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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    The Impact of Genomic and Traditional Selection on the Contribution of Mutational Variance to Long-Term Selection Response and Genetic Variance
    Mulder, Herman A. ; Lee, Sang Hong ; Clark, Sam ; Hayes, Ben J. ; Werf, Julius H.J. van der - \ 2019
    Genetics 213 (2019)2. - ISSN 0016-6731 - p. 361 - 378.
    de novo mutation - genetic variance - genomic selection - response to selection - selection strategies

    De novo mutations (DNM) create new genetic variance and are an important driver for long-term selection response. We hypothesized that genomic selection exploits mutational variance less than traditional selection methods such as mass selection or selection on pedigree-based breeding values, because DNM in selection candidates are not captured when the selection candidates' own phenotype is not used in genomic selection, DNM are not on SNP chips and DNM are not in linkage disequilibrium with the SNP on the chip. We tested this hypothesis with Monte Carlo simulation. From whole-genome sequence data, a subset of ∼300,000 variants was used that served as putative markers, quantitative trait loci or DNM. We simulated 20 generations with truncation selection based on breeding values from genomic best linear unbiased prediction without (GBLUP_no_OP) or with own phenotype (GBLUP_OP), pedigree-based BLUP without (BLUP_no_OP) or with own phenotype (BLUP_OP), or directly on phenotype. GBLUP_OP was the best strategy in exploiting mutational variance, while GBLUP_no_OP and BLUP_no_OP were the worst in exploiting mutational variance. The crucial element is that GBLUP_no_OP and BLUP_no_OP puts no selection pressure on DNM in selection candidates. Genetic variance decreased faster with GBLUP_no_OP and GBLUP_OP than with BLUP_no_OP, BLUP_OP or mass selection. The distribution of mutational effects, mutational variance, number of DNM per individual and nonadditivity had a large impact on mutational selection response and mutational genetic variance, but not on ranking of selection strategies. We advocate that more sustainable genomic selection strategies are required to optimize long-term selection response and to maintain genetic diversity.

    Genome-wide association studies for tick resistance in Bos taurus × Bos indicus crossbred cattle : A deeper look into this intricate mechanism
    Otto, Pamela I. ; Guimarães, Simone E.F. ; Verardo, Lucas L. ; Azevedo, Ana Luísa S. ; Vandenplas, Jeremie ; Soares, Aline C.C. ; Sevillano, Claudia A. ; Veroneze, Renata ; Fatima A. Pires, Maria de; Freitas, Célio de; Prata, Márcia Cristina A. ; Furlong, John ; Verneque, Rui S. ; Martins, Marta Fonseca ; Panetto, João Cláudio C. ; Carvalho, Wanessa A. ; Gobo, Diego O.R. ; Silva, Marcos Vinícius G.B. da; Machado, Marco A. - \ 2018
    Journal of Dairy Science 101 (2018)12. - ISSN 0022-0302 - p. 11020 - 11032.
    breed of origin - gene network - genetic variance - Gir × Holstein crossbred
    Rhipicephalus (Boophilus) microplus is the main cattle ectoparasite in tropical areas. Gir × Holstein crossbred cows are well adapted to different production systems in Brazil. In this context, we performed genome-wide association study (GWAS) and post-GWAS analyses for R. microplus resistance in an experimental Gir × Holstein F2 population. Single nucleotide polymorphisms (SNP) identified in GWAS were used to build gene networks and to investigate the breed of origin for its alleles. Tick artificial infestations were performed during the dry and rainy seasons. Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) and single-step BLUP procedure was used for GWAS. Post-GWAS analyses were performed by gene ontology terms enrichment and gene transcription factors networks, generated from enriched transcription factors, identified from the promoter sequences of selected gene sets. The genetic origin of marker alleles in the F2 population was assigned using the breed of origin of alleles approach. Heritability estimates for tick counts were 0.40 ± 0.11 in the rainy season and 0.54 ± 0.11 in dry season. The top ten 0.5-Mbp windows with the highest percentage of genetic variance explained by SNP markers were found in chromosomes 10 and 23 for both the dry and rainy seasons. Gene network analyses allowed the identification of genes involved with biological processes relevant to immune system functions (TREM1, TREM2, and CD83). Gene-transcription factors network allowed the identification of genes involved with immune functions (MYO5A, TREML1, and PRSS16). In resistant animals, the average proportion of animals showing significant SNPs with paternal and maternal alleles originated from Gir breed was 44.8% whereas the proportion of animals with both paternal and maternal alleles originated from Holstein breed was 11.3%. Susceptible animals showing both paternal and maternal alleles originated from Holstein breed represented 44.6% on average, whereas both paternal and maternal alleles originated from Gir breed animals represented 9.3%. This study allowed us to identify candidate genes for tick resistance in Gir × Holstein crossbreds in both rainy and dry seasons. According to the origin of alleles analysis, we found that most animals classified as resistant showed 2 alleles from Gir breed, while the susceptible ones showed alleles from Holstein. Based on these results, the identified genes may be thoroughly investigated in additional experiments aiming to validate their effects on tick resistance phenotype in cattle.
    Non-genetic variance in pigs: genetic analysis of reproduction and production traits
    Sell-Kubiak, E.B. - \ 2015
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Piter Bijma; Herman Mulder. - Wageningen : Wageningen University - ISBN 9789462573291 - 186
    varkens - dierveredeling - voortplanting - dierlijke productie - genetische analyse - genotypische variatie - genomica - fenotypische variatie - pigs - animal breeding - reproduction - animal production - genetic analysis - genetic variance - genomics - phenotypic variation

