Systematic differences in the response of genetic variation to pedigree and genome-based selection methods

Heidaritabar, Marzieh; Vereijken, Addie; Muir, William M.; Meuwissen, Theo H. E.; Cheng, Hans H.; Megens, Hendrik‐Jan; Groenen, Martien A. M.; Bastiaansen, J.W.M.

doi:10.1038/hdy.2014.55

Cited by 28 publications

(38 citation statements)

References 28 publications

(35 reference statements)

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“…In this study, we use the fixation index ( F ST , Holsinger & Weir, ) to estimate the level of genetic differentiation and to detect the SNPs under selection between the early and late selection lines. In other selection line studies, it has been used successfully, for example in chicken, where the F ST method detected regions with changes in allele frequencies (i.e., signatures of selection) between lines bred for either meat or eggs (Boschiero et al, ) and between three different lines of egg layers (Heidaritabar et al, ). An additional “sliding window analysis,” where a window of a certain length slides along the genotypes, checks whether SNPs under selection cluster in certain genomic regions (Tajima, ).…”

Section: Introductionmentioning

confidence: 99%

Genetic and phenotypic responses to genomic selection for timing of breeding in a wild songbird

et al. 2019

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The physiological mechanisms underlying avian seasonal timing of reproduction, a life‐history trait with major fitness consequences, are not well understood. Comparing individuals that have been selected to differ in their timing of breeding may prove to be a promising in studying these mechanisms, making selection lines a valuable tool. We created selection lines for early and late timing of breeding in great tits (Parus major) using genomic selection, that is selection based on multi‐marker genotypes rather than on the phenotype. We took in nestlings (F1 generation) from wild broods of which the mother was either an extremely early (“early line”) or extremely late (“late line”) breeder. These chicks were then genotyped and, based on their “genomic breeding values” (GEBVs), we selected individuals for early and late line breeding pairs to produce the F2 generation in captivity. The F2 offspring was hand‐reared, genotyped and selected to produce an F3 generation, which were then again genotyped and selected. This way we obtained laying dates in aviaries for F1, F2 and F3 birds. We studied the genetic response to the artificial selection and found increased genetic differentiation between the early and late reproducing selection lines over generations (F1–F3), indicated by both diverging GEBVs and increased fixation indices (FST). We studied the phenotypic response to selection for birds breeding in outdoor breeding aviaries. We found that early line birds laid earlier than late line birds, and this difference increased over the generations (F1–F3), with non‐significant line effects for the F1 and F2, but highly significant line differences for the F3. We also assessed whether there was correlated selection on two traits that are potentially part of the mechanisms underlying seasonal timing: the endogenous free‐running period of the day/night clock (tau) and basal metabolic rate, but found no correlated selection. We have successfully created selection lines on seasonal timing in a wild bird species and obtained an instrument for future studies to investigate the physiological mechanisms underlying timing of breeding, and the genetic variation in these mechanisms, an essential component for evolutionary change in timing of reproduction. A free Plain Language Summary can be found within the Supporting Information of this article.

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Section: Introductionmentioning

confidence: 99%

Genetic and phenotypic responses to genomic selection for timing of breeding in a wild songbird

et al. 2019

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“…On the beginning of chromosome 12, we identified another bin with a high rIBD signal, hinting at a locus that contains Asian introgressed haplotypes. This region overlaps the FASN gene that was previously described as fatty acid synthase and an important gene involved in fat deposition [42]. In addition to the genes described in this paragraph, our 11 regions that were used in the association analysis can be found in the 25 bins that span the top 1% of introgressed regions in the genome.…”

Section: (B) Fat-related Genesmentioning

confidence: 99%

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

et al. 2015

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Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.

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“…In GP, the proportion of variance explained by the markers, and how well the distribution of mutational effects is known, is crucial for GP to work well (Goddard 2009); but there is also a need to control inbreeding in genomic selection (Sonesson et al 2012;Toro et al 2014). Genomic selection can lead to acceleration erosion of variation at specific loci in the genome (Heidaritabar et al 2014), and its efficiency may be hampered by maintaining diversity (Clark et al 2013). Recent simulation results (MacLeod et al 2014) indicate that resequencing data could recover the missing genetic variance, and a better accuracy in the prediction is achieved with resequencing data for populations with large Ne.…”

Section: Impact Of Management On Selection Goalsmentioning

confidence: 99%

Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

et al. 2015

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Conservation and breeding programs aim at maintaining the most diversity, thereby avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, the most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequencing data and use them in population management. We analyzed the resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analyzing the demographic history of Sus cebifrons, we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analyzed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness, and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved the best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs.

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Systematic differences in the response of genetic variation to pedigree and genome-based selection methods

Cited by 28 publications

References 28 publications

Genetic and phenotypic responses to genomic selection for timing of breeding in a wild songbird

Genetic and phenotypic responses to genomic selection for timing of breeding in a wild songbird

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

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