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Insights in the Global Genetics and Gut Microbiome of Black Soldier Fly, Hermetia illucens: Implications for Animal Feed Safety Control
Khamis, Fathiya M. ; Ombura, Fidelis L.O. ; Akutse, Komivi S. ; Subramanian, Sevgan ; Mohamed, Samira A. ; Fiaboe, Komi K.M. ; Saijuntha, Weerachai ; Loon, Joop J.A. Van; Dicke, Marcel ; Dubois, Thomas ; Ekesi, Sunday ; Tanga, Chrysantus M. - \ 2020
Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
16S-metagenomics - genetic diversity - gut microbiome - Hermetia illucens - mitochondrial COI gene
The utilization of the black soldier fly (BSF) Hermetia illucens L. for recycling organic waste into high-quality protein and fat biomass for animal feeds has gained momentum worldwide. However, information on the genetic diversity and environmental implications on safety of the larvae is limited. This study delineates genetic variability and unravels gut microbiome complex of wild-collected and domesticated BSF populations from six continents using mitochondrial COI gene and 16S metagenomics. All sequences generated from the study linked to H. illucens accessions KM967419.1, FJ794355.1, FJ794361.1, FJ794367.1, KC192965.1, and KY817115.1 from GenBank. Phylogenetic analyses of the sequences generated from the study and rooted by GenBank accessions of Hermetia albitarsis Fabricius and Hermetia sexmaculata Macquart separated all samples into three branches, with H. illucens and H. sexmaculata being closely related. Genetic distances between H. illucens samples from the study and GenBank accessions of H. illucens ranged between 0.0091 and 0.0407 while H. sexmaculata and H. albitarsis samples clearly separated from all H. illucens by distances of 0.1745 and 0.1903, respectively. Genetic distance matrix was used to generate a principal coordinate plot that further confirmed the phylogenetic clustering. Haplotype network map demonstrated that Australia, United States 1 (Rhode Island), United States 2 (Colorado), Kenya, and China shared a haplotype, while Uganda shared a haplotype with GenBank accession KC192965 BSF from United States. All other samples analyzed had individual haplotypes. Out of 481,695 reads analyzed from 16S metagenomics, four bacterial families (Enterobactereaceae, Dysgonomonadaceae, Wohlfahrtiimonadaceae, and Enterococcaceae) were most abundant in the BSF samples. Alpha-diversity, as assessed by Shannon index, showed that the Kenyan and Thailand populations had the highest and lowest microbe diversity, respectively; while microbial diversity assessed through Bray Curtis distance showed United States 3 (Maysville) and Netherlands populations to be the most dissimilar. Our findings on genetic diversity revealed slight phylogeographic variation between BSF populations across the globe. The 16S data depicted larval gut bacterial families with economically important genera that might pose health risks to both animals and humans. This study recommends pre-treatment of feedstocks and postharvest measures of the harvested BSF larvae to minimize risk of pathogen contamination along the insect-based feed value chain.
Genebank Operation in the Arena of Access and Benefit-Sharing Policies
Brink, Martin ; Hintum, Theo van - \ 2020
Frontiers in Plant Science 10 (2020). - ISSN 1664-462X
Access and Benefit-Sharing (ABS) - conservation - Convention on Biological Diversity (CBD) - genebanks - genetic diversity - International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) - Nagoya Protocol
Since the 1990s, the exchange of genetic resources has been increasingly regulated. The Convention on Biological Diversity (CBD), the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) and the Nagoya Protocol recognize that countries have sovereign rights over their genetic resources and provide a framework for domestic legislations on Access and Benefit-Sharing (ABS). However, within the rules of these international agreements, countries can follow their own interpretations and establish their own rules and regulations, resulting in restricted access to genetic resources and limited benefit-sharing, effects that are contrary to the objectives of these agreements. Although the ITPGRFA’s Multilateral System of Access and Benefit-Sharing provides opportunities for easier access to plant genetic resources for food and agriculture (PGRFA), plant genebanks face increasing complexity in their operation. Adding material to genebank collections has become more difficult, not only because collecting missions need to be negotiated with national and local authorities, but also because acquiring material from other collections is only possible if the origin of the material is properly documented and is done in compliance with regulations. Genebanks may only provide access to their own collections if the material that is to be released is distributed in compliance with a) the conditions under which the material was received and b) the national laws of the country where the genebank is located. The only way genebanks can deal with this new complexity, apart from ceasing to add or distribute material, is by setting up proper procedures to document the origin of every accession and the conditions for their use and further distribution. To prevent a further decrease in access to PGRFA, complexity must be fought. Applying the ITPGRFA’s Standard Material Transfer Agreement (SMTA) only, even for material that does not fall under the ITPGRFA, would simplify matters. The scope of the ITPGRFA could be expanded to include all crops. Furthermore, certain ambiguities (e.g. regarding in situ material and wild species) could be resolved. Finally, compliance with the ITPGRFA should be improved and better monitored.
Phenotypic Variation of Cell Wall Composition and Stem Morphology in Hemp (Cannabis sativa L.): Optimization of Methods
Petit, Jordi ; Gulisano, Agata ; Dechesne, Annemarie ; Trindade, Luisa M. - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
Cannabis sativa - cell wall - fiber quality - genetic diversity - hemp - phenotyping methods - stem morphology
The growing demands for sustainable fibers have stimulated the study of genetic diversity in the quality of hemp fiber (Cannabis sativa L.). Nevertheless, the lack of high-throughput phenotyping methods that are suited for the analysis of hemp fiber, hampers the analysis of many accessions, and consequently the breeding for this complex trait. In the present report, we developed and optimized the throughput of five methods to study the diversity in hemp fiber quality including cell wall extraction, biochemical composition of cell wall polysaccharides, quantification of lignin, quantification of crystalline polysaccharides and morphology of the stems. Six hemp accessions contrasting for cell wall properties were used to assess the throughput and suitability of these methods for genetic studies. The methods presented revealed to be highly repeatable, with low coefficients of variation between technical replicates. With these methods we were able to detect significant phenotypic variation in cell wall composition and stem morphology between the six accessions. In addition, the throughput of the methods has been upgraded to a level that enables their use for phenotyping cell wall traits in breeding programs. The cell wall extraction was optimized to extract enough material for the complete characterization of the cell wall of hemp while reducing the time for the entire analysis. The throughput of the stem morphological analysis was improved by decreasing the timing of fixation, infiltration, and embedding of mature and dry hemp stems. Notwithstanding, our methods already have the potential to phenotype large number of accessions in a relatively short period of time. Our methods will enable exploration of genetic diversity of fiber quality and will contribute to the development of new hemp varieties with advanced quality of fibers.
Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley
Bustos-Korts, Daniela ; Dawson, Ian K. ; Russell, Joanne ; Tondelli, Alessandro ; Guerra, Davide ; Ferrandi, Chiara ; Strozzi, Francesco ; Nicolazzi, Ezequiel L. ; Molnar-Lang, Marta ; Ozkan, Hakan ; Megyeri, Maria ; Miko, Peter ; Çakır, Esra ; Yakışır, Enes ; Trabanco, Noemi ; Delbono, Stefano ; Kyriakidis, Stylianos ; Booth, Allan ; Cammarano, Davide ; Mascher, Martin ; Werner, Peter ; Cattivelli, Luigi ; Rossini, Laura ; Stein, Nils ; Kilian, Benjamin ; Waugh, Robbie ; Eeuwijk, Fred A. van - \ 2019
The Plant Journal 99 (2019)6. - ISSN 0960-7412 - p. 1172 - 1191.
adaptation - barley - common garden trials - exome sequence haplotypes - genetic diversity - genotype-by-environment interactions - H. vulgare ssp. vulgare
Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.
Culturally embedded practices of managing banana diversity and planting material in central Uganda
Kilwinger, F.B.M. ; Rietveld, A.M. ; Groot, J.C.J. ; Almekinders, C.J.M. - \ 2019
Journal of Crop Improvement 33 (2019)4. - ISSN 1542-7528 - p. 456 - 477.
Agro-biodiversity - genetic diversity - Musa sp - seed sourcing strategies - seed system interventions
Formal seed systems aim to provide farmers with high-quality planting material that meets evolving demands and cultivation challenges. East African banana (Musa sp.) systems rely strongly on informal seed exchange. For seed system interventions to have a larger and more sustainable impact in such a context, it is necessary to better understand the informal seed system. We studied the management and replacement dynamics around banana suckers and mats by smallholder farmers in Central Uganda. Data were collected through Focus Group Discussions (n = 4) and semi-structured interviews (n = 23). This study showed that, on average, banana farmers grew 10 different banana cultivars to ensure year-round harvesting and to accommodate multiple consumption and cultural needs. They included cultivars from the formal seed system within their portfolios of banana cultivars while also conserving cultivar diversity. Farmers used a broad array of evaluation criteria to select suckers and preferred to use known sources to assure plant quality. Household characteristics, such as age or wealth, are determinants of mat management and replacement. We concluded that a flexible blend of formal-informal approaches to developing the banana seed system is needed to meet the multiple needs of farm households and to support them in improving productivity and dealing with emerging challenges.
Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs
Upadhyay, Maulik ; Bortoluzzi, Chiara ; Barbato, Mario ; Ajmone-Marsan, Paolo ; Colli, Licia ; Ginja, Catarina ; Sonstegard, Tad S. ; Bosse, Mirte ; Lenstra, Johannes A. ; Groenen, Martien A.M. ; Crooijmans, Richard P.M.A. - \ 2019
Evolutionary Applications 12 (2019)5. - ISSN 1752-4563 - p. 951 - 963.
admixture - African taurine - cattle - genetic diversity - haplotype - indicine ancestry - SNPs - southern European
The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might account for the presence of non-European cattle ancestry in these cattle breeds.
Value of the Dutch Holstein Friesian germplasm collection to increase genetic variability and improve genetic merit
Doekes, H.P. ; Veerkamp, R.F. ; Bijma, P. ; Hiemstra, S.J. ; Windig, J. - \ 2018
Journal of Dairy Science 101 (2018)11. - ISSN 0022-0302 - p. 10022 - 10033.
conservation - dairy cow - gene bank collection - genetic diversity - genetic improvement
National gene bank collections for Holstein Friesian (HF) dairy cattle were set up in the 1990s. In this study, we assessed the value of bulls from the Dutch HF germplasm collection, also known as cryobank bulls, to increase genetic variability and improve genetic merit in the current bull population (bulls born in 2010–2015). Genetic variability was defined as 1 minus the mean genomic similarity (SIMSNP) or as 1 minus the mean pedigree-based kinship (fPED). Genetic merit was defined as the mean estimated breeding value for the total merit index or for 1 of 3 subindices (yield, fertility, and udder health). Using optimal contribution selection, we minimized relatedness (maximized variability) or maximized genetic merit at restricted levels of relatedness. We compared breeding schemes with only bulls from 2010 to 2015 with schemes in which cryobank bulls were also included. When we minimized relatedness, inclusion of genotyped cryobank bulls decreased mean SIMSNP by 0.7% and inclusion of both genotyped and nongenotyped cryobank bulls decreased mean fPED by 2.6% (in absolute terms). When we maximized merit at restricted levels of relatedness, inclusion of cryobank bulls provided additional merit at any level of mean SIMSNP or mean fPED except for the total merit index at high levels of mean SIMSNP. Additional merit from cryobank bulls depended on (1) the relative emphasis on genetic variability and (2) the selection criterion. Additional merit was higher when more emphasis was put on genetic variability. For fertility, for example, it was 1.74 SD at a mean SIMSNP restriction of 64.5% and 0.37 SD at a mean SIMSNP restriction of 67.5%. Additional merit was low to nonexistent for the total merit index and higher for the subindices, especially for fertility. At a mean SIMSNP of 64.5%, for example, it was 0.60 SD for the total merit index and 1.74 SD for fertility. In conclusion, Dutch HF cryobank bulls can be used to increase genetic variability and improve genetic merit in the current population, although their value is very limited when selecting for the current total merit index. Anticipating changes in the breeding goal in the future, the germplasm collection is a valuable resource for commercial breeding populations.