    Abstract

    Sell-Kubiak, E. (2015). Non-genetic variance in pigs: genetic analysis of reproduction and production traits. PhD thesis, Wageningen University, The Netherlands

    The main objective of this thesis was to study the origin of random variance in reproduction and production traits of pigs. In pig breeding for many traits it is important not only to improve the reproduction and production trait itself, but also its variation. The variance of traits can be used to improve pigs’ productivity, and potentially also to improve uniformity of traits. Results presented in Chapters 2 and 3 show that the proposed approach to explore the origin of common litter variance was not successful. The impact of various sow features on growth rate and feed intake of grow-finish pigs was very small. More importantly, sow features did not explain the phenotypic variance due to common litter effects found in production traits of pigs. In Chapters 4 and 5 the residual variance of birth weight and litter size were found to have a genetic component. The genetic coefficient of variation at residual standard deviation level (GCVSDe) was proposed as a measure of expressing the potential response to selection (Chapter 4). For both traits the estimated GCVSDe was about 10%, indicating sufficient potential for response to selection. In Chapter 4 it was shown that analyzing variation in traits with Double Hierarchical Generalized Linear model (DHGLM) was highly comparable with the conventional analysis of standard deviation of a trait. The correlation between the additive genetic effects for birth weight and the residual variance was 0.6 (Chapter 4), whereas for litter size (TNB) and its residual variance (varTNB) this correlation was 0.5 (Chapter 5). Those moderate correlations are an important indication of the direction of correlated selection response in the mean of those traits. In Chapter 5 in a genome-wide association study for litter size variation, the significant SNPs explained 0.83% of total genetic variance in TNB and 1.44% in varTNB. The most significant SNP explained 0.4% of genetic variance in TNB (chromosome 11) and 0.5% in varTNB (chromosome 7). One of the possible candidate genes for varTNB on chromosome 7 is heat shock protein (HSPCB). Studying the residual variance of traits with DHGLM has a great potential to serve as an alternative to conventional analysis to study and to select for improved uniformity of various traits. Lastly, Chapter 6 focuses on discussion of the findings of this thesis and their overall importance for pig breeding, as well as highly relevant topics for breeding uniform and robust pigs (macro-micro sensitivity analysis and application of genomic selection).

    Cooperative and uniform fish? : social interactions and variability in live body weight in the GIFT strain (Nile tilapia, Oreochromic niloticus) in Malaysia
    Khaw, H.L. - \ 2015
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Piter Bijma; R.W. Ponzoni. - Wageningen : Wageningen University - ISBN 9789462572157 - 161
    oreochromis niloticus - sociaal gedrag - lichaamsgewicht - variatie - genetische effecten - inteelt - kenmerken - heritability - genotype-milieu interactie - genotypische variatie - genetische verbetering - veredelingsprogramma's - visteelt - maleisië - oreochromis niloticus - social behaviour - body weight - variation - genetic effects - inbreeding - traits - heritability - genotype environment interaction - genetic variance - genetic improvement - breeding programmes - fish culture - malaysia

    Abstract

    Khaw, HL. (2014). Cooperative and uniform fish? Social interactions and variability in live body weight in the GIFT strain (Nile tilapia, Oreochromic niloticus) in Malaysia. PhD thesis, Wageningen University, the Netherlands.

