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Background  Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for heights at withers and body sizes. Debao pony (DBP), a famous Chinese horse, is known for its small body size and lives in Guangxi mountains of southern China. In this study, we employed comparative population genomics to study the genetic basis underlying the small body size of DBP breed based on the whole genome sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index ( F  ST ), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (θπ), and further analyzed the results to find genomic regions under selection for body size-related traits.    Results  A number of protein-coding genes in windows with the top 1% values of  F  ST  (367 genes), XP-CLR (681 genes), and log 2  (θπ ratio) (332 genes) were identified. The most significant signal of positive selection was mapped to the  NELL1  gene, probably underlies the body size and development traits, and may also have been selected for short stature in the DBP population. In addition, some other loci on different chromosomes were identified to be potentially involved in the development of body size.    Conclusions  Results of our study identified some positively selected genes across the horse genome, which are possibly involved in body size traits. These novel candidate genes may be useful targets for clarifying our understanding of the molecular basis of body size and as such they should be of great interest for future research into the genetic architecture of relevant traits in horse breeding program.

Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony