Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep

Abstract

BackgroundOne of the approaches to detect genetics variants affecting fitness traits is to identify their surrounding genomic signatures of past selection. With established methods for detecting selection signatures and the current and future availability of large datasets, such studies should have the power to not only detect these signatures but also to infer their selective histories. Domesticated animals offer a powerful model for these approaches as they adapted rapidly to environmental and human-mediated constraints in a relatively short time. We investigated this question by studying a large dataset of 542 individuals from 27 domestic sheep populations raised in France, genotyped for more than 500,000 SNPs.ResultsPopulation structure analysis revealed that this set of populations harbour a large part of European sheep diversity in a small geographical area, offering a powerful model for the study of adaptation. Identification of extreme SNP and haplotype frequency differences between populations listed 126 genomic regions likely affected by selection. These signatures revealed selection at loci commonly identified as selection targets in many species (“selection hotspots”) including ABCG2, LCORL/NCAPG, MSTN, and coat colour genes such as ASIP, MC1R, MITF, and TYRP1. For one of these regions (ABCG2, LCORL/NCAPG), we could propose a historical scenario leading to the introgression of an adaptive allele into a new genetic background. Among selection signatures, we found clear evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. We confirmed this allelic heterogeneity in one case by resequencing the MC1R gene in three black-faced breeds.ConclusionsOur study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4447-x) contains supplementary material, which is available to authorized users.

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

“…Genes for aesthetic physical phenotypes including height, stature, coat and plumage colour are commonly encountered in genomic regions under selection in domestic animal populations since they are easily identifiable [42][43][44][45] . Conformation characteristics are among the most discernible traits in horses and are the principal observable traits on which Thoroughbreds are selected.…”

Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation

“…; Rochus et al . ). The Angora individuals and Iranian domestics formed a sub‐clade in the tree, whereas breeds originating from France and Switzerland (hereafter called Western populations for simplicity) formed a mostly unstructured sub‐tree.…”

“…Within each breed, we identified a set of unrelated individuals by pruning pairs of individuals that had a genomic kinship coefficient greater than 0.2 (Rochus et al . ). After quality control, 46 065 SNPs and 223 animals from eight French caprine breeds were kept.…”

Genomic assessment and phenotypic characteristics of F2 resource sheep population

“…Применение ДНК-чипов, основанных на генотипировании множественных SNP-маркеров, позволило проводить исследования генетического разнообразия и взаимоотношений многочисленных пород овец на полногеномном уровне [1,2], а также осуществлять поиск локусов, находящихся под давлением естественной селекции [3] и искусственного отбора [4]. Тем не менее, одно из самых важных в практическом аспекте применений -картирование локусов количественных признаков (QTL) и поиск генов-кандидатов, ассоциированных с хозяйственно полезными признаками, до сих пор является несколько отстающим по сравнению с аналогичными работами в свиноводстве и скотоводстве.…”

“…На основе проведения полногеномных ассоциативных исследований на 1743 головах овец был найден достоверный ассоциированный SNP (OAR6_41936490) [5]. В прилегающей области к данному SNP были локализованы три значимых гена-кандидата, связанных с признаками роста, строением каркаса и размером тела, живой массой и высотой у овец [4,5]: LAP3 (лейцин аминопетидаза), NCAPG (non-SMC комплекс конденсина I, субъединица G) и LCORL (лиганд-зависимый ядерный рецептор корепрессор-подобный). Кроме того, недавно было проведено полногеномное исследование ассоциации размеров тела, оцененного по десяти промерам, с генотипическими данными, в результате которого было детектировано 11 значимых SNPs, в том числе TP53, BMPR1A, PIK3R5, RPL26 и PRKDC [6].…”