Data from: The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity
Bortoluzzi, C. ; Crooijmans, R.P.M.A. ; Bosse, M. ; Hiemstra, S.J. ; Groenen, M. ; Megens, H.J.W.C. - \ 2018
Bantam - biodiversity - chicken - genetic diversity - molecular characterisation - traditional breed - Gallus gallus
Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams. Commercial white layers are used to contrast the impact of management strategy on genetic diversity and demography. A high proportion of alleles was found to be shared between large fowls and neo-bantams, suggesting gene flow during neo-bantams development. Population admixture analysis supports these findings, in addition to revealing introgression from neo-bantams of the same breed and of phenotypically similar breeds. The prevalence of long runs of homozygosity (ROH) confirms the importance of recent inbreeding. A high diversity in management, carried out in small breeding units explains the high heterogeneity in diversity and ROH profile displayed by traditional breeds compared to commercial lines. Population bottlenecks may explain the long ROHs in large fowls, while repetitive backcrossing for phenotype selection may account for them in neo-bantams. Our results highlight the importance of using markers to inform breeding programmes on potentially harmful homozygosity to prevent loss of genetic diversity. We conclude that bantamisation has generated unique and identifiable genetic diversity. However, this diversity can only be preserved in the near future through structured breeding programmes.
Genetic diversity of potato for nitrogen use efficiency under low input conditions in Ethiopia
Getahun, Baye Berihun - \ 2017
Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): C.G. van der Linden. - Wageningen : Wageningen University - ISBN 9789463436595 - 219
solanum tuberosum - potatoes - genetic diversity - nitrogen - plant breeding - ethiopia - nutrient use efficiency - solanum tuberosum - aardappelen - genetische diversiteit - stikstof - plantenveredeling - ethiopië - nutriëntengebruiksefficiëntie
Potato is a prime food security crop for smallholder farmers in the highland part of North western Ethiopia. In this region, nutrient availability, especially nitrogen (N) is a major constraint for crop productivity. To obtain insight in the possibility of improving potato for growth under low N input conditions in Ethiopia, we evaluated CxE diploid back cross population, modern European and Ethiopian potato cultivars and local Ethiopian cultivars for their ability to grow and produce tubers under low and high N input conditions. The experiments were conducted under rainfed and irrigation conditions. Eighty-eight Dutch cultivars and 9 Ethiopian cultivars were evaluated in three locations in North-western Ethiopia, in 2013 and in 2015. The two years represent two different growth seasons: rain-fed (June-October 2013) and irrigated cultivation (February-June 2015). Similarly 100 CxE diploid back cross potato genotypes were evaluated in both rainfed and irrigation production seasons in 2014. The Growth of the plants was monitored throughout the growth cycle using canopy cover measurements, with modelled canopy characteristics, and other agronomic traits were measured as per the description. The effect of season and location was further investigated by a GGE Biplot genotype-by-environment interaction analysis, and genetic factors determining phenotypic traits and yield were identified through QTL mapping and association mapping. Ethiopian cultivars showed a remarkable, environment-dependent difference in utilisation of the canopy for tuber production. While total photosynthetic capacity was higher in Ethiopian cultivars than in Dutch cultivars in rainfed production season at Injibara, tuber production was higher in Dutch cultivars. This low radiation use efficiency was not observed in the other rain-fed location (Debre-Tabor). A Genotype by Environment analysis using GGE biplots demonstrates that, Irrespective of the N levels and locations, rainfed production season test environments were grouped as one mega environment and irrigation production season test environments as the other mega environment, indicating most of the variation for yield and nitrogen use efficiency (NUE) in the dataset may be caused by the effect of rain-fed vs irrigation season. Further trials are needed to confirm this result. The QTL mapping with the CxE diploid population and GWAS analysis with the Dutch cultivars discovered both season-environment and N-specific QTL as well as constitutive QTLs. Overall, N availability affects Dutch and Ethiopian cultivars differentially, with strong environmental interaction on canopy and yield traits. Rainfed and irrigated seasons in Ethiopia may require different breeding programs for improved yield under varying fertilizer levels. Both constitutive and environment-specific QTLs were identified that may be targets for breeding prorgams towards improved yield under Ethiopian cultivation conditions.
From species to trait evolution in Aethionema (Brassicaceae)
Mohammadin, Setareh - \ 2017
Wageningen University. Promotor(en): M.E. Schranz. - Wageningen : Wageningen University - ISBN 9789463431385 - 125
brassicaceae - evolution - rna - genomes - genetic diversity - phytogeography - glucosinolates - quantitative trait loci - next generation sequencing - brassicaceae - evolutie - rna - genomen - genetische diversiteit - plantengeografie - glucosinolaten - loci voor kwantitatief kenmerk - next generation sequencing
The plant family Brassicaceae (or crucifers) is an economically important group that includes many food crops (e.g. cabbages and radishes), horticultural species (e.g. Draba, Iberis, Lunaria), and model plant species (particularly Arabidopsis thaliana). Because of the fundamental importance of A. thaliana to plant biology, it makes the Brassicaceae an ideal system for comparative genomics and to test wider evolutionary, ecological and speciation hypotheses. One such hypothesis is the ‘Whole Genome Duplication Radiation Lag Time’ (WGD-RLT) model for the role of polyploidy on the evolution of important plant families such as the Brassicaceae. The WGD-RLT model indicates a higher rate of diversification of a core-group compared to its sister group, due to a lag time after a whole genome duplication event that made it possible for novel traits or geo- or ecological events to increase the core groups diversification rate.
