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

Keanning Li ¹Bingxing An ¹Mang Liang ¹Tianpeng Chang ¹Tianyu Deng ²Lili Du ¹Sheng Cao ³Yueying Du ⁴Hongyan Li ⁵Lingyang Xu ¹Lupei Zhang ¹Xue Gao ¹Junya LI ¹Huijiang Gao¹

扫码查看

作者信息

1. Laboratory of Molecular Biology and Bovine Breeding,Institute of Animal Sciences,Chinese Academy of Agricultural Sciences,Beijing 100193,China
2. Laboratory of Molecular Biology and Bovine Breeding,Institute of Animal Sciences,Chinese Academy of Agricultural Sciences,Beijing 100193,China;Shaanxi Key Laboratory of Molecular Biology for Agriculture,College of Animal Science and Technology,Northwest A&F University,Yangling 712100,China
3. Laboratory of Molecular Biology and Bovine Breeding,Institute of Animal Sciences,Chinese Academy of Agricultural Sciences,Beijing 100193,China;College of Computer and Information Engineering,Tianjin Agricultural University,Tianjin 300384,China
4. Laboratory of Molecular Biology and Bovine Breeding,Institute of Animal Sciences,Chinese Academy of Agricultural Sciences,Beijing 100193,China;College of Animal Science and Technology,Qingdao Agricultural University,Qingdao 266109,China
5. Tongliao Animal Agriculture Development Service Center,Tongliao 028000,China
折叠

Abstract

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 |Aβb|＞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 accuracy of genomic prediction.

Key words

multi-omics data/features prescreening/eQTL mapping/Huaxi cattle/genomic selection

引用本文复制引用

基金项目

国家自然科学基金(31872975)

Science and Technology Project of Inner Mongolia Autonomous Region,China(2020GG0210)

Program of National Beef Cattle and Yak Industrial Technology System,China(CARS-37)

出版年

2024

农业科学学报(英文)

中国农业科学院农业信息研究所

农业科学学报(英文)

CSTPCD

影响因子：0.576

ISSN：2095-3119

参考文献量44

段落导航