Genetic structure and relationships among 11 cattle populations using indel markers
2018
Yamanaka, H. (Kobe University, Kobe (Japan). Graduate School of Agricultural Science, Laboratory of Animal Breeding and Genetics) | Sasazaki, S. | Moe, H.H. | Lwin, M. | Shimogiri, T. | Mannnen, H.
In the present study, we developed indel markers in domestic cattle. We selected each one indel of 29 autosomes in the dbSNP database and genotyped 29 indels using 16 individuals from Bos taurus and Bos indicus. PCR amplification and polymorphism were observed in 26 indel markers. Out of the 26 indel markers, we genotyped polymorphic 8 indels with clear band detected by agarose gel in 11 cattle populations (4 Bos indicus populations : native cattle in Cambodia, Bangladesh, Laos and Bhutan. 7 Bos taurus populations : native cattle in Mongolia and Kazakhstan, and cattle breeds of Hanwoo, Japanese Black, Japanese Holstein, Angus and Hereford) and investigated genetic structure, relationships and diversity in 11 cattle populations. Genetic index of average gene diversity over loci showed higher genetic diversity in Mongolian (0.337) and Kazakhstani (0.379) native cattle than the other populations. Bos indicus populations (0.172-0.241) and Japanese Black (0.217) indicated relatively low genetic diversity. UPGMA-tree and the PC1 (58.3%) of principal component analysis clearly distinguished between Bos taurus and Bos indicus populations. In the STRUCTURE analysis, the maximum likelihood estimation is shown at K = 4. In addition, at K >= 4, Mongolian and Kazakhstani native cattle showed genetic admixture derived from multi-ancestors. These two countries are located in Eurasian Steps with Silk Road and Step Road, suggesting genetic exchange between cattle populations through trade routes. In conclusion, a set of 8 indel markers revealed well genetic structure and relationships based on breed histories and geographical locations.
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