Abstract
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 ~50 kb in crossbred and 170 kb in purebred populations, while average r2 values ≥0.3 were respectively observed in the ~10 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.
Highlights
Genomic selection (GS) has been widely used to estimate the breeding values in various fields, such as animal and plant breeding programs (Newell and Jannink, 2014; Liu and Chen, 2017; Weller et al, 2017)
The average minor allele frequency (MAF) over all autosomes was 0.29 ± 0.13 in purebred and 0.32 ± 0.12 in crossbred populations, and the purebred had the higher percentage of SNPs with MAF in the range 0.05–0.1 than that of the crossbred (Figure S2)
The results showed the average r2 of Linkage disequilibrium (LD) increased with the increase of MAF across the studies breeds, especially a rapidly declining trend of r2 values were detected at short distances (
Summary
Genomic selection (GS) has been widely used to estimate the breeding values in various fields, such as animal and plant breeding programs (Newell and Jannink, 2014; Liu and Chen, 2017; Weller et al, 2017). Ne can serve as an essential parameter for determining the GS accuracy in livestock species (Daetwyler et al, 2010). In this regard, several modern technologies, such as genome-wide SNP array and highthroughput sequencing created new opportunities to estimate the LD extent and Ne in livestock (Qanbari et al, 2010; Biegelmeyer et al, 2016) and human (Tenesa et al, 2007; Park, 2011). Understanding of the LD extent and Ne in the buffalo population is essential for the application of GS technology
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