Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Genes

Mina Park¹  Taejeong Choi¹  DeukHwan Lee²  Hossein Mehrban³  Masoumeh Naserkheil⁴  Chungil Cho⁵  Noelia Ibáñez-Escriche⁶ 

[1] Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea;Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si, Gyeonggi-do 17579, Korea;Department of Animal Science, Shahrekord University, Shahrekord 88186-34141, Iran;Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran;Hanwoo Genetic Improvement Center, NongHyup Agribusiness Group Inc, Seosan 31948, Korea;Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 València, Spain;

关键词: carcass traits;    yearling weight;    weighted single-step genomic procedures;    SNP window;    Hanwoo cattle;   

DOI  :  10.3390/genes12020266

来源: DOAJ

【 摘 要 】

The weighted single-step genomic best linear unbiased prediction (GBLUP) method has been proposed to exploit information from genotyped and non-genotyped relatives, allowing the use of weights for single-nucleotide polymorphism in the construction of the genomic relationship matrix. The purpose of this study was to investigate the accuracy of genetic prediction using the following single-trait best linear unbiased prediction methods in Hanwoo beef cattle: pedigree-based (PBLUP), un-weighted (ssGBLUP), and weighted (WssGBLUP) single-step genomic methods. We also assessed the impact of alternative single and window weighting methods according to their effects on the traits of interest. The data was comprised of 15,796 phenotypic records for yearling weight (YW) and 5622 records for carcass traits (backfat thickness: BFT, carcass weight: CW, eye muscle area: EMA, and marbling score: MS). Also, the genotypic data included 6616 animals for YW and 5134 for carcass traits on the 43,950 single-nucleotide polymorphisms. The ssGBLUP showed significant improvement in genomic prediction accuracy for carcass traits (71%) and yearling weight (99%) compared to the pedigree-based method. The window weighting procedures performed better than single SNP weighting for CW (11%), EMA (11%), MS (3%), and YW (6%), whereas no gain in accuracy was observed for BFT. Besides, the improvement in accuracy between window WssGBLUP and the un-weighted method was low for BFT and MS, while for CW, EMA, and YW resulted in a gain of 22%, 15%, and 20%, respectively, which indicates the presence of relevant quantitative trait loci for these traits. These findings indicate that WssGBLUP is an appropriate method for traits with a large quantitative trait loci effect.

【 授权许可】

Unknown