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

Frontiers in Genetics

Peng Guo¹  Lei Xu²  Ling Xu²  Hongwei Li²  Peinuo Zhou²  Han Gao²  Zezhao Wang²  Xue Gao²  Wentao Cai²  Yan Chen²  Lupei Zhang²  Lingyang Xu²  Huijiang Gao³  Junya Li³  Bo Zhu³ 

[1] College of Computer and Information Engineering, Tianjin Agricultural University, Tianjin, China;Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China;National Centre of Beef Cattle Genetic Evaluation, Beijing, China;

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

DOI  :  10.3389/fgene.2021.665382

来源: DOAJ

【 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 (∼1.4 and 1.9% for GHBLUP and GHBLUP+GBLUP, respectively). We found that the accuracies using haploblock approach varied with different LD thresholds. The LD thresholds (r2 ≥ 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.

【 授权许可】

Unknown