Population genetic analysis of the domestic Bactrian camel in China by RAD‐seq

Abstract

Restriction site‐associated DNA sequencing (RAD‐seq) is one of the most effective high‐throughput sequencing technologies for SNP development and utilization and has been applied to studying the origin and evolution of various species. The domestic Bactrian camels play an important role in economic trade and cultural construction. They are precious species resources and indispensable animals in China's agricultural production. Recently, the rapid development of modern transportation and agriculture, and the deterioration of the environment have led to a sharp decline in the number of camels. Although there have been some reports on the evolution history of the domestic Bactrian camel in China, the origin, evolutionary relationship, and genetic diversity of the camels are unclear due to the limitations of sample size and sequencing technology. Therefore, 47 samples of seven domestic Bactrian camel species from four regions (Inner Mongolia, Gansu, Qinghai, and Xinjiang) were prepared for RAD‐seq analysis to study the evolutionary relationship and genetic diversity. In addition, seven domestic Bactrian camel species are located in different ecological zones, forming different characteristics and having potential development value. A total of 6,487,849 SNPs were genotyped. On the one hand, the filtered SNP information was used to conduct polymorphism mapping construction, LD attenuation analysis, and nucleotide diversity analysis. The results showed that the number of SNPs in Dongjiang camel was the highest, the LD coefficient decayed the fastest, and the nucleotide diversity was the highest. It indicates that Dongjiang camel has the highest genetic diversity. On the other hand, the filtered SNPs information was used to construct the phylogenetic tree, and FST analysis, inbreeding coefficient analysis, principal component analysis, and population structure analysis were carried out. The results showed that Nanjiang camel and Beijiang camels grouped together, and the other five Bactrian camel populations gathered into another branch. It may be because the mountains in the northern part of Xinjiang and the desert in the middle isolate the two groups from the other five groups.

Development of Genomic Resources and Identification of Genetic Diversity and Genetic Structure of the Domestic Bactrian Camel in China by RAD Sequencing

“…The STRUCTURE program 3 (in order to ensure the independence of SNP marks, we used PLINK software to filter 865,774 SNPs according to LD intensity, the remaining 12,046 loci were used for structure analysis, -indep-pairwise 250 10 0.1, 250 kb window, the step size of 10 SNPs, r 2 is <1) was used for analysis of population structure. We predefined the number of genetic clusters from K = 2 to K = 6 (BURNIN = 5,000 times, NUMREPS = 100,000), and repeated each K -value three times ( Liu et al, 2019 ). Next, we used the POPHELPER software 4 to calculate the value of Δ K ; then, we used the CLUMPP software 5 to combine the results of three repetitions ( Schraiber and Akey, 2015 ).…”

Exploring the genomic resources of seven domestic Bactrian camel populations in China through restriction site-associated DNA sequencing

“…Ming et al [10] sequenced the whole genome of 128 camels across Asia and revealed origin and migration of domestic Bactrian camels. Additionally, Liu et al [11] used single nucleotide polymorphisms (SNPs) to study the genetic diversity and genetic structure of seven domestic Bactrian camel populations; our study clarified the phylogenetic relationships of these populations, laying a foundation for the protection of their biodiversity.…”

Development of Single Nucleotide Polymorphism (SNP) Markers for Analysis of Population Structure and Invasion Pathway in the Coconut Leaf Beetle Brontispa longissima (Gestro) Using Restriction Site-Associated DNA (RAD) Genotyping in Southern China

“…The phylogenetic tree is a branch map or tree that describes the order of evolution between groups, indicating the evolutionary relationship between groups [32]. The theoretical methods for constructing phylogenetic trees are mainly Neighbor-joining (NJ) and Maximum likelihood (ML).…”