Integrating large-scale meta-analysis of genome-wide association studies improve the genomic prediction accuracy for combined pig populations
文献类型： 外文期刊
作者： Cai, Xiaodian 1 ; Zhang, Wenjing 1 ; Gao, Ning 2 ; Wei, Chen 1 ; Wu, Xibo 3 ; Si, Jinglei 3 ; Gao, Yahui 1 ; Li, Jiaqi 1 ; Yin, Tong 4 ; Zhang, Zhe 1 ;
作者机构： 1.South China Agr Univ, Coll Anim Sci, Natl Engn Res Ctr Breeding Swine Ind, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Guangzhou, Peoples R China
2.Hunan Agr Univ, Coll Anim Sci & Technol, Changsha, Peoples R China
3.Guangxi State Farmd Yongxin Anim Husb Grp Co Ltd, Nanning, Peoples R China
4.Justus Liebig Univ, Inst Anim Breeding & Genet, Giessen, Germany
关键词： combined population; genomic prediction; heritability enrichment; meta-analysis of genome-wide association studies
期刊名称：JOURNAL OF ANIMAL BREEDING AND GENETICS （ 影响因子：1.9； 五年影响因子：2.6 ）
ISSN： 0931-2668
年卷期： 2025 年 142 卷 2 期
页码：
收录情况： SCI
摘要： The strategy of combining reference populations has been widely recognized as an effective way to enhance the accuracy of genomic prediction (GP). This study investigated the efficiency of genomic prediction using prior information and combined reference population. In total, prior information considering trait-associated single nucleotide polymorphisms (SNPs) obtained from meta-analysis of genome-wide association studies (GWAS meta-analysis) was incorporated into three models to assess the performance of GP using combined reference populations. Two different Yorkshire populations with imputed whole genome sequence (WGS) data (9,741,620 SNPs), named as P1 (1259 individuals) and P2 (1018 individuals), were used to predict genomic estimated breeding values for three live carcass traits, including backfat thickness, loin muscle area, and loin muscle depth. A 10 x 5 fold cross-validation was used to evaluate the prediction accuracy of 203 randomly selected candidate pigs from the P2 population and the reference population consisted of the remaining pigs from P2 and the stepwise added pigs from P1. By integrating SNPs with different p-value thresholds from GWAS meta-analysis downloaded from PigGTEx Project, the prediction accuracy of GBLUP, genomic feature BLUP (GFBLUP) and GBLUP given genetic architecture (BLUP|GA) were compared. Moreover, we explored effects of reference population size and heritability enrichment of genomic features on the prediction accuracy improvement of GFBLUP and BLUP|GA relative to GBLUP. The prediction accuracy of GBLUP using all WGS markers showed average improvement of 4.380% using the P1 + P2 reference population compared with the P2 reference population. Using the combined reference population, GFBLUP and BLUP|GA yielded 6.179% and 5.525% higher accuracies than GBLUP using all SNPs based on the single reference population, respectively. Positive regression coefficients were estimated in relation to the improvement in prediction accuracy (between GFBLUP/BLUP|GA and GBLUP) and the size of the reference as well as the heritability enrichment of genomic features. Compared to the classic GBLUP model, GFBLUP and BLUP|GA models integrating GWAS meta-analysis information increase the prediction accuracy and using combined populations with enlarged reference population size further enhances prediction accuracy of the two approaches. The heritability enrichment of genomic features can be used as an indicator to reflect weather prior information is accurately presented.
- 相关文献
作者其他论文 更多>>
-
A resource of longitudinal RNA-seq data of Holstein cow rumen, duodenum, and colon epithelial cells during the lactation cycle
作者：Gao, Yahui;Liu, George E.;Li, Cong-jun;Baldwin, Ransom L.;Gao, Yahui;Ma, Li;Gao, Yahui
关键词：Holstein cattle; Gene expression; Gastrointestinal tract tissues; Lactation; Functional genome; Molecular genetics
-
Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs
