Estimating chromosomal genetic diversity of Kuchinoshima feral cattle using high density SNP chip

Abstract

Kuchinoshima cattle are unique feral cattle in Kuchinoshima Island in Kagoshima prefecture. We genotyped 54K SNPs for Kuchinoshima cattle, Japanese Black, Japanese Brown and Japanese Holstein using high density SNP chip to estimate genetic diversity and genetic structure in Kuchinoshima cattle. Average minor allele frequency in Kuchinoshima cattle was lower (0.089) than those of the other populations (0.181-0.251). Ratio of monomorphic SNPs for each chromosome in Kuchinoshima cattle ranged from 47.7% (BTA24) to 72.3% (BTA20). Subsequently, we investigated expected heterozygosity in each chromosome, and observed six monomorphic regions longer than 5Mb, especially, the longest region extended 12.80Mb. This study revealed the extremely low genetic diversity of Kuchinoshima cattle, due to founder effect derived from a few ancestral individuals and genetic drift caused by small population with below 100 animals lasting for a long time in Kuchinoshima Island.