Analysis of genetic relationship and inbreeding coefficient of HetianQing donkey based on simplified genome sequencing

A total of 32 individual samples of Hetian Qing donkeys were collected in this study, including 4 male donkeys and 28 female donkeys. Genotype data were collected by the Simplified Genome Sequencing (GBS) technology, and then genetic diversity, genetic structure, inbreeding degree and family analysis were carried out. The results showed that a total of 55399 SNP loci were detected, and the genotype detection rate of individuals was ≥ 90%; There are 45557 SNP loci through quality control, of which 95.5% are polymorphic; The average effective allele number is 0.048, the polymorphism information content is 0.273, and the average minimum allele frequency is 0.250; The average observed heterozygosity was 0.347, and the average expected heterozygosity was 0.340; The average IBS (state homology) genetic distance was 0.268; There are 49 ROHs (homozygous fragments of genome length), 73.47% of which are between 1 and 5 Mb in length. The average length of each ROH is 1.75 Mb, and the average inbreeding coefficient is 0.003; The 32 Hetian Qing donkeys can be divided into 6 families, and the individual number of each family is significantly different. To sum up, the Hetian Qing donkey population has low heterozygosity, low inbreeding degree, few families, and large differences in the number of individuals in each family, which is easy to cause the loss of genetic diversity.