Aethionema is the species-poor sister genus of the core Brassicaceae and hence is at an important comparative position to analyse trait and genomic evolution of the species-rich core group. Aethionema species occur mainly in the western Irano-Turanian region, which is concordantly the biodiversity hotspot of the Brassicaceae family. Moreover comparing Aethionema to the Brassicaceae core group can help us to understand and test the ‘WGD-RLT’ model. However to be able to do so we first need to know more about Aethionema. In this thesis, I investigated various levels of evolutionary change (from macro, to micro to trait evolution) within the genus Aethionema, with a major focus the emerging model species Aethionema arabicum.
Next generation sequencing has made it possible to use the genomes of many species in a comparative framework. However, the formation of proteins and enzymes, and in the end the phenotype of the whole plant, relies on transcription from particular regions of the genome including genes. Hence, the transcriptome makes it possible to assess the functional parts of the genome. However, the functional part of the genome not only relies on the protein coding genes. Gene regulatory elements like promoters and long non-coding RNAs function as regulators of gene expression and hence are involved in increasing or decreasing transcription. In Chapter 2 I used the transcriptome of four different Aethionema species to understand the lineage specificity of these long non-coding RNAs. Moreover in a comparison with the Brassicaceae core group and Brassicaceae’s sister family the Cleomaceae I show that although the position of long non-coding RNAs can be conserved, their sequences do not have to be.
Most of the Aethionema species occur in the Irano-Turanian region, a politically instable region, making it hard for scientist to collect from. However the natural history collections made throughout the last centuries are a great resource. Combing these collections with the newest sequencing techniques, e.g. next generation sequencing, have allowed me to infer the phylogeny of ~75% of the known Aethionema species in a time calibrated and historical biogeographical framework. Hence, I was able to establish that Aethionema species likely originated from the Anatolian Diagonal and that major geological events like the uplift of the Turkish and Iranian plateau have had a hand in their speciation (Chapter 3).
To examine species-level processes I sequenced and analysed transcriptomes of eight Ae. arabicum accessions coming from Cyprus, Iran and Turkey to investigate population structure, genetic diversity and local adaptation (Chapter 4). The most prominent finding was a ploidy difference between the Iranian and Turkish/Cypriotic lines, whereby the former were (allo)tetraploid and the latter diploid. The tetraploid Iranian lines seem to have one set of alleles from the Turkish/Cypriotic gene-pool. However we do not know where the other alleles come from. In addition to the differences in ploidy level there are also differences in glucosinolate defence compounds between these two populations (Iranian vs Turkish/Cypriotic), with the Iranian lines lacking the diversity and concentration of indolic glucosinolates that the Turkish/Cypriotic lines have. This chapter serves as a good resource and starting point for future research in the region, maybe by using the natural history collections that are at hand.
Glucosinolates (i.e. mustard oils) are mainly made by Brassicales species, with their highest structural diversity in the Brassicaceae. In Chapter 5, I examined two Ae. arabicum lines (CYP and TUR) and their recombinant inbred lines to assess glucosinolate composition in different tissues and throughout the plants development. The levels of glucosinolates in the leaves changed when Ae. arabicum went from vegetative to a reproductive state. Moreover, a major difference in glucosinolate content (up to 10-fold) between CYP and TUR indicates a likely regulatory pathway outside of the main glucosinolate biosynthesis pathway. Multi-trait and multi-environment QTL analyses based on leaves, reproductive tissues and seeds identified a single major QTL. Fine mapping this region reduced the interval to only fifteen protein coding genes, including the two most intriguing candidates: FLOWERING LOCUS C (FLC) and the sulphate transporter SULTR2;1. These findings show an interesting correlation between development and defence.
Finally, Chapter 6 gives a final discussion of this thesis and its results. It brings the different topics together, put them in a bigger picture and look forward to new research possibilities.
Genetics of equine insect bite hypersensitivity and genetic diversity in horses
Shrestha, Merina - \ 2017
Wageningen University. Promotor(en): Henk Bovenhuis; D.J. de Koning, co-promotor(en): Bart Ducro; A.M. Johansson. - Wageningen : Wageningen University - ISBN 9789463430166
paarden - equus - insectenbeten - overgevoeligheid - diergenetica - genetische diversiteit - genetische variatie - allergische reacties - horses - equus - insect bites - hypersensitivity - animal genetics - genetic diversity - genetic variation - allergic reactions
Genetic variation contributing to the phenotypic variation was utilized in this thesis to understand the genetic background of a complex trait IBH, and to understand genetic diversity and relationships between various horse populations.
IBH is the most common skin allergic disorder in horses, caused by bites of midges, predominantly Culicoides species. It affects various horse breeds worldwide. With no effective treatment, IBH degrades horse health and causes economic loss. In this thesis, we used genome-wide SNPs to identify regions contributing to genetic variance of IBH susceptibility. We also investigated influence of increased number of horses and dense SNPs on identification of genomic regions associated to IBH susceptibility. Multiple genomic regions with small effects were observed in Studies I-III. Interesting genomic regions in the Icelandic horse population across the studies I and II, was observed on chromosomes 1, 7, 10, 15 and 17. The percentage of the genetic variance explained by top ten windows increased from 3.07% (Study I) to 6.56% (Study II). Novel genomic regions were identified when number of Icelandic horses was increased in Study II. Using dense SNPs on the Exmoor pony population we identified novel genomic regions, on chr 8, associated to IBH susceptibility, though with borderline significance.
