat might be reduced in T-cell stimulatory epitopes that cause celiac disease because of the absence of the D-genome. We tested gluten protein extracts from 103 tetraploid wheat accessions (obtained from the Dutch CGN genebank and from the French INRA collection) including landraces, old, modern, and domesticated accessions of various tetraploid species and subspecies from many geographic origins. Those accessions were typed for their level of T-cell stimulatory epitopes by immunoblotting with monoclonal antibodies against the a-gliadin epitopes Glia-a9 and Glia-a20. In the first selection, we found 8 CGN and 6 INRA accessions with reduced epitope staining. Fourteen of the 57 CGN accessions turned out to be mixed with hexaploid wheat, and 5 out of the 8 selected CGN accessions were mixtures of two or more different gluten protein chemotypes. Based on single seed analysis, lines from two CGN accessions and one INRA accession were obtained with significantly reduced levels of Glia-a9 and Glia-a20 epitopes. These lines will be further tested for industrial quality and may contribute to the development of safer foods for celiac patients.
Variatie in vee : biodiversiteit op de boerderij bedreigd
Zegwaard, A. ; Buiter, R. ; Oldenbroek, J.K. ; Everdingen, J. - \ 2010
Den Haag : Stichting Bio-Wetenschappen en Maatschappij (Cahier / Bio-Wetenschappen en Maatschappij 29e jrg., nr. 3) - ISBN 9789073196599 - 88
genetische bronnen van diersoorten - zeldzame rassen - domesticatie - huisdieren - genetica - rassen (dieren) - dierveredeling - genetische diversiteit - in-situ conservering - bedreigde rassen - agrarische geschiedenis - ex-situ conservering - animal genetic resources - rare breeds - domestication - domestic animals - genetics - breeds - animal breeding - genetic diversity - in situ conservation - endangered breeds - agricultural history - ex situ conservation
Op de boerderij wordt de diversiteit van het leven bedreigd. Steeds minder dieren krijgen steeds meer nakomelingen. Een gebrek aan genetische variatie in het gevolg. Door inteelt kunnen gezondheidsproblemen ontstaan, en ongemerkt kunnen bepaalde eigenschappen verdwijnen. Ook de variatie in ons landschap en zelfs op ons bord verdwijnt. Dit cahier biedt een helder overzicht van de stand van de wetenschap rond het behoud van zeldzame huisdierrassen.
Het paard in Nederland
Weerdt, M. de; Oldenbroek, J.K. - \ 2010
Wageningen : Centrum voor Genetische Bronnen Nederland (CGN) (CGN rapport 17) - 44
paarden - paardenrassen - gelderlander (paardenras) - paardenfokkerij - domesticatie - zeldzame rassen - fries (paardenras) - groninger paard - nederlands trekpaard - horses - horse breeds - gelderland (horse breed) - horse breeding - domestication - rare breeds - frisian (horse breed) - groningen horse - dutch draught horse
Paardenrassen, die hun oorsprong hebben in Nederland, zijn het Friese paard, het Gelderse paard, de Groninger en het Nederlands trekpaard. Dit verslag over de rol en de toekomst van de Nederlandse paardenrassen beschrijft de domesticatie van het paard en het ontstaan en de ontwikkeling van deze rassen. Daarna komt de huidige paardenfokkerij aan bod. Het verslag wordt afgerond met een hoofdstuk over het belang van het behoud van deze rassen.
Are pigs sensitive to variability in food rewards?
Jonge, F.H. de; Ooms, M. ; Kuurman, W.W. ; Maes, J.H.R. ; Spruijt, B.M. - \ 2008
Applied Animal Behaviour Science 114 (2008)1-2. - ISSN 0168-1591 - p. 93 - 104.
animal-welfare - starlings preferences - foraging strategies - sus-scrofa - behavior - domestication - choice - predictability - reinforcement - motivation
Pigs are non-specialist feeders with high capacities to adapt their diets within wide limits to prevailing and unpredictable conditions. Under husbandry conditions however, pigs are usually fed under extremely predictable conditions, i.e. with highly uniform and standardized diets, ad libitum or at standardized times. Although pigs, in this way, obtain their food with the lowest amount of effort and costs, studies in various different species have shown that animals may prefer to work for food, rather than receiving food for free. In addition, recent studies showed that animals may also be sensitive to risk and variance associated with food sources which may be expressed as a preference for unpredictable over predictable schedules when working for food in an operant task (risk-sensitive foraging). Since feeding is an important aspect of the daily animal husbandry routine which is likely to have a high impact on animal welfare, it is important to know whether (domesticated) pigs also prefer to work for unpredictable as opposed to predictable feeding schedules under husbandry conditions. For that purpose, nine gilts (Finish Landrace x York) were trained to respond in a two-choice operant task. In Test 1, pigs could choose between response options associated with either a FI-8 s schedule (predictable delay) or a VI-8 s reinforcement schedule (unpredictable delay). In Test 2 they could choose between choice options associated with the delivery of either a predictable food item (identical at all times) or an unpredictable food item (differing in nature across trials), delivered according to a FI-8 s schedule. Based upon natural foraging strategies of pigs it was expected that that pigs would prefer the unpredictable options in each test. However, the results from our experiment did not support this hypothesis. Factors that may influence the pig's sensitivity to variability in food rewards, are discussed.
