Whole-genome resequencing provides insights into the diversity and adaptation to desert environment in Xinjiang Mongolian cattle

Abstract

Abstract Background: Xinjiang Mongolian cattle is an indigenous breed living in the Taklimakan Desert and with small body size. However, the genomic diversity, origin, and genetic basis underlying the adaptation to the desert environment have been poorly studied. Results: We analyzed patterns of Xinjiang Mongolian cattle genetic variation by sequencing 20 genomes and comparing them to the 136 genomes of 10 representative breeds worldwide. We found the highest nucleotide diversity associated with the lower inbreeding coefficient, the lowest linkage disequilibrium, and the highest effective population size in Xinjiang Mongolian cattle. The genomic diversity pattern could be explained by the Bos taurusclade property of Xinjiang Mongolian cattle with a limited introgression of Bos indicus genes. More importantly, we identify signatures of convergent selection in desert animals (Xinjiang Mongolian cattle, camel and sheep originating from the Taklimakan Desert region) including genes, GO terms, and/or KEGG pathways controlling water reabsorption and osmoregulation, metabolic regulation and energy balance,and small body size. Conclusions: Our results imply that Xinjiang Mongolian cattle might have acquired distinct genomic diversity by virtue of the introgression of Bos indicus, which helps understand the demographic history. The identification of selective signals can provide novel insights into the genomic basis underlying the adaptation of Xinjiang Mongolian cattle to the desert environment.