Population structure of Lantang pig evaluated using SNP chip

To protect and utilize the germplasm resource of Lantang pig，Illumina CAUPorince 50K SNP chip was used to analyze the population structure of 139 Lantang pigs. The results showed the average call rate of all the pigs was 98.24%，suggesting the SNP Chip was very suitable for Chinese indigenous pig breeds. The average genetic distance was 0.3326±0.0339，and furthermore，both PCA and G matrix revealed some Lantang pigs shared close genetic relationship. These Lantang pigs could be divided into five families，assigned as family A，B，C，D and E， separately，but only family A，B，C and D had stock boars. Two kinds of haplotypes were found on Y chromosome among Lantang pigs，all the individuals of family A and B belonged to haplotype A while family C and D belonged to haplotype B. A total of 1 680 ROHs were detected in Lantang pigs，the amount of ROH with 10～20 Mb size had the highest frequency which reached 44.52%. The average number of ROH per pig was 12.09±5.90，and the average total length of ROH for each pig was 246.90（±170.93）Mb. These results revealed a real population structure of a Lantang pig population in genetic level using the SNP chip，which provided a robust tool for the conversation， development and utilization of indigenous pig breeds.