Analysis of Genetic Diversity and Population Structure of Tarim and Junggar Bactrian Camels Based on Simplified GBS Genome Sequencing

SIMPLE SUMMARY: Camels have a high tolerance to hunger, thirst, cold, and drought, as well as the ability to travel over long distances. They are indispensable animals for agricultural production in desert areas in China. Old World camels have served humans in uses such as cross-continental caravans; transporting people and goods; connecting different cultures; providing milk, meat, and wool; and serving as draught animals. In view of the severe reduction in Bactrian camel germplasm resources, people now realize that it is particularly important to scientifically evaluate and protect the genetic integrity and diversity of native species. At the same time, there is a growing demand for intensive and sustainable meat and milk production. Using modern genomic tools for selection to improve milk and wool production is warranted. In this study, GBS technology was used to analyze the genetic diversity and genetic structure of Tarim and Junggar camels, and identify the genes important in their evolution. On this basis, the effects of resource conservation were evaluated by analyzing the differences between individuals and populations at the genome level. Screening candidate genes that may be responsible for the biological characteristics of Bactrian camels will aid research into genetic resource protection, important economic traits, and the mechanisms underlying biological characteristics, molecular breeding, and disease. ABSTRACT: In view of the severe reduction in Bactrian camel germplasm resources, scientific evaluation, protection, and utilization is particularly important. Therefore, it is necessary to investigate the genetic diversity and genetic structure of this species, and identify the genes that have played important roles in its evolution. In this study, 21,971 SNPs were identified in 118 domestic Bactrian camels from the Tarim (n = 60) and Junggar (n = 58) populations using simplified GBS genome sequencing. The results show that Tarim and Junggar Bactrian camels have high nucleotide diversity. A phylogenetic tree constructed using structural analysis, principal component analysis (PCA), and the adjacency method (NJ) showed that Tarim and Junggar Bactrian camels were clustered together. The selection signals revealed that the Tarim and Junggar Bactrian camels shared 108 genes under positive selection, including WNT1, WNT10B, CD14, SEC61A2, DPAGT1, FOXO6, etc. These selected genes were widely involved in the immune system, embryonic development, lipid metabolism, and other processes. From a genomic analysis perspective, the genetic relationship between TLM and ZGE camels is close, with an average Fst of 0.048 and a relatively low average differentiation coefficient between the two populations. In addition, shared selected genes in the long-term depression pathway were significantly enriched in Tarim and Junggar. These findings will offer support and assistance for the exploration of genetic resource preservation, economically significant traits, and the mechanisms underlying biological characteristics, molecular breeding, and disease.