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| Population structure of Lantang pig evaluated using SNP chip |
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| DOI：10.16768/j.issn.1004-874X.2018.06.018 |
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| Abstract: |
| 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. |
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