Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle

文献类型： 外文期刊

第一作者： Li, Hongwei

作者： Li, Hongwei;Zhu, Bo;Xu, Ling;Wang, Zezhao;Xu, Lei;Zhou, Peinuo;Gao, Han;Chen, Yan;Gao, Xue;Zhang, Lupei;Gao, Huijiang;Cai, Wentao;Xu, Lingyang;Li, Junya;Zhu, Bo;Gao, Huijiang;Li, Junya;Guo, Peng

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关键词： genomic prediction; prediction accuracy; LD; haplotype; Chinese Simmental beef cattle

期刊名称：FRONTIERS IN GENETICS （ 影响因子：4.599； 五年影响因子：4.888 ）

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年卷期： 2021 年 12 卷

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收录情况： SCI

摘要： A haplotype is defined as a combination of alleles at adjacent loci belonging to the same chromosome that can be transmitted as a unit. In this study, we used both the Illumina BovineHD chip (HD chip) and imputed whole-genome sequence (WGS) data to explore haploblocks and assess haplotype effects, and the haploblocks were defined based on the different LD thresholds. The accuracies of genomic prediction (GP) for dressing percentage (DP), meat percentage (MP), and rib eye roll weight (RERW) based on haplotype were investigated and compared for both data sets in Chinese Simmental beef cattle. The accuracies of GP using the entire imputed WGS data were lower than those using the HD chip data in all cases. For DP and MP, the accuracy of GP using haploblock approaches outperformed the individual single nucleotide polymorphism (SNP) approach (GBLUP_In_Block) at specific LD levels. Hotelling's test confirmed that GP using LD-based haplotypes from WGS data can significantly increase the accuracies of GP for RERW, compared with the individual SNP approach (similar to 1.4 and 1.9% for G(H)BLUP and G(H)BLUP+GBLUP, respectively). We found that the accuracies using haploblock approach varied with different LD thresholds. The LD thresholds (r(2) >= 0.5) were optimal for most scenarios. Our results suggested that LD-based haploblock approach can improve accuracy of genomic prediction for carcass traits using both HD chip and imputed WGS data under the optimal LD thresholds in Chinese Simmental beef cattle.

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