Abstract:

To accelerate the progress of molecular breeding of Chinese donkeys, this study collected whole genome resequencing data from 251 adult donkeys across 27 donkey breeds and combined it with the results of genetic variation research on important traits of domestic donkeys at home and abroad, designed a 40K liquid chip based on targeted sequencing genotype detection technology for domestic donkeys. The results showed that the variation sites (45 893 SNPs and 1 InDel) in the 40K liquid chip of the domestic donkey were distributed within the domestic donkey genome, with an average spacing of 61.8 kb. Genotyping test was performed on 210 adult Dezhou female donkeys, achieving a detection rate of 98.4%-99.2% across all samples. The average sequencing depth of the loci was 133×, and 42 575 loci had minor allele frequency greater than 0.35. The chip was used for breed identification in 20 donkey-hide samples and preliminarily verified its usability. In summary, the 40K liquid chip developed in this study, the first large-scale genotype detection tool for domestic donkeys, has the advantages of high loci density, good polymorphism, high detection rate, and strong application. It can be used for early molecular marker-assisted selection and breed identification of domestic donkeys, further improving the breeding efficiency.

Key words: domestic donkey, genotyping detection by target sequencing, liquid chip, breeding