In Study IV, pre-conceived understanding about evolutionary history of horse populations matched obtained results from investigation of genetic relationships within Dutch warmblood populations (pairwise mean FST ≤ 0.070), and within pony-like populations (pairwise mean FST ≤ 0.078). Horse populations with similar genetic background might share similar genetic components for IBH susceptibility. The Friesian horse population had lowest diversity (mean inbreeding coefficients: fi: 30.4%, fiROH= 22.2%) in Study IV and was genetically distinct (FST ranged from 0.13 to 0.17). This might be a result of a history of several population bottlenecks and selection on a closed breeding scheme. Low diversity in immunity related genes, observed in the Friesian horse population, might have led to increased prevalence of IBH. Similarly, low susceptibility of IBH in a warmblood population, KWPN sport horse population might be due to high genetic diversity ( =-6.9%). High genetic diversity in KWPN sport horse population might be a result of an open breeding scheme and interbreeding with other warmblood populations.
Data from: Distinguishing migration events of different timing for wild boar in the Balkans
Alexandri, Panoraia ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Groenen, M. ; Goedbloed, D.J. ; Herrero Medrano, J.M. ; Rund, L.A. ; Schook, Lawrence B. ; Chatzinikos, Evangelos ; Triantaphyllidis, Costas ; Triantafyllidis, Alexander - \ 2016
Wageningen University & Research
SNPs - population genetics - recent migration - genetic diversity - mammal - microsatellites - Sus scrofa
Aim: We compared the power of different nuclear markers to investigate genetic structure of southern Balkan wild boar. We distinguished between historic events, such as isolation in different refugia during glacial periods, from recent demographic processes, such as naturally occurring expansions. Location: Southern Balkans/Greece. Methods: We sampled 555 wild boars from 20 different locations in southern Balkans/Greece. All individuals were analysed with 10 microsatellites and a subgroup of 91 with 49,508 single nucleotide polymorphisms (SNPs). Patterns of genetic structure and demographic processes were assessed with Bayesian clustering, linkage disequilibrium and past effective population size estimation analysis. Results: Both microsatellite and SNP data analyses detected genetic structure caused by historic events and support the existence of three groups in the studied area. A hybrid zone between two of the groups was also detected. We also showed that genome-wide SNP data analysis can identify recent events in bottlenecked populations. Main conclusions: We inferred the three groups diverged ~50,000–10,000 yr bp when populations contracted to different refugia. Our findings strengthened the evidence that the southern Balkan area was a glacial refugium including further local smaller refugia. Genome-wide genotyping inferred a recent population expansion that can mimic a ‘refugium within refugium’ scenario. It seems that microsatellite data tend to overestimate genetic structure when genetic drift happens in bottlenecked populations over a short distance. Therefore, genome-wide SNPs are more powerful at inferring phylogeography in natural populations, resolving inconsistencies from mitochondrial and microsatellite data sets.
Genenweelde in oorsprongsgebieden essentieel voor toekomstige voedselzekerheid
Struik, Paul ; Hintum, Theo van - \ 2016
food security - genetic diversity - field crops - gene banks - plant breeding - genetic engineering - biodiversity - malus - varieties - kazakhstan - middle east
Behoud van genetische diversiteit is een belangrijk wapen om in te spelen op veranderingen in de leefomstandigheden van landbouwgewassen. Genenbanken vormen een onmisbare basis voor plantenveredeling, maar bieden onvoldoende waarborg voor toekomstige voedselzekerheid. Ook de lokale genenweelde in de oorsprongsgebieden moet behouden blijven, maar die wordt bedreigd door verstedelijking, verwaarlozing en klimaatverandering, constateert Michiel Löwik.
Werken aan diversiteit in tarwe en groenten : voor meer variatie op het veld, in het winkelschap en op het bord
Nuijten, Edwin ; Lammerts van Bueren, Edith - \ 2016
Driebergen : Louis Bolk Instituut (Publicatie / Louis Bolk Instituut 2016-030 LbP) - 20
kwekers - biologische landbouw - rassen (planten) - tarwe - zaden - plantenveredeling - groenten - genetische diversiteit - diversiteit - biologische plantenveredeling - growers - organic farming - varieties - wheat - seeds - plant breeding - vegetables - genetic diversity - diversity - organic plant breeding
Van 2014 tot 2016 heeft het Louis Bolk Instituut onderzoek gedaan naar de mogelijkheden van een breder assortiment in gewassen voor de teler (op het veld) en voor de consument (op het bord). Aanleiding voor het onderzoek is dat het aantal rassen dat aangepast is aan biologische teeltomstandigheden (rassen die dus zonder gebruik van kunstmest en bestrijdingsmiddelen kunnen) beperkt is en blijft. Veel veredelingsbedrijven kunnen vanwege de ontwikkelingskosten geen aparte rassen ontwikkelen voor een kleine markt. Meestal worden rassen uit het bestaande (gangbare) assortiment geselecteerd voor biologische vermeerdering. Bovendien zijn biologische telers en handelaren meegegaan in de huidige eisen voor hoge opbrengst en uniforme eindproducten. Het aanbieden van zaadvaste rassen in plaats van bijvoorbeeld hybride rassen is daarmee commercieel niet meteen vanzelfsprekend. Divers en Dichtbij Van 2014 tot 2016 heeft het Louis Bolk Instituut onderzoek gedaan naar de mogelijkheden van een breder assortiment in gewassen voor de teler (op het veld) en voor de consument (op het bord). Dit onderzoek is samen met Estafette Odin BV en de biologische dynamische telers GAOS in Swifterbant, De Groenen Hof in Esbeek en de Maatschap Dames en Heren Vos in Kraggenburg uitgevoerd. Het doel van dit project Divers en Dichtbij was de diversiteit op het veld en op het bord te vergroten. Daarmee bedoelen we niet alleen meer verschillende rassen, maar vooral andere type rassen of populaties die zelf meer genetische variatie bezitten. Dat kan door te kiezen voor zaadvaste rassen bij groentegewassen en populaties bij granen. Tot nu toe is populatieveredeling alleen toegepast bij granen en nog niet of nauwelijks bij groentegewassen (zie voor definities Box 1 op pagina 7). Dit betekent ook een keuze voor andere manieren van veredelen en selecteren. Aanleiding voor het onderzoek is dat het aantal rassen dat aangepast is aan biologische teeltomstandigheden (rassen die dus zonder gebruik van kunstmest en bestrijdingsmiddelen kunnen) beperkt is en blijft. Veel veredelingsbedrijven kunnen vanwege de ontwikkelingskosten geen aparte rassen ontwikkelen voor een kleine markt. Meestal worden rassen uit het bestaande (gangbare) assortiment geselecteerd voor biologische vermeerdering. Bovendien zijn biologische telers en handelaren meegegaan in de huidige eisen voor hoge opbrengst en uniforme eindproducten. Het aanbieden van zaadvaste rassen in plaats van bijvoorbeeld hybride rassen is daarmee commercieel niet meteen vanzelfsprekend. En toch heeft ons brede speurwerk in dit project wel degelijk een aantal interessante zaadvaste rassen opgeleverd! Want gelukkig zijn er in Europa en Amerika diverse biologische veredelaars actief in het veredelen van zaadvaste rassen en populaties. De informatie in deze brochure is bedoeld voor telers en andere ketenpartijen om meer te leren over de mogelijkheden van zaadvaste rassen bij groenten en populaties bij tarwe.