    Social interactions are present everywhere in the living world. Such social interactions may lead to indirect genetic effects (IGE), which are heritable effects of an individual on trait values of the other individuals its interacts with. IGEs may affect the direction and magnitude of response to selection in breeding programs. Moreover, social interactions may affect variability of traits. In aquaculture, competition for resources inflates size variation within populations. In this thesis, we used the Genetically Improved Farmed Tilapia (GIFT; Oreochromis niloticus) strain to investigate the genetic basis for social interactions and variability in harvest weight for tropical finfish. Social interaction experiments were established for quantifying the genetic and non-genetic indirect effects on harvest weight in the GIFT strain. We found evidence for IGEs on harvest weight, and a negative direct-indirect genetic correlation, which suggesting heritable competitive interactions for harvest weight in GIFT. Hence, breeding schemes may need to be adapted to avoid an increase in competition. A stochastic simulation study was conducted to examine the effect of BLUP selection on the rate of inbreeding for socially affected traits. The rates of inbreeding for scenarios with IGEs were greater than for scenarios without IGE. Therefore, with IGEs there is a greater need for a selection algorithm that restricts the increase of mean kinship. In aquaculture industry, there is a wide range of commercial production environments, which may leads to genotype by environment (GxE) interaction, for example due to differential social interactions. The GIFT fish were tested in ponds and cages to study the GxE interaction. The genetic correlations between environments (0.73 to 0.85, for harvest weight and body measurements) indicate little GxE-interaction. The data collected from the social interaction experiments were also used to investigate the presence of genetic variation in uniformity for harvest weight. The genetic coefficient of variation for standard deviation of harvest weight (0.17) shows that uniformity of harvest weight is heritable and can be increased by selective breeding. In the General Discussion of this thesis, the uniformity study was extended to incorporate IGE. The result indicates that more cooperative fish are not necessary more uniform for harvest weight. Overall, our results suggest that genetic improvement in fish breeding programs can be increased by accounting for social interactions.

    The potential of genomic selection to support local breed conservation
    Calus, Mario - \ 2014
    animal breeding - genotypes - phenotypes - genetic variance - genomics - genetic correlation - irish republic - beef cows - animal genetic resources - breeds
    Genetic baculovirus determinants for pathogenicity, virulence and transmission
    Serrano, A. - \ 2014
    Wageningen University. Promotor(en): Just Vlak; P. Caballero, co-promotor(en): Gorben Pijlman; D. Munoz. - Wageningen : Wageningen University - ISBN 9789462571358 - 160
    baculovirus - spodoptera exigua multiple nucleopolyhedrovirus - genetische analyse - genotypische variatie - pathogeniteit - virulentie - genen - biologische bestrijding - insectenplagen - baculovirus - spodoptera exigua multiple nucleopolyhedrovirus - genetic analysis - genetic variance - pathogenicity - virulence - genes - biological control - insect pests
    Fokkerij geeft antwoord op vragen maatschappij
    Greef, K.H. de; Hiemstra, S.J. ; Kool, E. - \ 2014
    V-focus 2014 (2014)1. - ISSN 1574-1575 - p. 28 - 29.
    varkenshouderij - dierenwelzijn - varkens - dierveredeling - staartbijten - varkensfokkerij - diergenetica - genotypische variatie - duurzame veehouderij - pig farming - animal welfare - pigs - animal breeding - tail biting - pig breeding - animal genetics - genetic variance - sustainable animal husbandry
    De fokkerij kan een belangrijke bijdrage leveren aan het oplossen van een probleem als berengeur en het begrijpen van staartbijten. Naast deze twee maatschappelijke vraagstukken zijn er veel meer vragen waarop het samenwerkingsverband Breed4Food antwoord wil geven. Dit artikel beschrijft doorbraken, die Breed- 4Food wil realiseren in de varkensfokkerij om daarmee bij te dragen aan een economisch en maatschappelijk duurzame houderij.
    'Intraspecific pathogen variation' Verslag KNPV/Plantum/EPS-eendagsconferentie : Wageningen, 22 januari 2013
    Folkertsma, R.T. ; Goverse, A. ; Posthuma, E. ; Gilijamse, T. - \ 2013
    Gewasbescherming 44 (2013)2. - ISSN 0166-6495 - p. 32 - 34.
    plantenziekteverwekkers - genetische variatie - genotypische variatie - dna-sequencing - moleculaire technieken - moleculaire genetica - plantenziekten - conferenties - plant pathogens - genetic variation - genetic variance - dna sequencing - molecular techniques - molecular genetics - plant diseases - conferences
    Dinsdag 22 januari 2013 werd in Wageningen een eendagsconferentie gehouden getiteld ‘Intraspecific pathogen variation - implications and opportunities’. Deze conferentie werd georganiseerd naar aanleiding van discussies over het werken met intraspecifieke variatie voor diagnostiek en veredeling binnen de Nematodenwerkgroep van de KNPV en de Isolaten-beheerwerkgroep van Plantum. Het doel van de bijeenkomst was a.) onderzoekers uit de private en de publieke sector samenbrengen om recente ontwikkelingen te bespreken in fundamentele en toegepaste aspecten van het werken met intraspecifieke variatie, en b.) het stimuleren van uitwisselen van ideeën binnen en tussen beide groepen, voor mogelijke vervolginitiatieven.
    Multivariate phenotypic divergence due to the fixation of beneficial mutations in experimentally evolved lineages of a filamentous fungus
    Schoustra, S.E. ; Punzalan, D. ; Dali, R. ; Rundle, H.D. ; Kassen, R. - \ 2012
    PLoS ONE 7 (2012)11. - ISSN 1932-6203
    variance-covariance matrices - genetic variance - aspergillus-nidulans - adaptive radiation - life-history - evolution - selection - fitness - adaptation - populations
    The potential for evolutionary change is limited by the availability of genetic variation. Mutations are the ultimate source of new alleles, yet there have been few experimental investigations of the role of novel mutations in multivariate phenotypic evolution. Here, we evaluated the degree of multivariate phenotypic divergence observed in a long-term evolution experiment whereby replicate lineages of the filamentous fungus Aspergillus nidulans were derived from a single genotype and allowed to fix novel (beneficial) mutations while maintained at two different population sizes. We asked three fundamental questions regarding phenotypic divergence following approximately 800 generations of adaptation: (1) whether divergence was limited by mutational supply, (2) whether divergence proceeded in relatively many (few) multivariate directions, and (3) to what degree phenotypic divergence scaled with changes in fitness (i.e. adaptation). We found no evidence that mutational supply limited phenotypic divergence. Divergence also occurred in all possible phenotypic directions, implying that pleiotropy was either weak or sufficiently variable among new mutations so as not to constrain the direction of multivariate evolution. The degree of total phenotypic divergence from the common ancestor was positively correlated with the extent of adaptation. These results are discussed in the context of the evolution of complex phenotypes through the input of adaptive mutations
    The genetics of the metabolome in Brassica rapa
    Pino del Carpio, D. - \ 2010
    Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Guusje Bonnema. - [S.l. : S.n. - ISBN 9789085857211 - 168
    brassica campestris - koolsoorten - metabolieten - genexpressie - genetische regulatie - genotypische variatie - genetische diversiteit - genetische merkers - selectiemethoden - metabolomica - brassica campestris - cabbages - metabolites - gene expression - genetic regulation - genetic variance - genetic diversity - genetic markers - selection methods - metabolomics
    In this thesis the metabolic variation in Brassica rapa is described based on results of metabolic profiling of a core collection of 168 accessions representing the different crop types and geographical origin and a Doubled Haploid population. In Chapter 2 we describe the genetic and phenotypic variation of this core collection to explore the possibility of following association mapping methods to identify genes involved in metabolic regulation. We explored through a genome wide and candidate gene approach different association mapping methods in a core collection in Chapters 3 and 4 respectively and in Chapter 5 we combined the QTL analysis of targeted and untargeted metabolites profiled through LC-MS with expression QTLs following a genetical genomics approach aiming to detect genes underlying the metabolite QTL. The genetic diversity evaluated through the screening of AFLP and SSR markers was correlated with classification of accessions using morphological and metabolic trait values. The relationship between accessions in groups was compared using hierarchical clustering and the STRUCTURE program. Using Random Forests classification a set of metabolites was selected that differentiated the different sub groups as determined by STRUCTURE (Chapter 2). Based on the classification into subpopulations using the STRUCTURE program we included the subpopulations as a correction term in our statistical model for association studies (Chapter 3). Additionally, because of the increasing amount of data that will be soon available through sequencing technology we tested the use of Random Forests in the search for marker-trait association for the isoprenoids pathway. Using the results obtained with the linear models as implemented in TASSEL and the results obtained in Random Forests we found a set of 16 significant markers with potential use for marker assisted selection in breeding for several isoprenoidsThe determination of map positions through synteny prediction and genetic mapping of a group of genes from the glucosinolate pathway lead us to identify Myb28 and MAM as candidate genes mapping under a previously detected major QTL for glucosinolates We followed an association mapping approach to investigate their role in the variation in glucosinolates in the core collection by profiling 37 SSR markers, which included markers linked to these candidate genes and markers distributed along different positions in linkage group A03 (Chapter 4). Interestingly, not only MAM and Myb28, but the AOP and GS-OH genes involved in side chain modification and Myb29 in transcriptional regulation were also associated with glucosinolate levels. A genetical genomics approach was followed to identify candidate genes for variation inmetabolites of six biosynthetic pathways: carotenoids, tocopherols, folates, glucosinolates, flavonoids and phenylpropanoids, based on the co-localization analysis and comparison between metabolic (m)QTLs and expression (e)QTLs (Chapter 5). A Doubled Haploid (DH) population was profiled for metabolite content and variation through targeted and LC-MS untargeted approaches. Additionally, the same population was profiled for transcript variation with a newly developed 105K Cogenics array assembled using mainly EST sequences from three species: B. napus, B. rapa and B. oleracea. Co-localization of eQTLs and mQTLs for several isoprenoids (tocopherols and carotenoids) and glucosinolates lead us to the identification of candidate genes for these pathways. However, further work is needed to identify the gene or genes underlying a major cluster of QTLs for 112 centrotypes derived from the LC-MS untargeted data. The results obtained through this combined approach and considerations that need to be taken into account when performing these types of studies with regard to identification of paralogues and the use of a multi Brassica species microarray for transcript profiling in Brassica rapa are discussed.In the final Chapter, the combined use of core collections encompassing the genetic diversity within B. rapa and biparental DH populations to unravel the genetic regulation of the metabolome are discussed.
    Genotypische diversiteit en rhizosfeerkolonisatie van DAPG-producerende Pseudomonas spp.
    Bergsma-Vlami, M. - \ 2009
    Gewasbescherming 40 (2009)3. - ISSN 0166-6495 - p. 117 - 118.
    genotypische variatie - pseudomonas - soorten - antibiotica - biologische bestrijding - gewasbescherming - genetic variance - pseudomonas - species - antibiotics - biological control - plant protection
    Het antibioticum 2,4-diacetylphloroglucinol (DAPG) speelt een belangrijke rol in biologische bestrijding van verschillende plantenpathogenen door fluorescerende Pseudomonas-soorten. DAPG-producerende Pseudomonas-stammen zijn effectief in biologische bestrijding, maar hun saprofytisch vermogen is vaak variabel met als gevolg dat ook de mate van ziekteonderdrukking niet altijd consistent is
    Heat-shock effects on photosynthesis and sink-source dynamics in wheat (Triticum aestivum L.)
    Schapendonk, A.H.C.M. ; Xu, H.Y. ; Putten, P.E.L. van der; Spiertz, J.H.J. - \ 2007
    NJAS Wageningen Journal of Life Sciences 55 (2007)1. - ISSN 1573-5214 - p. 37 - 54.
    hittetolerantie - weerstand van huidmondjes - fluorescentie - veroudering - tarwe - triticum aestivum - genotypische variatie - fotosynthese - gewasopbrengst - heat tolerance - stomatal resistance - fluorescence - senescence - wheat - triticum aestivum - genetic variance - photosynthesis - crop yield - high-temperature stress - grain-growth - irrigated environment - yield - cereals - quality - traits - productivity - limitations - maturation
    To assess the mechanisms causing genotypic differences in heat tolerance of wheat (Triticum aestivum L.), physiological responses to a heat shock in a vegetative (`end of tillering¿) or a reproductive (`early grain filling¿) stage were studied. Three cultivars ¿ Lavett, Ciano-79 and Attila ¿ differing in adaptation to heat were grown in a glasshouse at a day/night temperature regime of 15/10 °C and a 12-h daylength from sowing to `end of tillering¿ and next at two day/night regimes of 25/20 and 18/13 °C under natural daylength. The heat-shock treatment consisted of an exposure of plants to temperatures raised gradually over a time-span of 12 hours to above 30 °C with a maximum of 38 °C during three hours at midday for three days either at the `end of tillering¿ or at `grain filling¿. A heat shock at the `end of tillering¿ strongly reduced the rate of leaf photosynthesis. A similar heat shock during `grain filling¿ decreased both rate of photosynthesis (source) and grain growth (sink). The rate of leaf photosynthesis was decreased by 40 to 70%, depending on cultivar and developmental stage. Photosynthesis fully recovered within 4 days after the heat-shock treatment was ended. The effects of the heat shock on biomass yield were more pronounced for treatments at `early grain filling¿ than at `end of tillering¿. However, the impact of a 3-day heat shock on biomass yield was less than the effects of the pre- and post-treatment growing temperature.
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