作者：Xu, Zhiting;Lin, Qing;Cai, Xiaodian;Zhong, Zhanming;Teng, Jinyan;Zeng, Haonan;Gao, Yahui;Wei, Chen;Zhou, Jun;Zhang, Wenjing;Zhang, Xiaoke;Shi, Shaolei;Wu, Jun;Diao, Shuqi;Liu, Yuqiang;Pan, Xiangchun;Feng, Xueyan;Liu, Ruiqi;Su, Zhanqin;Chang, Chengjie;Zhu, Qianghui;Wu, Yuwei;Zhang, Hao;Yuan, Xiaolong;Li, Jiaqi;Zhang, Zhe;Li, Bingjie;Gao, Yahui;Liu, George E.;Gao, Yahui;Ma, Li;Cai, Zexi;Bai, Zhonghao;Su, Guosheng;Sahana, Goutam;Lund, Mogens Sando;Fang, Lingzhao;Wang, Xiaoqing;Shi, Liangyu;Zhao, Fuping;Wang, Xue;Wang, Yi;Zhang, Zipeng;Ding, Xiangdong;Lin, Yu;Tang, Guoqing;Li, Mingzhou;Li, Xuewei;Liu, Shuli;Yin, Hongwei;Bai, Lijing;Li, Kui;Zhou, Zhongyin;Wang, Qishan;Pan, Yuchun;Xu, Zhong;Peng, Xianwen;Mei, Shuqi;Mo, Delin;Liu, Xiaohong;Chen, Yaosheng;Liu, Yang;Xiang, Ruidong;Xiang, Ruidong;Shen, Xia;Shen, Xia;Shen, Xia;Li, Pinghua;Huang, Ruihua;Li, Pinghua;Huang, Ruihua;Ballester, Maria;Crespo-Piazuelo, Daniel;Amills, Marcel;Clop, Alex;Amills, Marcel;Karlskov-Mortensen, Peter;Fredholm, Merete;Zhang, Qin;Zhao, Yunxiang
关键词：pig; meta-GWAS; PigGTEx; molQTL; complex traits
-
The antioxidative properties of thyme, cinnamon, and pomegranate oils in heat-stressed broilers
作者：Wang, Dingfa;Abouelezz, Khaled;Sayed, Mohamed Abdelhameed Mohamed;Galal, Ali Elsayed;Makled, Mohamed Nabil;Habib, Mohamed Ahmed;Abdelfattah, Mostafa Galal;Abouelezz, Khaled;Attaai, Abdelraheim Hassan;Ali, Abdalla Hassan Hussein;Wei, Chen
关键词：Thermal stress; Villus morphology; Antioxidative capacity; Phytogenic supplement; Broiler chicken
-
DPImpute: A Genotype Imputation Framework for Ultra-Low Coverage Whole-Genome Sequencing and its Application in Genomic Selection
作者：Zheng, Weigang;Wang, Chao;Dong, Wenjun;Liu, Yuwen;Zheng, Weigang;Wang, Chao;Dong, Wenjun;Liu, Yuwen;Zheng, Weigang;Ma, Wenlong;Chen, Zhilong;Wang, Chao;Sun, Tao;Dong, Wenjun;Zhang, Song;Tang, Zhonglin;Li, Kui;Liu, Yuwen;Zheng, Weigang;Ma, Wenlong;Chen, Zhilong;Wang, Chao;Sun, Tao;Dong, Wenjun;Zhang, Song;Tang, Zhonglin;Li, Kui;Liu, Yuwen;Zhang, Wenjing;Tang, Zhonglin;Liu, Yuwen;Zhao, Yunxiang
关键词：breeding models; genetic screening of embryos; genomic selection; genotype imputation; single cell genotype
-
Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis
作者：Gao, Yahui;Liu, George E.;Li, Cong-jun;Baldwin, Ransom L.;Gao, Yahui;Ma, Li;Gao, Yahui;Fang, Lingzhao
关键词：
-
Genetic regulation of gene expression across multiple tissues in chickens
作者：Guan, Dailu;Wang, Ying;Zhou, Huaijun;Bai, Zhonghao;Zhu, Di;Li, Houcheng;Buitenhuis, Albert Johannes;Sahana, Goutam;Lund, Mogens Sando;Fang, Lingzhao;Zhu, Xiaoning;Zhu, Di;Wang, Yuzhe;Hu, Xiaoxiang;Zhong, Conghao;Lan, Fangren;Li, Xiaochang;Sun, Congjiao;Yang, Ning;Zhong, Conghao;Lan, Fangren;Li, Xiaochang;Sun, Congjiao;Yang, Ning;Hou, Yali;Pan, Zhangyuan;Si, Wei;Diao, Shuqi;Gao, Yahui;Teng, Jinyan;Xu, Zhiting;Lin, Qing;Li, Zhenhui;Nie, Qinghua;Zhang, Xiquan;Zhang, Zhe;Yao, Yuelin;Yao, Yuelin;Zhao, Bingru;Gao, Yahui;Liu, George E.;Gao, Yahui;Zou, Dong;Wang, Ruizhen;Xu, Tianyi;Zhang, Zhang;Zou, Dong;Wang, Ruizhen;Xu, Tianyi;Zhang, Zhang;Wang, Ruizhen;Zhang, Zhang;Yin, Hongwei;Shi, Shourong;Shao, Dan;Degalez, Fabien;Lagarrigue, Sandrine;Wang, Mingshan;Peng, Minsheng;Wang, Mingshan;Peng, Minsheng;Rocha, Dominique;Charles, Mathieu;Smith, Jacqueline;Watson, Kellie;Warren, Wesley;Frantz, Laurent;Frantz, Laurent;Larson, Greger;Lamont, Susan J.;Si, Wei;Zhao, Xin;Li, Bingjie;Zhang, Haihan;Luo, Chenglong;Shu, Dingming;Qu, Hao;Luo, Wei;Li, Zhenhui;Nie, Qinghua;Zhang, Xiquan;Li, Zhenhui;Nie, Qinghua;Zhang, Xiquan;Xiang, Ruidong;Xiang, Ruidong;Xiang, Ruidong;Liu, Shuli;Cheng, Hans
关键词：
-
Preliminary exploration of mRNA, lncRNA, and miRNA expressions in the bovine jejunum unveils novel aspects of Mycobacterium avium subspecies paratuberculosis infections
作者：Gao, Yahui;Han, Bo;Sun, Dongxiao;Gao, Yahui;Cao, Jie
关键词：Paratuberculosis; RNA-seq; sRNA-seq; Holstein cattle