The origin, versatility and distribution of azole fungicide resistance in the banana black Sigatoka pathogen Pseudocercospora fijiensis
Chong Aguirre, Pablo A. - \ 2016
Wageningen University. Promotor(en): Gert Kema; Pedro Crous. - Wageningen : Wageningen University - ISBN 9789462578791 - 289
pseudocercospora - plant pathogenic fungi - fungicides - pesticide resistance - defence mechanisms - genetic diversity - genetic mapping - sensitivity - musa - bananas - fungal diseases - disease control - pseudocercospora - plantenziekteverwekkende schimmels - fungiciden - resistentie tegen pesticiden - verdedigingsmechanismen - genetische diversiteit - genetische kartering - gevoeligheid - musa - bananen - schimmelziekten - ziektebestrijding
Pseudocercospora fijiensis causes black Sigatoka disease of banana. It is one of the most damaging threats of the crop requiring excessive fungicide applications for disease control as the major export “Cavendish” clones are highly susceptible. The consequence of this practice is the reduced efficacy of disease management strategies due to increasing levels of fungicide resistance. In this thesis the history and current practices of black Sigatoka disease management as well as the underlying mechanisms of fungicide resistance to a major group of fungicides are described. We discovered that both target site mutations and promotor insertions are crucial for modulating sensitivity. The more insertions, the higher the expression of the gene and the more resistant the strain. Using this information, we advocate modern monitoring techniques and improved disease control strategies as well as the urgent need for innovative banana breeding to develop resistant varieties for a sustainable global banana production.
Targets and tools for optimizing lignocellulosic biomass quality of miscanthus
Weijde, R.T. van der - \ 2016
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Luisa Trindade; Oene Dolstra. - Wageningen : Wageningen University - ISBN 9789462578388 - 231
miscanthus - bioethanol - biomass - biofuels - lignocellulose - fuel crops - plant breeding - cell walls - cell wall components - genetic diversity - genetic variation - biomass conversion - biobased economy - miscanthus - bioethanol - biomassa - biobrandstoffen - lignocellulose - brandstofgewassen - plantenveredeling - celwanden - celwandstoffen - genetische diversiteit - genetische variatie - biomassaconversie - biobased economy
Miscanthus is a perennial energy grass characterized by a high productivity and resource-use efficiency, making it an ideal biomass feedstock for the production of cellulosic biofuels and a wide range of other biobased value-chains. However, the large-scale commercialization of converting biomass into cellulosic biofuel is hindered by our inability to efficiently deconstruct the plant cell wall. The plant cell wall is a complex and dynamic structure and its components are extensively cross-linked into an unyielding matrix. The production of biofuel depends on the extraction, hydrolysis and fermentation of cell wall polysaccharides, which currently requires energetically and chemically intensive processing operations that negatively affect the economic viability and sustainability of the industry. To address this challenge it is envisioned that the bioenergy feedstocks can be compositionally tailored to increase the accessibility and extractability of cell wall polysaccharides, which would allow a more efficient conversion of biomass into biofuel under milder processing conditions.
Extensive phenotypic and genetic diversity in cell wall composition and conversion efficiency was observed in different miscanthus species, including M. sinensis, M. sacchariflorus and interspecific hybrids between these two species. In multiple experiments a twofold increase in the release of fermentable sugars was observed in ‘high quality’ accessions compared to ‘low quality’ accessions. The exhaustive characterization of eight highly diverse M. sinensis genotypes revealed novel and distinct breeding targets for different bioenergy conversion routes. The key traits that contributed favourably to the conversion efficiency of biomass into biofuel were a high content of hemicellulosic polysaccharides, extensive cross-linking of hemicellulosic polysaccharides (revealed by a high content of trans-ferulic acids and a high ratio of arabinose-to-xylose), a low lignin content and extensive incorporation of para-coumaric acid into the lignin polymer.
