Abstract
Simple SummaryThroughout horse industry modernization, sport horse breeds have been genetically evolved in accordance to their abilities in sport disciplines providing an opportunity to study selection signatures in the genome level. Future selection strategies of sport horse breeds can be optimized by improving our knowledge of genomic signatures of selection. The main goals of this study are identifying and investigating the genes and their biological pathways underlying selective pressures in sport and non-sport horse breeds. Here, we detected 49 genes as selective signals using fixation index, nucleotide diversity and Tajima’s D approaches. Intriguingly, our findings in functional enrichment analysis revealed the selection footprints related to musculoskeletal system development. Detected candidate genes and biological pathways in this study may be helpful to widen our perspective in recent breeding efforts and genomic evolutionary mechanisms in sport horse breeds.Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic regions under selective pressures in sport horse breeds. The major goal of this study was to shed light on genomic regions and biological pathways under selective pressures in sport horses. In this study, whole-genome sequences of 16 modern sport and 35 non-sport horses were used to investigate the genomic selective signals of sport performance, by employing fixation index, nucleotide diversity, and Tajima’s D approaches. A total number of 49 shared genes were identified using these approaches. The functional enrichment analysis for candidate genes revealed novel significant biological processes related to musculoskeletal system development, such as limb development and morphogenesis, having been targeted by selection in sport breeds.
Highlights
The livestock species have been shaped by humans according to their needs and purposes since the beginning of domestication process
The high-quality paired-end reads of 51 sport and non-sport horses obtained from NextSeq
We detected the genomic regions under selective pressure in sport horse breeds, using whole-genome comparative analyses
Summary
The livestock species have been shaped by humans according to their needs and purposes since the beginning of domestication process. In order to improve athletic performance of horses, the selection programs based on modern methods started in the late 20th century, in Europe, by warmblood horse breeding organizations [2]. The identification of genomic regions that have been subjected to selective pressure as signatures of selection is one of the approaches to screen the candidate genes for economic traits in horses [3,10] and other livestock species [5,12,13]. Detecting the candidate genes for traits such as reproduction [14], racing performance [15], body size [10,16,17], and type [18] was the main objective in recent horse signatures of selection studies. It can be useful to optimize the single nucleotide polymorphism (SNP) arrays that are widely used in breeding programs based on genomic evaluation
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