Prescreening of large-effect markers with multiple strategies improves the accuracy of genomic prediction  

作　　者：Keanning Li Bingxing An Mang Liang Tianpeng Chang Tianyu Deng Lili Du Sheng Cao Yueying Du Hongyan Li Lingyang Xu Lupei Zhang Xue Gao Junya LI Huijiang Gao 

机构地区：[1]Laboratory of Molecular Biology and Bovine Breeding,Institute of Animal Sciences,Chinese Academy of Agricultural Sciences,Beijing 100193,China [2]Shaanxi Key Laboratory of Molecular Biology for Agriculture,College of Animal Science and Technology,Northwest A&F University,Yangling712100,China [3]College of Computer and Information Engineering,Tianjin Agricultural University,Tianjin 300384,China [4]College of Animal Science and Technology,Qingdao Agricultural University,Qingdao 266109,China [5]Tongliao Animal Agriculture Development Service Center,Tongliao 028000,China

出　　处：《Journal of Integrative Agriculture》2024年第5期1634-1643,共10页农业科学学报（英文版）

基　　金：This research was supported by the National Natural Science Foundations of China(31872975);the Science and Technology Project of Inner Mongolia Autonomous Region,China(2020GG0210);the Program of National Beef Cattle and Yak Industrial Technology System,China(CARS-37).

摘　　要：Presently,integrating multi-omics information into a prediction model has become a ameliorate strategy for genomic selection to improve genomic prediction accuracy.Here,we set the genomic and transcriptomic data as the training population data,using BSLMM,TWAS,and eQTL mapping to prescreen features according to |β_(b)|>0,top 1%of phenotypic variation explained(PVE),expression-associated single nucleotide polymorphisms(eSNPs),and egenes(false discovery rate(FDR)<0.01),where these loci were set as extra fixed effects(named GBLUP-Fix)and random effects(GFBLUP)to improve the prediction accuracy in the validation population,respectively.The results suggested that both GBLUP-Fix and GFBLUP models could improve the accuracy of longissimus dorsi muscle(LDM),water holding capacity(WHC),shear force(SF),and pH in Huaxi cattle on average from 2.14 to 8.69%,especially the improvement of GFBLUP-TWAS over GBLUP was 13.66%for SF.These methods also captured more genetic variance than GBLUP.Our study confirmed that multi-omics-assisted large-effects loci prescreening could improve the accuracyofgenomic prediction.

关 键 词：multi-omics data features prescreening eQTL mapping Huaxi cattle genomic selection 

分 类 号：S813.3[农业科学—畜牧学]