Lignin is widely recognized as one of the key factors conveying recalcitrance against enzymatic deconstruction of the cell wall. The incorporation of para-coumaric acid into the lignin polymer is hypothesized to make lignin more easily degradable during alkaline pretreatment, one of the most widely applied processing methods that is used to pretreat biomass prior to enzymatic hydrolysis. Previous studies have shown that reducing lignin content is often implicated in reduced resistance of plants to lodging. We hypothesize that extensively cross-linked hemicellulosic polysaccharides may fulfil a similar function in supporting cell wall structural rigidity and increasing the content of hemicellulosic polysaccharides may be a way to reduce lignin content without adversely affecting cell wall rigidity. This strategy can be used to improve biomass quality for biobased applications, as hemicellulosic polysaccharides are more easily degradable during industrial processing than lignin. Furthermore, hemicellulosic polysaccharides adhere to cellulose, which negatively affects the level of cellulose crystallinity. Crystalline cellulose is harder to degrade than its more amorphous form. Therefore the reduction of cellulose crystallinity is another mechanism through which increasing the content of hemicellulosic polysaccharides positively contributes to cell wall degradability. These results provided new insights into the traits that may be targeted to improve the quality of lignocellulose feedstocks.
However, evaluation of complex biochemical traits for selection purposes is hindered by the fact that their accurate quantification is a costly, lengthy and laborious procedure. To overcome these limitations an accurate and high-throughput method was developed based on near-infrared spectroscopy. Through extensive calibration we developed accurate prediction models for a wide range of biomass quality characteristics, which may be readily implemented as a phenotyping tool for selection purposes.
Additionally, progress through breeding may substantially be improved by marker-assisted selection, which will reduce the need for the evaluation of genotype performance in multi-year field trials. To this end, a biparental M. sinensis mapping population of 186 individuals was developed and genotyped using a genotyping-by-sequencing approach. A total of 564 short-sequence markers were used to construct a new M. sinensis genetic map. Cell wall composition and conversion efficiency were observed to be highly heritable and quantitatively inherited properties. This is the first genetic study in miscanthus to map quantitative trait loci (QTLs) for biomass quality properties and is a first step towards the application of marker-assisted selection for biomass quality properties.
Through the evaluation of a diverse set of miscanthus genotypes in multiple locations we demonstrated that in addition to genotypic variation, growing conditions may have a substantial influence on cell wall composition and conversion efficiency. While further research is needed to identify which specific environmental parameters are responsible for the observed effects, these results clearly indicate that the environmental influence on biomass quality needs to be taken into account in order to match genotype, location and end-use of miscanthus as a lignocellulose feedstock. Moreover, significant genotype-by-environment interaction effects were observed for cell wall composition and conversion efficiency, indicating variation in environmental sensitivity across genotypes. Although the magnitude of the genotypic differences was small in comparison to genotype and environmental main effects, this affected the ranking of accession across environments. Stability analysis indicated some stable accessions performed relatively across diverse locations.
In addition to trialing miscanthus in diverse locations, we also evaluated miscanthus biomass quality under drought conditions for a number of reasons: 1) drought stress is linked to a differential expression of cell wall biosynthesis genes, 2) incidence of drought events is increasing due to climate change, 3) irrigation is likely to be uneconomical during the cultivation of miscanthus and 4) miscanthus has many characteristics that make it a crop with a good potential for cultivation on marginal soils, where abiotic stresses such as drought may prevail. Drought stress was shown to result in a large reduction in cell wall and cellulose content and a substantial increase in hemicellulosic polysaccharides and cellulose conversion rates. We hypothesized that the reduction in cellulose content was due to an increase in the production of osmolytes, which are well-known for their role in plant protection against drought. The results indicated that drought stress had a positive effect on the cell wall degradability of miscanthus biomass.
Overall the compendium of knowledge generated within the framework of this thesis provided insights into the variation in biomass quality properties in miscanthus, increased our understanding of the molecular, genetic and environmental factors influencing its conversion efficiency into biofuel and provided tools to exploit these factors to expand the use of miscanthus as a lignocellulose feedstock.
Flinke uitbreiding genenbank voor Nederlandse paardenrassen
Hoving, A.H. ; Wit, A.A.C. de; Sulkers, H. - \ 2016
Zeldzaam huisdier 41 (2016)1. - ISSN 0929-905X - p. 20 - 21.
genenbanken - paardenrassen - genetische diversiteit - zeldzame rassen - gene banks - horse breeds - genetic diversity - rare breeds
Het Centrum voor Genetische Bronnen Nederland (CGN) bewaart sperma
van Nederlandse paardenrassen in de genenbank voor landbouwhuisdieren.
Doel is het veiligstellen van de genetische diversiteit binnen
Potato breeding in the Netherlands: successful collaboration between farmers and commercial breeders
Almekinders, C.J.M. ; Mertens, L. ; Loon, Jan van; Lammerts Van Bueren, E. - \ 2016
Farming Matters 32 (2016)Special Issue April. - ISSN 2210-6499 - p. 34 - 37.
potatoes - table potatoes - plant breeding - netherlands - cooperation - farmers - genetic diversity - firms - agricultural law - new variety - organic farming - aardappelen - consumptieaardappelen - plantenveredeling - nederland - samenwerking - boeren - genetische diversiteit - firma's - agrarisch recht - nieuwe variëteit - biologische landbouw
The Dutch potato breeding model, which involves a partnership between farmers and commercial breeding companies in a modern, Western context, is unique. While there are other examples of collaborative relationships between farmers and breeders in Europe, the Dutch potato breeding model stands out in terms of its long track record, the involvement of the private sector, and the institutional integration of the relationship which up to today facilitates access to genetic materials and financial benefit sharing.
Development of a breeding strategy for nitrogen use efficiency in spinach (Spinacia oleracea L.)