Genetic analysis of results of a Swedish behavior test on German Shepherd Dogs and Labrador Retrievers1
Waaij, E.H. van der; Wilsson, E. ; Strandberg, E. - \ 2008
Journal of Animal Science 86 (2008). - ISSN 0021-8812 - p. 2853 - 2861.
performance traits - sexual-behavior - breed - selection - season - domestication - heritability - adolescents - parameters - position
The objectives of this study were to estimate genetic parameters and the influence of systematic effects on behavior test results in dogs. Behavior test results on 1,813 Labrador Retrievers (LR) and 2,757 German Shepherd Dogs (GSD) were analyzed. The behavior test included observations on courage, defense drive, prey drive, nerve stability, temperament, cooperation, affability, and gun shyness. Sex and age influenced most of the traits, and seasons of birth and testing and litter size and composition influenced some of the traits. Apart from defense drive in GSD, and courage, nerve stability, hardness, and affability in LR, all traits were heritable, with heritabilities ranging from 0.14 for hardness to 0.38 for affability in GSD, and from 0.03 for affability to 0.56 for gun shyness in LR. Genetic correlations ranged from 1.00 (LR) and 0.95 (GSD) between courage and hardness to ¿0.01 (LR) and ¿0.03 (GSD) between gun shyness and defense drive. Most genetic correlations were positive. Correlations with cooperation were mainly negative, especially in GSD. Genetic correlations between courage and defense drive in LR (0.26) and GSD (0.80), between courage and prey drive in LR (0.27) and GSD (0.65), between affability and nerve stability in LR (0.09) and GSD (0.64), between affability and temperament in LR (¿0.24) and GSD (0.39), and between cooperation and hardness in LR (0.28) and GSD (¿0.67) were significantly different between the breeds. Genetic parameters for defense drive and cooperation in GSD and hardness and gun shyness in LR were genetically different between the sexes. Results of this study indicate that correction for systematic effects is essential when making selection decisions. Estimating breeding values would be a good solution, incorporating both correction for systematic effects and using all genetic links. Genetic parameters need to be estimated for each breed separately.
Linkage Disequilibrium Decay and Haplotype Block Structure in the Pig
Amaral, A.J. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Heuven, H.C.M. ; Groenen, M.A.M. - \ 2008
Genetics 179 (2008)1. - ISSN 0016-6731 - p. 569 - 579.
human genome - microsatellite markers - disease genes - sus-scrofa - domestication - breeds - populations - diversity - extent - map
Linkage disequilibrium (LD) may reveal much about domestication and breed history. Ail investigation was conducted, to analyze the extent of LD, haploblock partitioning, and haplotype diversity within haploblocks across several pig breeds from China and Europe and in European wild boar. In total, 371 single-nucleotide-polymorph isms located in three genomic regions were genotyped. The extent of LD differed significantly between European and Chinese breeds, extending tip to 2 cM in Europe and up to 0.05 cM in China. In European breeds, LD extended over large haploblocks tip to 400 kb, whereas in Chinese breeds the extent of LD was smaller and generally did not exceed 10 kb. The European wild boar showed an intermediate level of LD between Chinese and European breeds. In Europe, the extent of LD also differed according to genomic region. Chinese breeds showed a higher level of haplotype diversity and shared high levels of frequent haplotypes with Large White, Landrace, and Duroc. The extent of LD differs between both centers of pig domestication, being higher in Europe. Two hypotheses can explain these findings. First, the European ancestral stock had a higher level of LD. Second, modern breeding programs increased the extent of LD in Europe and caused differences of LD between genomic regions. Large White, Landrace, and Duroc showed evidence of past introgression from Chinese breeds.
Phenotypic and genetic analysis of the Triticum monococcum - Mycosphaerella graminicola interaction
Jing, H.C. ; Lovell, D. ; Gutteridge, R. ; Jenk, D. ; Kornyukhin, D. ; Mitrofanova, O.P. ; Kema, G.H.J. ; Hammond-Kosack, K.E. - \ 2008
New Phytologist 179 (2008)4. - ISSN 0028-646X - p. 1121 - 1132.
anamorph septoria-tritici - blotch pathogen - winter-wheat - disease resistance - aestivum l. - identification - inheritance - cultivars - genome - domestication
Here, the aim was to understand the cellular and genetic basis of the Triticum monococcum-Mycosphaerella graminicola interaction. Testing for 5 yr under UK field conditions revealed that all 24 T. monococcum accessions exposed to a high level of natural inocula were fully resistant to M. graminicola. When the accessions were individually inoculated in the glasshouse using an attached leaf seeding assay and nine previously characterized M. graminicola isolates, fungal sporulation was observed in only three of the 216 interactions examined. Microscopic analyses revealed that M. graminicola infection was arrested at four different stages post-stomatal entry. When the inoculated leaves were detached 30 d post inoculation and incubated at 100% humidity, abundant asexual sporulation occurred within 5 d in a further 61 interactions. An F2 mapping population generated from a cross between T. monococcum accession MDR002 (susceptible) and MDR043 (resistant) was inoculated with the M. graminicola isolate IPO323. Both resistance and in planta fungal growth were found to be controlled by a single genetic locus designated as TmStb1 which was linked to the microsatellite locus Xbarc174 on chromosome 7Am. Exploitation of T. monococcum may provide new sources of resistance to septoria tritici blotch disease.
