Genome-wide DAPC-based genetic structure, linkage disequilibrium, and effective population size in indigenous buffaloes of Northeastern and Central India.

The Indian buffalo population makes a significant component of rural livelihood and dairy economics and has different genetic makeup from the diverse evolutionary processes. The purpose of this study is to determine the amount of genomic variation, linkage disequilibrium (LD), and effective population size (Ne) and genetic relationship of seven buffalo populations living in the Northeast of India and nearby areas by using high-density SNP array. Our study included 327 animals that represented Tripura (n = 53), Meghalaya (n = 43), Manipuri (n = 23), Luit (n = 126), Kalahandi (n = 24), Chilika (n = 36), and Chhattisgarhi (n = 22) populations was genotyped and 621,789 high quality SNPs were obtained after strict quality control filtering. DAPC, pairwise FST, and PCA analyses of population structure showed that the populations were moderately defined by genetic groups. DAPC differentiated clusters which were consistent with patterns of shared ancestry, and there was low to middle differentiation as indicated by FST, especially between populations of Chhattisgarhi, Chilika, Kalahandi, and Meghalaya. The relationships were also supported by PCA that exhibited overlapping and distinct patterns of groups that portrayed the genomic structure. The process of estimating genome-wide linkage disequilibrium involved the utilization of 20 kb intermaker distance bins that range between 10 and 250 kb. Tripura, Manipuri and Chilika buffalo population had a relatively greater LD in the majority of the distance classes, when compared to Luit and Meghalaya which had a more rapid LD decay. It is expected that these trends are manifested by variations in recombination and demographic processes in the past, and not necessarily because of inbreeding itself. Recent Ne estimates for Ne in Manipuri and Tripura were lower, whereas the Ne in Meghalaya, Luit, and Kalahandi was relatively high indicating relatively stable demographic histories. These findings generally describe the population of northeastern Indian buffalos at the genome-wide scale and offer baseline data regarding conservation and breeding goals that would preserve genetic diversity in the long run.