SNPs AND InDels Detection and selection signals identification of alxa bactrian camel by whole-genome resequencing

Abstract

Alxa Bactrian camel has been raised as an economic and transportation animal in Alxa, Inner Mongolia, China. In a long period of evolution and artificial selection, it has formed many specific physiological characteristics that enable the production of beneficial items such as milk, meat and fur despite in the harsh environment. At the present the Bactrian camel genome is still a draft genome assembled only at scaffold level but the genetic diversity in multiple re-sequenced Bactrian camels has not been investigated yet. In this study, we evaluated the genetic features of SNPs and InDels and conducted selection signals identification to detect specific genes associated with adaptation to the environment and muscle growth of Alxa Bactrian camel by whole-genome resequencing. By next-generation sequencing technology, a total of 367.98 Gb high-quality paired-end reads were generated. On an average, 81.65% of the reference genome sequence was covered with mapping depth of 10-fold. From these data, 6, 759, 073 SNPs and 976, 715 InDels were identified and 15, 037 genes were detected, which revealed wide genetic variations and complex genetic features related to adaptation mechanism of Alxa Bactrian camel in harsh environments. By selective signals analysis, we identified 111 genomic regions, including 70 candidate genes such as BCO1, AKR1D1, SVOPL, SMS, PHEX, PCYT1B, POLA1, and MEGF10, which are potentially involved in environment adaptability and muscle growth. Generally, these results provide a framework and comprehensive insights for further genetic studies in the Bactrian camel population and research on genes, which would provide a better understanding of economically important traits and environment adaptability in Bactrian camel and further provide a scientific basis for the selective breeding of Alxa Bactrian camel.