The effect of direct and indirect defenses in two wild brassicaceous plant species on a specialist herbivore and its gregarious endoparasitoid
Gols, R. ; Witjes, L.M.A. ; Loon, J.J.A. van; Posthumus, M.A. ; Dicke, M. ; Harvey, J.A. - \ 2008
Entomologia Experimentalis et Applicata 128 (2008)1. - ISSN 0013-8703 - p. 99 - 108.
parasitoid diaeretiella-rapae - cotesia-rubecula - pieris-rapae - trophic level - host-plant - sequestration - infochemicals - domestication - generalist - induction
Most studies on plant defenses against insect herbivores investigate direct and indirect plant defenses independently. However, these defenses are not necessarily mutually exclusive. Plant metabolites can be transmitted through the food chain and can also affect the herbivore's natural enemies. A conflict may arise when a natural enemy is attracted to a plant that is suboptimal in terms of its own fitness. In addition, plant defenses are often studied in cultivated plant species in which artificial selection may have resulted in reduced resistance against insect herbivores. In this study, we investigated both direct and indirect plant defenses in two closely related wild brassicaceous plant species, Brassica nigra L. and Sinapis arvensis L. The herbivore Pieris brassicae L. (Lepidoptera: Pieridae), which is specialized on brassicaceous plant species, developed faster and attained higher pupal mass when reared on B. nigra than on S. arvensis. In contrast, Cotesia glomerata L. (Hymenoptera: Braconidae), which is a gregarious endoparasitoid of P. brassicae caterpillars, developed equally well on P. brassicae irrespective of the food plant on which its host had been reared. The feeding strategy of the parasitoid larvae, that is, selectively feeding on hemolymph and fat body, is likely to allow for a much wider host-size range without affecting the size or development time of the emerging parasitoids. In flight chamber experiments, C. glomerata, which had an oviposition experience in a host that fed on Brussels sprout, exhibited significant preference for host-damaged B. nigra over host-damaged S. arvensis plants. Headspace analysis revealed quantitative and qualitative differences in volatile emissions between the two plant species. This parasitoid species may use a range of cues associated with the host and the host's food plant in order to recognize the different plant species on which the host can feed. These results show that there is no conflict between direct and indirect plant defenses for this plant¿host¿parasitoid complex.
Molding maize: the shaping of a crop diversity landscape in the western highlands of Guatemala
Etten, J. van - \ 2006
Journal of Historical Geography 32 (2006)4. - ISSN 0305-7488 - p. 689 - 711.
domestication - intensification - ethnography - subsistence - population - conquest - indians - mexico
Today¿s domesticated plants not only embody past humanenature interactions, but also reflect social history. Human seed exchange, replacement and loss are important forces in shaping crop diversity. This essay explores regional history in relation to the shaping of maize diversity in the western highlands of Guatemala. This is an area of exceptional maize heterogeneity and a peripheral part of the region where maize was domesticated. Maize diversity seems to have developed through geographic isolation in networks of seed exchange that were generally very local in scope. However, recent studies on Mexican maize suggest otherwise. However, few studies have examined crop diversity or seed exchange from a historical perspective. A closer examination of regional history suggests which processes might be important for shaping the present geographical distribution of maize diversity. Seeds were occasionally transported over longer distances. As a consequence, maize diversity is geographically not characterised by sharp differences between farming communities; the main differences are to be found in regional occurrences. This challenges antimodern ideas of closed, local native ecologies. Consequently, the conservation of maize genetic resources is a challenge, but not entirely contradictory with its transforming socio-economic context.
Re-evaluating the taxonomic status of Phaeoisariopsis griseola, the causal agent of angular leaf spot of bean
Crous, P.W. ; Liebenberg, M.M. ; Braun, U. ; Groenewald, J.Z. - \ 2006
Studies in Mycology 55 (2006). - ISSN 0166-0616 - p. 163 - 173.
phaseolus-vulgaris - genetic diversity - uromyces-appendiculatus - variability - wild - origin - mycosphaerella - domestication - landraces - virulence
Angular leaf spot of Phaseolus vulgaris is a serious disease caused by Phaeoisariopsis griseola, in which two major gene pools occur, namely Andean and Middle-American. Sequence analysis of the SSU region of nrDNA revealed the genus Phaeoisariopsis to be indistinguishable from other hyphomycete anamorph genera associated with Mycosphaerella, namely Pseudocercospora and Stigmina. A new combination is therefore proposed in the genus Pseudocercospora, a name to be conserved over Phaeoisariopsis and Stigmina. Further comparisons by means of morphology, cultural characteristics, and DNA sequence analysis of the ITS, calmodulin, and actin gene regions delineated two groups within P. griseola, which are recognised as two formae, namely f. griseola and f. mesoamericana.