Chan Navarrete, J.R. - \ 2016
Wageningen University. Promotor(en): Edith Lammerts van Bueren, co-promotor(en): Oene Dolstra; Gerard van der Linden. - Wageningen : Wageningen University - ISBN 9789462577961 - 161
spinacia oleracea - spinach - plant breeding - nitrogen - nutrient use efficiency - genetic mapping - nitrogen fertilizers - fertilizer application - genetic diversity - nitrogen response - spinacia oleracea - spinazie - plantenveredeling - stikstof - nutriëntengebruiksefficiëntie - genetische kartering - stikstofmeststoffen - bemesting - genetische diversiteit - stikstofrespons
Spinach (Spinacia oleracea L.) is one of the most consumed leafy vegetables worldwide and it is considered to be highly nutritious. Spinach is a short-cycle leafy crop that has a high demand for nitrogen in order to rapidly come to a harvestable product that has the required dark green colour within a reasonable harvest window. In commercial production of spinach the recovery of N is poor, which may result in environmental pollution. To increase sustainability of both organic and conventional spinach cultivation there is a need to reduce the dependency on high levels of nitrogen. Growers therefore urgently need cultivars with a satisfactory yield under reduced N input conditions. Nitrogen use efficiency (NUE), defined as the ability to produce high biomass per unit N applied, is low in spinach. The present study aims to evaluate spinach genotypes for selectable traits under varying N supply and provide tools and knowledge to facilitate the development of varieties with good yield, quality and stability under low N input. To minimise environmental variation affecting the identification of traits related to NUE a screening method was developed using a hydroponics system. The genetic diversity for NUE related traits was first studied with 24 commercial cultivars under contrasting levels of N supply based on the Ingestad model with a steady-state N application. This demonstrated that the hydroponics screening strategy as a pre-screening tool enabled reliable detection of heritable variation among cultivars for NUE-related traits under optimal as well as suboptimal N input. Shoot dry weight and leaf area were preferred selectable traits for the detection of heritable differences contributing to NUE in spinach. The effect of N application strategy was examined in seven cultivars grown under hydroponics conditions with low and high N levels supplied either as a single bulk N application resembling N fertilization in field cultivation, or a steady-state N application according to Ingestad. The latter application strategy provided more stable and reproducible conditions for determination of genetic differences in NUE under low N conditions for a short-cycle leafy vegetable crop. Several tools for molecular genetic evaluation of NUE in spinach were provided as well, including a SNP marker set for marker-assisted breeding, a genetic mapping population with a corresponding genetic map, and the identification of two major QTL regions contributing to growth under low N conditions. With these tools, an efficient strategy for breeding for NUE efficiency in spinach would include screening under controlled conditions at high and low N using leaf area, biomass and root to shoot ratio as selectable traits, and QTL identification of genetic factors that can be targeted and combined using marker-assisted selection. An in depth genotype by environment interaction analysis using six field trials showed that environmental factors like temperature, soil, and management strongly influence nitrogen availability in the soil in a short cycle crop like spinach. This severely complicates selection and breeding for NUE of spinach under field conditions, and emphasizes the importance of performing trials under better controllable conditions for genetic dissection of NUE and discovery of genetic factors contributing to NUE. It also underscores the importance of validating these findings in various field trials. Multi-environment field trials with different levels of N fertilization will then allow selection of cultivars that combine stable performance under various low input growing conditions with high yields under more favorable conditions.
Conservation genetics of the frankincense tree
Bekele, A.A. - \ 2016
Wageningen University. Promotor(en): Frans Bongers, co-promotor(en): Rene Smulders; K. Tesfaye Geletu. - Wageningen : Wageningen University - ISBN 9789462576865 - 158
boswellia - genomes - dna sequencing - tropical forests - genetic diversity - genetic variation - genetics - forest management - plant breeding - boswellia - genomen - dna-sequencing - tropische bossen - genetische diversiteit - genetische variatie - genetica - bosbedrijfsvoering - plantenveredeling
Boswellia papyrifera is an important tree species of the extensive Combretum-Terminalia dry tropical forests and woodlands in Africa. The species produces a frankincense which is internationally traded because of its value as ingredient in cosmetic, detergent, food flavor and perfumes productions, and because of its extensive use as incense during religious and cultural ceremonies in many parts of the world. The forests in which B. papyrifera grows are increasingly overexploited at the expense of the economic benefit and the wealth of ecological services they provide. Populations of B. papyrifera have declined in size and are increasingly fragmented. Regeneration has been blocked for the last 50 years in most areas and adult productive trees are dying. Projections showed a 90% loss of B. papyrifera trees in the coming 50 years and a 50% loss of frankincense production in 15 years time.
This study addressed the conservation genetics of B. papyrifera. Forty six microsatellite (SSR) markers were developed for this species, and these genetic markers were applied to characterize the genetic diversity pattern of 12 B. papyrifera populations in Ethiopia. Next to this, also the generational change in genetic diversity and the within-population genetic structure (FSGS) of two cohort groups (adults and seedlings) were studied in two populations from Western Ethiopia. In these populations seedlings and saplings were found and natural regeneration still takes place, a discovery that is important for the conservation of the species.
Despite the threats the populations are experiencing, ample genetic variation was present in the adult trees of the populations, including the most degraded populations. Low levels of population differentiation and isolation-by-distance patterns were detected. Populations could be grouped into four genetic clusters: the North eastern (NE), Western (W), North western (NW) and Northern (N) part of Ethiopia. The clusters corresponded to environmentally different conditions in terms of temperature, rainfall and soil conditions. We detected a low FSGS and found that individuals are significantly related up to a distance of 60-130 m.
Conservation of the B. papyrifera populations is urgently needed. The regeneration bottlenecks in most existing populations are an urgent prevailing problem that needs to be solved to ensure the continuity of the genetic diversity, species survival and sustainable production of frankincense. Local communities living in and around the forests should be involved in the use and management of the forests. In situ conservation activities will promote gene flow among fragmented populations and scattered remnant trees, so that the existing level of genetic diversity may be preserved. Geographical distance among populations is the main factor to be considered in sampling for ex situ conservation. A minimum of four conservation sites for B. papyrifera is recommended, representing each of the genetic clusters. Based on the findings of FSGS analyses, seed collection for ex situ conservation and plantation programmes should come from trees at least 100 m, but preferably 150 m apart.