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

Abstract

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.

Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens

“…All detected variants (~ 18.6 million SNPs) were then filtered to be supported by a minimum genotype quality of 40 and minimum mapping quality of 25. In order to avoid potential sequencing errors, all identified loci with more than two alleles and within clusters (> 3 SNP in a 10-bp window) were removed for the subsequent analyses [ 26 ]. After filtering out low-quality reads, around 14.56 million variants were retained for all individuals (Additional file 1 : Table S2).…”

A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses

“…We sequenced the genomes of 48 ponies and nine horses at an average depth of coverage of ∼11.1× and combined them with 130 genomes previously characterized 7 , 8 ( Data S1 A; STAR Methods ). Our dataset includes 52 Chinese ponies from four breeds, 100 Chinese native horses from 12 breeds, 23 imported Falabella ponies, seven Thoroughbred horses, and five Przewalski’s horses.…”

“…The 57 genomes sequenced in this study were complemented with a previously released data consisting of 113 individual horse genomes 8 and 17 Debao ponies, 7 providing a panel of 187 genomes. The ancient genome time-series was obtained from Fages and collaborators 19 and included genome-wide sequence data from 245 equine subfossils from across Eurasia and spanning the last six millennia.…”

“… 4 , 5 Whether the same genetic pathways also drive the small body size of Chinese ponies, which show striking anatomical differences to Shetland ponies, 6 remains unclear. 2 , 7 To test this, we combined whole-genome sequences of 187 horses across China. Statistical analyses revealed top association between genetic variation at the T-box transcription factor 3 ( TBX3 ) and the body size.…”

Whole-genome resequencing infers genomic basis of giant phenotype in Siamese fighting fish (<i>Betta splendens</i>)

“…Bmp8a is associated with bone differentiation and morphogenesis ( Wozney, 2002 ). In domestic chickens and ponies, mutations in bone morphogenetic protein genes can cause body size variation ( Nanaei et al, 2020 ; Wang et al, 2016 ). Thus, our data suggest that bmp8a may be a candidate gene for the giant phenotype.…”