Incorporating kernelized multi-omics data improves the accuracy of genomic prediction  

作　　者：Mang Liang Bingxing An Tianpeng Chang Tianyu Deng Lili Du Keanning Li Sheng Cao Yueying Du 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,People’s Republic of China

出　　处：《Journal of Animal Science and Biotechnology》2023年第1期88-97,共10页畜牧与生物技术杂志（英文版）

基　　金：funds from the National Natural Science Foundations of China(32172693);the Program of National Beef Cattle and Yak Industrial Technology System(CARS-37)。

摘　　要：Background:Genomic selection(GS)has revolutionized animal and plant breeding after the first implementation via early selection before measuring phenotypes.Besides genome,transcriptome and metabolome information are increasingly considered new sources for GS.Difficulties in building the model with multi-omics data for GS and the limit of specimen availability have both delayed the progress of investigating multi-omics.Results:We utilized the Cosine kernel to map genomic and transcriptomic data as n×n symmetric matrix(G matrix and T matrix),combined with the best linear unbiased prediction(BLUP)for GS.Here,we defined five kernel-based prediction models:genomic BLUP(GBLUP),transcriptome-BLUP(TBLUP),multi-omics BLUP(MBLUP,M=ratio×G+(1-ratio)×T),multi-omics single-step BLUP(mss BLUP),and weighted multi-omics single-step BLUP(wmss BLUP)to integrate transcribed individuals and genotyped resource population.The predictive accuracy evaluations in four traits of the Chinese Simmental beef cattle population showed that(1)MBLUP was far preferred to GBLUP(ratio=1.0),(2)the prediction accuracy of wmss BLUP and mss BLUP had 4.18%and 3.37%average improvement over GBLUP,(3)We also found the accuracy of wmss BLUP increased with the growing proportion of transcribed cattle in the whole resource population.Conclusions:We concluded that the inclusion of transcriptome data in GS had the potential to improve accuracy.Moreover,wmss BLUP is accepted to be a promising alternative for the present situation in which plenty of individuals are genotyped when fewer are transcribed.

关 键 词：BLUP Cosine kernel Genomic prediction TRANSCRIPTOME 

分 类 号：S813[农业科学—畜牧学]