Abstract
Arunachali yak, the only registered yak breed of India, is crucial for the economic sustainability of pastoralist Monpa community. This study intended to determine the genomic diversity and to identify signatures of selection in the breed. Previously available double digest restriction-site associated DNA (ddRAD) sequencing data of Arunachali yak animals was processed and 99,919 SNPs were considered for further analysis. The genomic diversity profiled based on nucleotide diversity, π (π = 0.041 in 200 bp windows), effective population size, Ne (Ne = 83) and Runs of homozygosity (ROH) (predominance of shorter length ROHs) was found to be optimum. Subsequently, 207 regions were identified to be under selective sweeps through de-correlated composite of multiple signals (DCMS) statistic which combined three individual test statistics viz. π, Tajima’s D and |iHS| in non-overlapping 100 kb windows. Mapping of these regions revealed 611 protein-coding genes including KIT, KITLG, CDH12, FGG, FGA, FGB, PDGFRA, PEAR1, STXBP3, olfactory receptor genes (OR5K3, OR5H6 and OR1E1) and taste receptor genes (TAS2R1, TAS2R3 and TAS2R4). Functional annotation highlighted that biological processes like platelet aggregation and sensory perception were the most overrepresented and the associated regions could be considered as breed-specific signatures of selection in Arunachali yak. These findings point towards evolutionary role of natural selection in environmental adaptation of Arunachali yak population and provide useful insights for pursuing genome-wide association studies in future.
Highlights
Mammalian body has evolved certain anatomical, physiological, haematological and morphological adaptations in order to cope up with the stressors of long-term exposure to cold and hypoxic conditions of high altitudes [1,2,3,4,5,6,7,8]
A total of 96.46 million raw reads of Arunachali yak were obtained for the analysis
SphI and MluCI restriction enzymes were used for creating reduced representation libraries of the samples
Summary
Mammalian body has evolved certain anatomical (enlarged heart and lungs, shorter tongue), physiological (increased oxygen availability in blood, lower metabolic rate), haematological (modifications in haemoglobin structure to improve oxygen affinity, increased average platelet volume and plasma fibrinogen concentrations) and morphological (small body size, distinct coat features like colour, texture and length) adaptations in order to cope up with the stressors of long-term exposure to cold and hypoxic conditions of high altitudes [1,2,3,4,5,6,7,8] Most of these adaptations are genetically fixed in highlanders, conferring them protection against adverse climatic conditions [9]. Elucidation of these regions subjected to positive selection in yak genome can help in maintaining genetic diversity and unravelling causal variants and genes subjected to selection
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