Breeding for improved welfare in pigs: a conceptual framework and its use in practice
Kanis, E. ; Belt, H. van den; Groen, A.F. ; Schakel, J. ; Greef, K.H. de - \ 2004
Animal Science 78 (2004)2. - ISSN 1357-7298 - p. 315 - 329.
feather pecking behavior - reproductive-performance - coping strategies - animal-welfare - farm-animals - selection - sows - motivation - domestication - heritability
Welfare of animals can be defined as the kind of feelings the environmental conditions bring about in the animals. These feelings depend on the needs of the animals and their degree of satisfaction. Needs of animals, and so their welfare, are partly genetically determined. Therefore, welfare can be changed by breeding. The aim of this study was to investigate how welfare of pigs under modern intensive farm conditions can be improved by genetic selection, with emphasis on the precise definition of the breeding goal and determination of the animal characteristics on which selection can be based in practice. The existing thermoregulation model was used to develop a conceptual framework that describes welfare of growing pigs and production sows with respect to each of their needs as a curvilinear function of the respective environmental conditions. The framework assumes that welfare in terms of feelings is reflected by the physiological and behavioural mechanisms the pig has to activate in order to cope with the various environmental conditions it encounters. Based on those physiological and behavioural responses to changing conditions, five welfare zones can be distinguished for each need. Breeding goals for welfare were defined in terms of the transition points between these welfare zones, such that future pigs would better cope with unfavourable or unfamiliar farming conditions, therewith quickening the domestication process, to some extent. However, as long as genetic parameters for these transition points are not available, more common welfare-related characteristics like temperament, stress resistance and robustness can be included in the breeding goal, as an alternative. For selection among potential breeding candidates, transition points between welfare zones can be determined in sib tests, thereby also collecting the data for estimating genetic parameters. As a cheaper alternative, breeding candidates could be tested under hard conditions and selected on their coping success. In addition, various behavioural tests and operant conditioning tests ( to test a pig's motivation to change its actual environment) can be carried out. Under common conditions on the farm, problems associated with coping (like incidences of diseases, injuries, and stereotypies) and/or other relevant traits ( e. g. saliva cortisol levels, longevity and even production traits) should be recorded routinely and used as selection index information. Selection for improved welfare should lead to more tolerant pigs that are better able to cope with possible unfavourable farm conditions by a more efficient use of the adaptation mechanisms they already possess. It should, however, not result in lowering husbandry standards. More research is needed to assess genetic correlations among various welfare aspects and with production traits to prevent undesired side effects in future populations of pigs.
Forest Gardens as an 'intermediate' land-use system in the nature-culture continuum: Characteristics and future potential
Wiersum, K.F. - \ 2004
Agroforestry Systems 61-62 (2004)1. - ISSN 0167-4366 - p. 123 - 134.
agroforestry system - management - domestication - indonesia - sumatra - areas - trees - nepal
Forest gardens are reconstructed natural forests, in which wild and cultivated plants coexist, such that the structural characteristics and ecological processes of natural forests are preserved, although the species composition has been adapted to suit human needs. These agroforests include a range of modified and transformed forests, and form an integral part of local land-use systems. They lie between natural forests and tree-crop plantations in terms of their structure and composition, and low intensity of forest extraction systems and the high intensity plantation systems in terms of their management intensity. Their management is characterized by combined use of silvicultural and horticultural operations, and spatial and temporal variations. These ecologically sustainable systems are often dynamic in species composition in response to changing socioeconomic conditions. Evolved over a long period of time as a result of local community's creativity, forest gardens have still received little attention in agroforestry research, just as in the case of the more intensively domesticated homegardens. The study of forest gardens offers good opportunities for obtaining a better understanding of the 'nature-analogous' agroforestry systems and for developing multifunctional agroforestry systems combining production and biodiversity values.
