Abstract
Artificial selection has played a critical role in animal breeding. Detection of artificial selection footprints in genomic regions can provide insights for understanding the function of specific phenotypic traits and better guide animal breeding. To more fully understand the relationship between genomic composition and phenotypic diversity arising from breed development, a genome-wide scan was conducted using an OvineSNP50 BeadChip and integrated haplotype score and fixation index analyses to detect selection signatures on the X chromosome in three sheep breeds. We identified 49, 34, and 55 candidate selection regions with lengths of 27.49, 16.47, and 25.42 Mb in German Mutton, Dorper, and Sunit sheep, respectively. Bioinformatics analysis showed that some of the genes in these regions with selection signatures, such as BMP15, were relevant to reproduction. We also identified some selection regions harboring genes that had human orthologs, including BKT, CENPI, GUCY2F, MSN, PCDH11X, PLP1, VSIG4, PAK3, WAS, PCDH19, PDHA1, and SRPX2. The VSIG4 and PCDH11X genes are associated with the immune system and disease, PDHA1 is associated with biosynthetic related pathways, and PCDH19 is expressed in the nervous system and skin. These genes may be useful as candidate genes for molecular breeding.
Highlights
Artificial selection has played a significant role in the domestication of livestock
Two studies found that artificial selection changed sheep coat pigmentation, horn morphology and growth developmental traits [3,4] using a genome scan of recent positive selection signatures in three sheep populations
Other selection signals are found in genomic regions such as quantitative trait loci and genes associated with production traits, including reproduction, growth, and fat deposition
Summary
Artificial selection has played a significant role in the domestication of livestock. The iHS is based on linkage disequilibrium theory and can detect regions with a rapidly increased frequency of the derived allele at selected sites [9]. The X chromosome in sheep contains several genes relevant to desirable breeding traits, including those related to tail fat deposition [19], further indicating that this is a good target chromosome for examining selection signatures in sheep. In the present study, within-population (iHS) and between-population (FST) methods were used to search the whole X chromosome in three breeds of sheep for signatures of positive selection using the OvineSNP50 BeadChip array, followed by candidate gene enrichment analysis and gene annotation to elucidate the biological functions of the selection signature
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