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

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

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  • 国家科技期刊平台
  • NETL
  • NSTL
  • 万方数据
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.

multi-omics datafeatures prescreeningeQTL mappingHuaxi cattlegenomic selection

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

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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

College of Computer and Information Engineering,Tianjin Agricultural University,Tianjin 300384,China

College of Animal Science and Technology,Qingdao Agricultural University,Qingdao 266109,China

Tongliao Animal Agriculture Development Service Center,Tongliao 028000,China

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国家自然科学基金Science and Technology Project of Inner Mongolia Autonomous Region,ChinaProgram of National Beef Cattle and Yak Industrial Technology System,China

318729752020GG0210CARS-37

2024

10.1016/j.jia.2023.11.048

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
年,卷(期)：2024.23(5)
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