Data from: Genome-wide SNP data revealed the extent of linkage disequilibrium, persistence of phase and effective population size in purebred and crossbred buffalo populations

Linkage disequilibrium (LD) is a useful parameter for guiding the accuracy
and power of both genome-wide association studies (GWAS) and genomic
selection (GS) among different livestock species. The present study
evaluated the extent of LD, persistence of phase and effective population
size (Ne) for the purebred (Mediterranean buffalo; n=411) and crossbred
[Mediterranean × Jianghan × Nili-Ravi buffalo, n=9; Murrah × Nili-Ravi ×
local (Xilin or Fuzhong) buffalo, n=36] buffalo populations using the 90K
Buffalo SNP genotyping array. The results showed that the average square
of correlation coefficient (r2) between adjacent SNP was 0.13 ± 0.19
across all autosomes for purebred and 0.09 ± 0.13 for crossbred, and the
most rapid decline in LD was observed over the first 200 kb. Estimated r2
≥ 0.2 extended up to approximately 50 kb in crossbred and 170 kb in
purebred populations, while average r2 values ≥ 0.3 were respectively
observed in the approximately 10 kb and 60 kb in the crossbred and
purebred populations. The largest phase correlation (RP,C = 0.47) was
observed at the distance of 100 kb, suggesting that this phase was not
actively preserved between the two populations. Estimated Ne for the
purebred and crossbred population at the current generation was 387 and
113 individuals, respectively. These findings may provide useful
information to guide the GS and GWAS in buffaloes.