Diversity makes a difference: Farmers managing inter- and intra-specific tree species diversity in Meru Kenya
Lengkeek, A.G. - \ 2003
University. Promotor(en): Jos van der Maesen. - [S.l.] : S.n. - ISBN 9058089363 - 171
trees - agroforestry - vitex - plant genetic resources - domestication - medicinal plants - biodiversity - kenya - east africa - on-farm research - bomen - genetische bronnen van plantensoorten - domesticatie - medicinale planten - biodiversiteit - oost-afrika
De Oeros: het spoor terug
Vuure, C. van - \ 2003
Wageningen : Wetenschapswinkel (Rapport / Wetenschapswinkel Wageningen UR nr. 186) - ISBN 906754678X - 346
bos primigenius - rundvee - evolutie - uitsterven - dierecologie - morfologie - domesticatie - plantensuccessie - bossen - habitats - natuurlijke historie - paleozoölogie - historische ecologie - cattle - evolution - extinction - animal ecology - morphology - domestication - plant succession - forests - natural history - palaeozoology - historical ecology
"In De oeros ontrafelt Cis van Vuure het spoor terug naar de oorsprong van de in 1627 uitgestorven oeros. Die kwam oorspronkelijk uit Zuidoost-Azië, zijn leefgebied strekte zich uit van Thailand tot West-Europa. De laatste oeros leefde in het gebied rondom de Centraal-Poolse plaats Jaktorów. Van Vuure speurde naar het spoor van de oeros via historische bronnen als tekeningen, boeken en runenverzen en bezoeken aan runderfokkerijen van onder meer Spaanse vechtstieren. De oeros is niet alleen een historisch interessante zoektocht, omdat Van Vuure in twee conclusies direct aansluit bij de huidige natuurdiscussie. De Heck-runderen die nu in de Nederlandse natuur grazen werden in de jaren 1920 door de gebroeders Heck gefokt naar het toen heersende beeld van de oeros. Volgens Van Vuure klopt daar echter weinig van. Volgens hem leek de oeros meer op een Spaans vechtrund. De stier van de oeros had een schofthoogte van 170 à 180 centimeter, de koe 150. Dat is veel groter dan de Heck-runderen. Volgens Van Vuure leefde de oeros in een landschap met dichte bossen, verschillende soorten moerassen en hoogvenen, vooral in de rivierdalen, kwelders en zeggemoerassen. Van Vuure baseert zich hiervoor onder meer op een runenvers uit de negende eeuw, waarin de os de bijnaam 'moerasloper' krijgt, op overleveringen dat oerossen in Egypte langs de Nijl leefden. Dat opent weer nieuwe perspectieven voor de discussie die ecoloog Frans Vera in 2000 opende over hoe het Nederlandse landschap er in vroeger tijden uit heeft gezien, en naar welk evenbeeld we de huidige natuur moeten vormen." (Recensie door Martin Woestenburg, 2003. http://www.woestenburg.nl/)
Wildheid gewogen : samenspel van ethologie en ethiek bij de de-domesticatie van grote grazers
Koene, P. ; Gremmen, B. - \ 2002
Wageningen [etc.] : Wageningen Universiteit [etc.] - ISBN 9789067546829 - 200
herbivoren - begrazing - natuurreservaten - domesticatie - wilde kuddes - dierenwelzijn - diergedrag - ethiek - bedrijfsvoering - herbivores - grazing - nature reserves - domestication - feral herds - animal welfare - animal behaviour - ethics - management
Towards domestication of Dimorphotheca pluvialis : studies on the genetic improvement of a potential oilseed crop for industrial applications
Hof, L. - \ 2000
Agricultural University. Promotor(en): P. Stam; Oene Dolstra. - S.l. : S.n. - ISBN 9789058082756 - 95
dimorphotheca - industriële gewassen - domesticatie - genetische verbetering - oliezaden - oilseeds - industrial crops - domestication - genetic improvement
<p>World-wide, but particularly in Western Europe and the USA, the interest in arable crops for non-food use has increased substantially over the past few decades. Surpluses of the major food crops and the industrial interest for renewable resources have led to research and development programmes aiming at the introduction of crops with industrial applications. Particularly vegetable oils with fatty acids containing functional groups are very attractive as substitutes for mineral oils used in the production of e.g. lubricants, surfactants, coatings and polymers. Therefore, in recent years much effort has been made to domesticate wild species containing such oils.</p><p>Although the domestication and development of each new oilseed crop requires a specific approach dependent on the characteristics of the plant species, the history of the crop and its potential uses, some generalisations can be made about the steps involved. Both for crop development (agricultural side) and product development (industrial side), four stages can be distinguished: exploration, examination, expansion and exploitation. A more detailed description of this concept, known as the '4-ex model', can be found in Chapter 1 of this thesis.</p><p>In 1986, the first of a series of projects on potential industrial crops in the Netherlands was launched. Around 40 oilseed species were evaluated for various agronomic characteristics as well as oil content and quality. After considering the industrial interest and agricultural potential, one of the species selected for further breeding research was <em>Dimorphotheca pluvialis</em> (L.) Moench. Seeds of this species contain ca 21% oil with approximately 60-65% dimorphecolic acid (Δ9-hydroxy,10t,12t-octadecadienoid acid). The highly reactive hydroxydiene structure provides this fatty acid with a unique functionality and properties, making it potentially suitable for application in e.g. pharmaceuticals, surfactants, coatings, plastic foams, polymers, fragrances and flavours.</p><p>Although species of the genus <em>Dimorphotheca</em> have been known in the Netherlands as garden ornamentals for several centuries, the use of <em>D. pluvialis</em> for the production of seed oil is completely new. With regard to its use as an arable crop no breeding activities have been reported earlier, and as such the species should be considered as undomesticated. In the exploration of its potential as an arable oilseed crop, several constraints were identified, e.g. a long and unsynchronised period of flowering and seed ripening, poor seed retention and rather low oil content of the seeds. Hence, reported seed and oil yields were erratic. Seed retention seemed difficult to quantify, and preliminary observations revealed little variation for this character. Given the relatively short duration of the projects on which this thesis is based, attention was therefore focused on other important yield limiting factors: flowering synchronisation and oil content. Emphasis was laid on genetic improvement of these traits by means of selection. The efficiency of selection was examined by determination of the response to selection and estimations of the heritability.