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
Deng, Tingxian, Huazhong Agricultural University
Liang, Aixin, Huazhong Agricultural University
Liu, Jiajia, Huazhong Agricultural University
Hua, Guohua, Huazhong Agricultural University
Ye, Tingzhu, Huazhong Agricultural University
Liu, Shenhe, Huazhong Agricultural University
Plastow, Graham, University of Alberta
Zhang, Chunyan, University of Alberta
Wang, Zhiquan, University of Alberta
Salzano, Angela, University of Alberta
Riaz, Hasan, COMSATS Institute of Information Technology
Liang, Xianwei, Chinese Academy of Agricultural Sciences
Yang, Liguo, Huazhong Agricultural University
Cassandro, Martino, University of Padua
Published Dec 18, 2018 on Dryad.
Cite this dataset
Deng, Tingxian et al. (2018). 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 [Dataset]. Dryad. https://doi.org/10.5061/dryad.310pf05
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.
buffalo SNPchip data
SNP data used in the LD analysis for purebred and crossbred buffalo populations. SNP chip data are in binary PLINK format.