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.
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