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

Abstract

The domestic Bactrian camel is a valuable livestock resource in arid desert areas. Therefore, it is essential to understand the roles of important genes responsible for its characteristics. We used restriction site-associated DNA sequencing (RAD-seq) to detect single nucleotide polymorphism (SNP) markers in seven domestic Bactrian camel populations. In total, 482,786 SNPs were genotyped. The pool of all remaining others were selected as the reference population, and the Nanjiang, Sunite, Alashan, Dongjiang, Beijiang, Qinghai, and Hexi camels were the target populations for selection signature analysis. We obtained 603, 494, 622, 624, 444, 588, and 762 selected genes, respectively, from members of the seven target populations. Gene Ontology classifications and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and the functions of these genes were further studied using Genecards to identify genes potentially related to the unique characteristics of the camel population, such as heat resistance and stress resistance. Across all populations, cellular process, single-organism process, and metabolic process were the most abundant biological process subcategories, whereas cell, cell part, and organelle were the most abundant cellular component subcategories. Binding and catalytic activity represented the main molecular functions. The selected genes in Alashan camels were mainly enriched in ubiquitin mediated proteolysis pathways, the selected genes in Beijiang camels were mainly enriched in MAPK signaling pathways, the selected genes in Dongjiang camels were mainly enriched in RNA transport pathways, the selected genes in Hexi camels were mainly enriched in endocytosis pathways, the selected genes in Nanjiang camels were mainly enriched in insulin signaling pathways, while the selected genes in Qinghai camels were mainly enriched in focal adhesion pathways; these selected genes in Sunite camels were mainly enriched in ribosome pathways. We also found that Nanjiang (HSPA4L and INTU), and Alashan camels (INO80E) harbored genes related to the environment and characteristics. These findings provide useful insights into the genes related to the unique characteristics of domestic Bactrian camels in China, and a basis for genomic resource development in this species.

Identification of selection signatures in Iranian dromedary and Bactrian camels using whole genome sequencing data

“…To identify regions under positive selection in the genome of ID and IB camels, we used two methods including population differentiation index (Fst) and cross-population extended haplotype homozygosity (XP-EHH) with 50 kb sliding window and 25 kb step size. The window size and step size were selected for this study based on previous studies on the genomes of dromedary 16 and Bactrian 17 camels. The Fst in each window and XP-EHH score for each SNP were estimated using VCFtools and Selscan v.2.0 80 , respectively.…”

“…In recent years, although many studies have been done to identify the selection signs in different species of domestic animals, including cattle 8 , 9 , sheep 10 , 11 , goat 12 , 13 and horse 14 , 15 , but the studies of Bahbahani et al 16 on Sudanese dromedary camels and Liu et al 17 on Chinese Bactrian camels are among the few cases in this field for camels. In the present study, we used whole genome sequencing (WGS) data to identify the selection footprints on the genome of Iranian dromedary (ID) and Iranian Bactrian (IB) camels as a step to better understand these valuable species.…”

Genetic structure and origin of emu populations in Japanese farms inferred from large-scale SNP genotyping based on double-digest RAD-seq

“…Restriction site-associated DNA sequencing (RAD-seq) is a robust and effective method for obtaining genome-wide SNP genotypes in a large number of samples and is used for population genetics 14 , 15 , quantitative trait locus (QTL) analysis 16 , 17 , and marker development 18 , 19 in eukaryotes, including non-model organisms. In this study, we performed large-scale SNP genotyping using RAD-seq and compared the genetic structures of three Japanese emu populations which were observed marked genetic differentiation in our previous report.…”

ddRAD sequencing based genotyping of six indigenous dairy cattle breeds of India to infer existing genetic diversity and population structure

“…ddRAD being a restriction digestion based reduced representation Next Generation Sequencing method fragments a target genome with both frequent and rare cutting restriction enzymes and such a strategy minimizes the hassles of uninformative and repetitive sequences, sequence assembly and SNP calling that accompanies with Whole genome sequencing (WGS). Evidently, ddRAD has been employed for the discovery of species-specific genome wide SNPs in economic, production and adaptation traits related candidate genes [20][21][22] . Furthermore, reduced representation methods based on whole genome sequencing of single individuals solve the problem of ascertainment bias 23 .…”