</p><p>For successful seed production, knowledge on the mode of reproduction of the crop is imperative. In the literature, <em>D. pluvialis</em> is described as a highly allogamous species, but little is known about the mode of pollen transfer. The influence of insects on several yield components was studied by comparing plant populations in the presence and absence of insects (Chapter 2). Exclusion of insects had a dramatic effect on the production of flowers and the duration of the flowering period. The total number of flowers at peak bloom was higher, and flowering continued longer in the absence of insects. Seed weight was somewhat higher, but seed set, seed yield and oil content were severely reduced under these circumstances, thousand seed weight was somewhat higher. The total seed and oil yield of insect-visited plots were, respectively, 4.5 and 5.5 times higher than those of insect-free plots. These results confirm the assumptions on the allogamous nature of the species and underline the importance of insect pollination for adequate seed yield in <em>D. pluvialis</em> .</p><p>Next to seed yield, oil content is a second important oil yield determining factor. High and stable oil yields of good quality are essential to provide industry with a constant supply. Three different populations of <em>D. pluvialis</em> were therefore subjected to mass selection for higher oil content (Chapter 3). After three cycles of selection at an intensity of 10%, for all three populations a significant increase in oil content was observed. Per selection cycle, an average gain in oil content ranging from 0.5% to 1.2% was achieved, depending on the population used. Realised heritabilities for this feature after three selection cycles in these populations ranged from 0.15 to 0.58. In Chapter 4, heritabilities for oil content were estimated from parent-offspring regression and half-sib family variance components. For this, forty plants were selected and progenies were tested twice, in two consecutive years. Heritability estimates from this experiment were moderately low: 0.34 from parent-offspring regression and 0.27 from variance components. If from this experiment 10% of the parental plants had been selected, an increase in oil content of 0.8% in one selection cycle would have been achieved. These values are in accordance with the values mentioned in Chapter 3. Although heritability estimates are specific for populations and environmental circumstances, it is likely that (mass) selection for increased oil content in general will be effective, particularly in the early generations. Considering the observed additive genetic variation in the populations, an average oil content of at least 30% seems feasible.</p><p>Particularly in combination with poor seed retention, the long, unsynchronised period of flowering and seed ripening is undesired. When a crop is harvested too early, yield losses occur due to incomplete setting and maturation of the seeds. When harvested too late, however, seed shattering will account for a severe reduction of seed yield. With regard to synchronisation of flowering, two main components can be distinguished; i.e. the synchronisation between plants and the synchronisation within plants. Synchronisation between plants is attained when plants of a population start flowering at the same time. Synchronisation within a plant is achieved when its flowers are produced in a short period of time. Both components are considered important for improvement of flowering synchronisation of the crop. Therefore, the flowering of individual plants was studied by counting the open flowers at regular time intervals (Chapter 5). It appeared that the flowering process of individual plants can be described mathematically by a logistic curve, obtained by the regression of the cumulative number of open flowers plotted against time. The curve is characterised by three parameters, corresponding with the total number of flowers produced by the plant, the rate of flowering development and the day at which peak bloom was reached. From these parameters, subsequently two other characteristics could be derived, namely onset of flowering and duration of flowering within the plant. Similar to the method described for oil content, heritabilities of the flowering traits were estimated by using parent-offspring regression and half-sib family variance components analyses. Onset of flowering and peak bloom showed high (&gt; 0.69) heritabilities for both methods and both years, and total number of flowers showed moderate to high (0.30 - 0.90) heritability values. For these traits considerable progress may be expected from mass selection, particularly in the early selection generations. Duration of flowering showed low to moderate values (0.25 - 0.45), and thus for improvement of this trait methods other than mass selection should be considered.</p><p>Duration of flowering, total number of flowers and onset of flowering do not seem to be correlated (Chapter 5). Oil content and onset of flowering also seem to be uncorrelated (Chapter 4). Selection for either of these traits will most likely not influence the others.