Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk production traits in Chinese buffalo breeds

摘要

The water buffalo is an important dual-purpose livestockthat is widespread throughout central and southernChina. However, there has been no characterizationof the population genetics of Chinese buffalo. Usingan Axiom buffalo genotyping array (Thermo FisherScientific, Wilmington, DE), we analyzed the geneticdiversity, linkage disequilibrium pattern, and signatureof selection in 176 Chinese buffaloes from 13 breeds.A total of 35,547 SNP passed quality control and wereused for further analyses. Population genetic analysisrevealed a clear separation between swamp and rivertypes. Ten Chinese indigenous breeds were clusteredinto the swamp group, the Murrah and Nili-Ravi breedswere clustered into the river group, and the crossbredbreed was closer to the river group. Genetic diversityanalysis showed that the swamp group had a lower averageexpected heterozygosity. Linkage disequilibriumdecay distance was much shorter in the swamp groupcompared with the river group, with an average squareof correlation coefficient value of 0.2 of approximately50 kb. Analysis of runs of homozygosity indicatedextensive remote and recent inbreeding within swampand river groups, respectively. Moreover, one genomicregion under selection was detected between the riverand swamp groups. Our findings contribute to ourunderstanding of the characterization of populationgenetics in Chinese buffaloes, which in turn may beused in buffalo breeding programs.