Analysis of the Genetic Relationship and Inbreeding Coefficient of the Hetian Qing Donkey through a Simplified Genome Sequencing Technology.

The Hetian Qing donkey is an excellent local donkey breed in Xinjiang. It is of great significance to accelerate breeding and the speed of breeding and rejuvenation, as well as to understand the genetic basis of the strategies and population. This study collected a total of 4 male donkeys and 28 female donkeys. It then obtained genotype data through Simplified Genomic Sequencing (GBS) technology for data analysis. The results detected a total of 55,399 SNP loci, and the genotype detection rate of individuals was ≥90%. A total of 45,557 SNP loci were identified through quality control, of which 95.5% were polymorphic. The average minimum allele frequency was 0.250. The average observed heterozygosity was 0.347. The average expected heterozygosity was 0.340. The average IBS (state homologous) genetic distance was 0.268. ROH: 49 (homozygous fragments), with 73.47% of the length between 1 and 5 Mb. The average per-strip ROH length was 1.75 Mb. The mean inbreeding coefficient was 0.003. The 32 Hetian green donkeys could be divided into six families. The number of individuals in each family is significant. To sum up, the Hetian Qing donkey population has low heterozygosity, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the subsequent process of seed protection, seed selection should be conducted according to the divided pedigree to ensure the long-term protection of the genetic resources of Hetian green donkeys.

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

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.