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

Abstract

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.