Strategies to improve genomic predictions for 35 duck carcass traits in an F2 population

作     者：Wentao Cai Jian Hu Wenlei Fan Yaxi Xu Jing Tang Ming Xie Yunsheng Zhang Zhanbao Guo Zhengkui Zhou Shuisheng Hou Wentao Cai;Jian Hu;Wenlei Fan;Yaxi Xu;Jing Tang;Ming Xie;Yunsheng Zhang;Zhanbao Guo;Zhengkui Zhou;Shuisheng Hou

作者机构：Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China Shandong New Hope Liuhe Group Co.Ltd.Qingdao 266108China College of Animal Science and TechnologyQingdao Agricultural UniversityQingdao 266109China College of Animal Science and TechnologyBeijing University of AgricultureBeijing 102206China 

出 版 物：《畜牧与生物技术杂志:英文版》 (Journal of Animal Science and Biotechnology)

年 卷 期：2023年第14卷第5期

页      面：1854-1868页

核心收录：

学科分类：0905[农学-畜牧学] 09[农学] 0901[农学-作物学] 

基　　金：supported by grants from the Key Technologies Research on New Breed of Broiler Poultry by Integration of Breeding,Reproduction and Promotion(2021CXGC010805-02) Taishan Industry Leadership Talent Project of Shandong province in China(TSCY20190108) China Agriculture Research System of MOF and MARA(CARS-42) the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences(CXGC-IAS-09). 

主　　题：Bayesian model Carcass traits Duck Genome prediction Genomic relationship matrix Mark density 

摘      要：Background Carcass traits are crucial for broiler ducks,but carcass traits can only be measured postmortem.Genomic selection(GS)is an effective approach in animal breeding to improve selection and reduce costs.However,the performance of genomic prediction in duck carcass traits remains largely unknown.Results In this study,we estimated the genetic parameters,performed GS using different models and marker densi-ties,and compared the estimation performance between GS and conventional BLUP on 35 carcass traits in an F2 population of ducks.Most of the cut weight traits and intestine length traits were estimated to be high and moder-ate heritabilities,respectively,while the heritabilities of percentage slaughter traits were dynamic.The reliability of genome prediction using GBLUP increased by an average of 0.06 compared to the conventional BLUP method.The Permutation studies revealed that 50K markers had achieved ideal prediction reliability,while 3K markers still achieved 90.7%predictive capability would further reduce the cost for duck carcass traits.The genomic relationship matrix nor-malized by our true variance method instead of the widely used 2pi(1-pi)could achieve an increase in prediction reliability in most traits.We detected most of the bayesian models had a better performance,especially for BayesN.Compared to GBLUP,BayesN can further improve the predictive reliability with an average of 0.06 for duck carcass traits.Conclusion This study demonstrates genomic selection for duck carcass traits is promising.The genomic prediction can be further improved by modifying the genomic relationship matrix using our proposed true variance method and several Bayesian models.Permutation study provides a theoretical basis for the fact that low-density arrays can be used to reduce genotype costs in duck genome selection.