</p><p>Modern agriculture requires uniform plant populations. The currently available populations of <em>D. pluvialis</em> , however, most often originate from botanical gardens or gene banks and show considerable variation for morphological and agronomic traits. To improve morphological uniformity and to determine a preliminary ideotype for plant architecture, divergent mass selection for this character was carried out (Chapter 6). In order to minimise undesired side-effects due to assortative mating caused by variation in onset of flowering, selection for plant architecture was combined with selection for onset of flowering (earliness). Hence, six selection groups were distinguished: all possible combinations of two plant architecture types (erect and procumbent), with three earliness classes (early, middle and late). Three cycles of combined selection resulted in a significant response for both traits in both directions, even at a low selection pressure. In this experiment, selection for early flowering or procumbent architecture showed a better response and a higher heritability than selection for late flowering or erect plant architecture. The different plant architecture selections showed similar flowering development and seed yield. Therefore, from these results no conclusions on ideal architecture type with regard to breeding for increased yield could be drawn. However, for cultivation generally erect plant types are preferred. Earliness did have a significant effect on seed yield: early flowering types showed the highest yields. As the yield experiment was carried out only in one year, and genotype by environment interactions could not be assessed, no firm conclusions on ideotype with regard to earliness could be drawn. Nevertheless, (very) late flowering selections in general are undesired in the Netherlands because of an increased risk of experiencing unfavourable weather conditions during flowering and seed set.</p><p><em>D. pluvialis</em> seems well adapted to the climatic conditions of north-west Europe, and fits well in a crop rotation system with annuals (Chapter 7). Its susceptibility to soil-borne diseases should be taken into consideration, but so far this has not caused major crop damage. Other pests and diseases seem to be easily controlled by agrochemicals. Improvement of resistance to several diseases can most likely be achieved by breeding, and deserves further attention. Genotypes with quick soil cover and improved harvest index may contribute to a higher potential seed production. Apart from further selection for increased oil content and flowering synchronisation, special attention should be directed towards improvement of seed retention. Even under optimal harvest conditions, seed losses of 20% were reported, entirely due to shattering. For good oil quality, relatively expensive methods for oil recovery have to be used. At present, oil of <em>D. pluvialis</em> seems particularly suitable for use in products with a high added value. However, many potential applications have not been explored yet. The unique structure and functionalities of dimorphecolic acid call for further research!</p>
Domestication paysanne des arbres fruitiers forestiers : cas de Coula edulis Bail, Olacaceae, et de Tieghemella heckelii Pierre ex A. Chev., Sapotaceae, autour du Parc National de Taï, Côte d'Ivoire
Bonnéhin, L. - \ 2000
Agricultural University. Promotor(en): R.A.A. Oldeman; R.S.A.R. van Rompaey. - S.l. : S.n. - ISBN 9789051130409 - 140
tieghemella heckelii - olacaceae - bosbestanden - domesticatie - plantenvermeerdering - bosbomen - teelt - agroforestry - biodiversiteit - bosecologie - ivoorkust - nieuwe cultuurgewassen - forest resources - domestication - propagation - forest trees - cultivation - biodiversity - forest ecology - cote d'ivoire - new crops
<p>In Côte d'Ivoire agriculture has confined the forest to national parks and state forests. Forest species are disappearing from the rural landscape and the products of these species get ever rarer. Thus, the rural population goes out collecting these products in national parks and state forests, the access to which is legally is forbidden. This situation leads to numerous conflicts that threaten the long term conservation of these last forest relics. How to ensure this long term conservation and sustainable management of national parks and state forests, or simply of biodiversity in Côte d'Ivoire?</p><p>Maintaining local forest species in the rural landscape may contribute to biodiversity conservation. The path to follow is, that farmers themselves domesticate the forest species they are interested in.</p><p>Domestication is a process in several steps one being to bring into cultivation the wild plants. For this study, the following questions were raised :</p><UL><LI>Which are the forest species that farmers around Taï National Park want to domesticate and for what reasons?<LI>Are these species apt to be domesticated and is their propagation easy on the farm?<LI>How do the farmers conceive the domestication and which socio-cultural and economic factors determine their decisions?<LI>How do the forest species perform as to growth and development during on-farm domestication?</UL><p>To answer these questions, a number of enquiries, direct and participative observations and experiments on farms in the Taï region were undertaken.</p><p>After a participative analysis of local useful forest species in the rural environment, two fruit tree species have been selected, with the agreement of the farmers, to become the subject of this study. They are Makoré ( <em>Tieghemella heckelii,</em> Pierre ex A.Chev., <em></em> Sapotaceae) and Attia ( <em>Coula edulis</em> Baill., Olacaceae). Farmers found problems in obtaining seeds or seedlings of those for biological, ecological or phenological reasons, and this justified our choice. Biology, ecology and socioeconomic aspects of both species have been described.</p><p>On-farm propagation of the species in both vegetative and generative way, using simple techniques available to farmers was experimentally done</p><p>Both types of propagation were successful with Makoré:</p><UL><LI>Germination was rapid and abundant; germination levels up to 90% were reached four weeks after sowing in the tree nursery. These seedlings started branching after two months and measured between 25 and 68 cm high after 4 to 5 months in the nursery;<LI>layered branches developed roots after eight weeks;<LI>73% of cuttings developed roots in a sandy substrate and 41% on a sawdust substrate. No effect could be found of rooting hormone treatment;<LI>Plants reproduce AUBREVILLE's model, which is the basic architectural model of the species by vegetative propagation.</UL><p>With Attia:</p><UL><LI>germination was very slow; the germination strategy of the species is of the Durian type and seems to be suicidal, without success and negatively selective in tropical rain forest; germination levels attain 44 to 75% depending on the length of observation in the nursery. Seedlings branch in a sequential sylleptic way.<LI>the vegetative propagation of the species is not autonomous.</UL><p>Domestication is a very complex process that involves biological, ecological and economic aspects of the species under study as well as the socio-economic situation of the participating farmer. After having treated biological and economical aspects of the species the socio-economic situation of farmers that showed interest in domestication during the study was analysed. Domestication over time from protoculture to the actual cultivation of Makoré in the Taï region was discussed. Protoculture consists of caring for trees issued from natural regeneration and was practised until 1969. At that time forest resources were still abundant and planting trees was a taboo for the farmers. Between 1969 and 1989 the first timid steps were set towards really cultivating forest fruit trees. Farmers secretly planted local forest fruit trees. From 1990 on there has been a certain dynamism to start cultivating these trees, especially Makoré. Makoré seed oil was the primary motivation for domesticating Makoré for 79% of the farmers (N=49), 21% planting them for their seeds and their timber. Three quarters of Makoré farmers were men. Makoré is mainly planted intimately mixed with tree cash crops to optimize the labour factor. Land tenure and land and tree property rights did not seem to hamper domestication. Due to the very long germination period of Attia, it has not been possible to obtain enough seedlings to study the farmers' response to domestication. But the farmers' attitude towards propagation of this species has changed: they have seen germinated <em>C. edulis</em> seeds and they know now that generative propagation is possible.</p><p>Growth and development of Makoré seedlings on the farm were analysed in relation to the cultural system in which Makoré was introduced, and to light and mycorrhizae levels. Growth of Makoré seedlings was found to be positively correlated with the quantity of available light. The species is thus clearly a non-pioneer, but tolerant to full sunlight. In the cultural system 'fallow with <em>Chromolaena odorata</em> after rice culture', Makoré seedlings and saplings found the best ecological conditions during the first stages of development. All soils on which Makoré grew in the Taï region, contained mycorrhizal spores, the closed forest soils most of them. However, no correlation was found between spore density and seedling growth rate.</p><p>All the results were taken together in order to formulate the perspective of domestication by farmers of local forest fruit tree species. In general the cultural blockage against planting indigenous tree species has been dissolved amongst the farmers of the Taï region. The process of domestication thus has started to the west of Taï National Park. Thanks to this process agroforestry systems allowing the conservation or restoration of forest biodiversity in the rural landscape are now being developed in the region. The extension of the agroforestry techniques used by the farmers in this study is advised.</p>
Plant domestication and evolution : a monovular twin or not?
Raamsdonk, L.W.D. van - \ 1996
Wageningen : CPRO-DLO - 101
oorsprong - distributie - vestiging - wilde planten - genetica - genetische variatie - evolutie - soortvorming - immunogenetica - fylogenie - fylogenetica - relaties - gewassen - acclimatisatie - domesticatie - plantkunde - nieuwe cultuurgewassen - economische botanie - origin - distribution - establishment - wild plants - genetics - genetic variation - evolution - speciation - immunogenetics - phylogeny - phylogenetics - relationships - crops - acclimatization - domestication - botany - new crops - economic botany
Overzicht van begrazing met gedomesticeerde dieren in Nederland
Beije, H.M. ; Boer, W.J. den; Wijnhoven, A.L.J. - \ 1996
Bosbouwvoorlichting 35 (1996)7. - ISSN 0166-8986 - p. 84 - 85.
rundvee - domesticatie - geiten - begrazing - paarden - bedrijfsvoering - natuurbescherming - nederland - oorsprong - beleid - schapen - cattle - domestication - goats - grazing - horses - management - nature conservation - netherlands - origin - policy - sheep
Overzicht van beherende organisaties, begraasde oppervlakten, soorten grazers en aantallen grazers
Efforts to accelerate domestication of winged bean (Psophocarpus tetragonolobus (L.) DC.) by means of induced mutations and tissue culture
Klu, G.Y.P. - \ 1996
Agricultural University. Promotor(en): Evert Jacobsen; A.M. van Harten. - S.l. : Klu - ISBN 9789054856047 - 110
oorsprong - distributie - vestiging - psophocarpus tetragonolobus - plantenveredeling - straling - geïnduceerde mutaties - weefselkweek - embryokweek - wilde planten - gewassen - acclimatisatie - domesticatie - plantkunde - nieuwe cultuurgewassen - economische botanie - origin - distribution - establishment - plant breeding - radiation - induced mutations - tissue culture - embryo culture - wild plants - crops - acclimatization - domestication - botany - new crops - economic botany
This thesis describes mutation breeding and tissue culture techniques developed for accelerated domestication of winged bean ( <em>Psophocarpus</em><em>tetragonolobus</em> (L.) DC.). The tissue culture techniques, which are the first steps towards genetic transformation of the crop, include: (1) direct adventitious shoot formation from the axes of cotyledon explants; (2) direct simultaneous regeneration of adventitious shoots and somatic embryos; and (3) direct somatic embryogenesis on the wounds of cotyledon explants. An optimised mutation breeding technique for economic significance, based on the early selection of chlorophyll mutations generated from gamma-radiated seeds, has been developed. The use of this scheme has resulted in the recovery of seed coat colour mutants which have succesfully served as an indirect method for selecting changes in tannin content and nodulation. A desired mutant with reduced tannin content and improved nodulation was selected.
12.000 Jaar zaaien en oogsten, het resultaat : een handleiding bij de demonstratietuin
Peulen, A.P.C. ; Soest, L.J.M. van - \ 1995
Wageningen : CPRO-DLO - 16
genenbanken - genetische bronnen - germplasm - hulpbronnenbehoud - genetische bronnen van plantensoorten - gewassen - acclimatisatie - domesticatie - wilde planten - nederland - nieuwe cultuurgewassen - gene banks - genetic resources - resource conservation - plant genetic resources - crops - acclimatization - domestication - wild plants - netherlands - new crops
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