Incorporating Genome Annotation Into Genomic Prediction for Carcass Traits in Chinese Simmental Beef Cattle.

ABSTRACT: Various methods have been proposed for genomic prediction (GP) in livestock. These methods have mainly focused on statistical considerations and did not include genome annotation information. In this study, to improve the predictive performance of carcass traits in Chinese Simmental beef cattle, we incorporated the genome annotation information into GP. Single nucleotide polymorphisms (SNPs) were annotated to five genomic classes: intergenic, gene, exon, protein coding sequences, and 3'/5' untranslated region. Haploblocks were constructed for all markers and these five genomic classes by defining a biologically functional unit, and haplotype effects were modeled in both numerical dosage and categorical coding strategies. The first-order epistatic effects among SNPs and haplotypes were mode

SUBMITTER: Xu L 

PROVIDER: S-EPMC7243208 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature