Selection signatures for local and regional adaptation in Chinese Mongolian horse breeds reveal candidate genes for hoof health

Abstract

Background Thousands of years of natural and artificial selection since the domestication of the horse has shaped the distinctive genomes of Chinese Mongolian horse populations. Consequently, genomic signatures of selection can provide insights into the human-mediated selection history of specific traits and evolutionary adaptation to diverse environments. Here, we used genome-wide SNPs from five distinct Chinese Mongolian horse populations to identify genomic regions under selection for the population-specific traits, gait, black coat colour, and hoof quality. Other global breeds were used to identify regional-specific signatures of selection. Results We first identified the most significant selection peak for the Wushen horse in the region on ECA23 harbouring DMRT3, the major gene for gait. We detected selection signatures encompassing several genes in the Baicha Iron Hoof horse that represent good biological candidates for hoof health, including the CSPG4, PEAK1, EXPH5, WWP2 and HAS3 genes. In addition, an analysis of regional subgroups (Asian compared to European) identified a single locus on ECA3 containing the ZFPM1 gene that is a marker of selection for the major domestication event leading to the DOM2 horse clade. Conclusions Genomic variation at these loci in the Baicha Iron Hoof may be leveraged in other horse populations to identify animals with superior hoof health or those at risk of hoof-related pathologies. The overlap between the selection signature in Asian horses with the DOM2 selection peak raises questions about the nature of horse domestication events, which may have involved a prehistoric clade other than DOM2 that has not yet been identified.

Genomic insights into the population history and adaptive traits of Latin American Criollo cattle

“…Following this, the MINOTAUR R package [ 45 ] was used to calculate CSS statistics, which were then averaged over 20 kb windows to reduce spurious signals. In addition, a signal was only considered significant if at least one SNP in 0.1% of CSS scores was flanked by at least five other SNPs in the top 1% of CSS values [ 44 , 46 ].…”

Genomic Insights into the Population History and Adaptive Traits of Latin American Criollo Cattle

“…The resulting statistics were then averaged over 20 kb windows to reduce spurious signals. To further reduce the likelihood of spurious signals, a signal was only considered significant if at least one SNP in the 0.1% of CSS scores was flanked by at least five other SNPs in the top 1% of CSS values [54,[56][57][58].…”

“…Following this, the MINOTAUR R package [45] was used to calculate CSS statistics, which were then averaged over 20 kb windows to reduce spurious signals. In addition, a signal was only considered significant if at least one SNP in the 0.1% of CSS scores was flanked by at least five other SNPs in the top 1% of CSS values [44, 46].…”

The Characteristics, Distribution, Function, and Origin of Alternative Lateral Horse Gaits

“…Many East Asian breeds also pace including the Chakouyi, which do so with elevated and flexed front legs, Cheju (or Jeju), Datong, Hokkaido (or Dosanko), Mongolian Wushen (where it is called the joroo), Shan, and Tibetan. The hard pace is also found in the Bhutia (or Yuta), Spiti, and Zaniskari of India [ 35 , 36 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 ].…”