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

BMC Genomics
Hojjat Asadollahpour NanaeiYa-Ping Zhang

Abstract

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 (FST), 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. A number of protein-coding genes in windows with the top 1% values of FST (367 genes), XP-CLR (681 genes), and log2 (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 ot...Continue Reading

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Methods Mentioned

BETA
genotyping
PCA

Software Mentioned

Runs of Homozygosity
GSEA
ADMIXTURE
ENSEMBL Aligner
RealignerTargetCreator
: Profiler
GATK
UnifiedGenotyper
Genome Analysis Toolkit ( GATK )
SAMtools

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