Impact of linkage disequilibrium heterogeneity along the genome on genomic prediction and heritability estimation
文献类型： 外文期刊
作者： Ren, Duanyang 1 ; Cai, Xiaodian 1 ; Lin, Qing 1 ; Ye, Haoqiang 1 ; Teng, Jinyan 1 ; Li, Jiaqi 1 ; Ding, Xiangdong 2 ; Zhang, Zhe 1 ;
作者机构： 1.South China Agr Univ, Coll Anim Sci, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Guangzhou 510642, Peoples R China
2.China Agr Univ, Key Lab Anim Genet & Breeding, Natl Engn Lab Anim Breeding, Minist Agr & Rural Affairs,Coll Anim Sci & Techno, Beijing 100193, Peoples R China
期刊名称：GENETICS SELECTION EVOLUTION （ 影响因子：5.1； 五年影响因子：5.236 ）
ISSN： 0999-193X
年卷期： 2022 年 54 卷 1 期
页码：
收录情况： SCI
摘要： Background: Compared to medium-density single nucleotide polymorphism (SNP) data, high-density SNP data contain abundant genetic variants and provide more information for the genetic evaluation of livestock, but it has been shown that they do not confer any advantage for genomic prediction and heritability estimation. One possible reason is the uneven distribution of the linkage disequilibrium (LD) along the genome, i.e., LD heterogeneity among regions. The aim of this study was to effectively use genome-wide SNP data for genomic prediction and heritability estimation by using models that control LD heterogeneity among regions. Methods: The LD-adjusted kinship (LDAK) and LD-stratified multicomponent (LDS) models were used to control LD heterogeneity among regions and were compared with the classical model that has no such control. Simulated and real traits of 2000 dairy cattle individuals with imputed high-density (770K) SNP data were used. Five types of phenotypes were simulated, which were controlled by very strongly, strongly, moderately, weakly and very weakly tagged causal variants, respectively. The performances of the models with high- and medium-density (50K) panels were compared to verify that the models that controlled LD heterogeneity among regions were more effective with high-density data. Results: Compared to the medium-density panel, the use of the high-density panel did not improve and even decreased prediction accuracies and heritability estimates from the classical model for both simulated and real traits. Compared to the classical model, LDS effectively improved the accuracy of genomic predictions and unbiasedness of heritability estimates, regardless of the genetic architecture of the trait. LDAK applies only to traits that are mainly controlled by weakly tagged causal variants, but is still less effective than LDS for this type of trait. Compared with the classical model, LDS improved prediction accuracy by about 13% for simulated phenotypes and by 0.3 to similar to 10.7% for real traits with the high-density panel, and by similar to 1% for simulated phenotypes and by -0.1 to similar to 6.9% for real traits with the medium-density panel. Conclusions: Grouping SNPs based on regional LD to construct the LD-stratified multicomponent model can effectively eliminate the adverse effects of LD heterogeneity among regions, and greatly improve the efficiency of high-density SNP data for genomic prediction and heritability estimation.
- 相关文献
作者其他论文 更多>>
-
The toxic effects of tetracycline exposure on the physiological homeostasis of the gut-liver axis in grouper
作者：Duan, Yafei;Yang, Yukai;Li, Hua;Zhang, Zhe;Xiao, Meng;Nan, Yuxiu;Yang, Yukai;Chen, Xiaoying;Duan, Yafei;Li, Hua
关键词：Grouper; Antibiotics; Intestinal health; Metabolism; Physiology
-
Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs
作者：Wang, Yifei;Pan, Xiangchun;Liao, Weili;Shen, Qingpeng;Cai, Jiali;Gong, Wentao;Tian, Yuhan;Xu, Dantong;Li, Yipeng;Li, Jiaqi;Zhang, Zhe;Yuan, Xiaolong;Jin, Weiwei;Gong, Jing
关键词：
-
A compendium of genetic regulatory effects across pig tissues
作者：Teng, Jinyan;Gao, Yahui;Xu, Zhiting;Lin, Qing;Diao, Shuqi;Pan, Xiangchun;Wei, Chen;Zhang, Zhe;Zhang, Zhe;Gao, Yahui;Li, Cong-jun;Liu, George E.;Gao, Yahui;Gao, Yahui;Yin, Hongwei;Bai, Lijing;Yang, Liu;Yi, Guoqiang;Tang, Zhonglin;Li, Kui;Yin, Hongwei;Bai, Zhonghao;Bai, Zhonghao;Yu, Xiaoshan;Haley, Chris;Navarro, Pau;Tenesa, Albert;Fang, Lingzhao;Liu, Shuli;Zhao, Bingru;Yang, Wenjing;Ding, Xiangdong;Li, Xiujin;Pan, Zhangyuan;Yang, Wenjing;Guan, Dailu;Pan, Zhangyuan;Hou, Yali;Hou, Yali;Keel, Brittney N.;Rohrer, Gary A.;Lindholm-Perry, Amanda K.;Oliver, William T.;Ballester, Maria;Crespo-Piazuelo, Daniel;Quintanilla, Raquel;Rawlik, Konrad;Xia, Charley;Xia, Charley;Yao, Yuelin;Yao, Wenye;Karlskov-Mortensen, Peter;Fredholm, Merete;Amills, Marcel;Clop, Alex;Amills, Marcel;Godia, Marta;Clop, Alex;Giuffra, Elisabetta;Rocha, Dominique;Wang, Sheng;Rocha, Dominique;Dekkers, Jack C. M.;Kramer, Luke;Tuggle, Christopher K.;Corbett, Ryan;Charles, Mathieu;Pausch, Hubert;Hu, Xiaoxiang;Frantz, Laurent;Frantz, Laurent;Luo, Yonglun;Lin, Lin;Luo, Yonglun;Lin, Lin;Luo, Yonglun;Zhang, Zhe;Chen, Zitao;Cui, Leilei;Cui, Leilei;Cui, Leilei;Cui, Leilei;Cui, Leilei;Xiang, Ruidong;Xiang, Ruidong;Shen, Xia;Shen, Xia;Shen, Xia;Li, Pinghua;Huang, Ruihua;Tang, Guoqing;Li, Mingzhou;Zhao, Yunxiang;Jiang, Jicai;Yuan, Xiaolong;Liu, Xiaohong;Zhao, Shuhong;Zhao, Pengju;Zhao, Shuhong;Zhao, Pengju;Zhao, Pengju;Haley, Chris;Tenesa, Albert;Zhang, Qin;Tenesa, Albert
关键词：
-
Haplotype analysis of genomic prediction by incorporating genomic pathway information based on high-density SNP marker in Chinese yellow-feathered chicken
作者：Ye, Haoqiang;Bello, Semiu Folaniyi;Zhu, Qianghui;Kong, Shaofen;Zheng, Ming;Fang, Xiang;Xu, Haiping;Zhang, Xiquan;Nie, Qinghua;Ye, Haoqiang;Bello, Semiu Folaniyi;Zhu, Qianghui;Kong, Shaofen;Zheng, Ming;Fang, Xiang;Xu, Haiping;Zhang, Xiquan;Nie, Qinghua;Ye, Haoqiang;Xu, Zhenqiang;Bello, Semiu Folaniyi;Zhu, Qianghui;Kong, Shaofen;Zheng, Ming;Fang, Xiang;Jia, Xinzheng;Xu, Haiping;Zhang, Xiquan;Nie, Qinghua;Xu, Zhenqiang;Jia, Xinzheng
关键词：genomic prediction; haplotype; genomic annotation information; linkage disequilibrium; chicken
-
Investigation of potential genetic factors for growth traits in yellow-feather broilers using weighted single-step genome-wide association study
作者：Fang, Xiang;Ye, Haoqiang;Zhang, Siyu;Guo, Lijin;Xu, Yibin;Zhang, Dexiang;Nie, Qinghua;Guo, Lijin;Nie, Qinghua;Fang, Xiang;Ye, Haoqiang;Zhang, Siyu;Guo, Lijin;Xu, Yibin;Zhang, Dexiang;Nie, Qinghua;Fang, Xiang;Ye, Haoqiang;Zhang, Siyu;Guo, Lijin;Xu, Yibin;Zhang, Dexiang;Nie, Qinghua;Guo, Lijin;Nie, Qinghua
关键词：yellow-feather broiler; wssGWAS; pedigree; QTL; growth traits
-
PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs
作者：Zeng, Haonan;Zhang, Wenjing;Lin, Qing;Gao, Yahui;Teng, Jinyan;Xu, Zhiting;Cai, Xiaodian;Zhong, Zhanming;Wu, Jun;Liu, Yuqiang;Diao, Shuqi;Wei, Chen;Gong, Wentao;Pan, Xiangchun;Li, Zedong;Huang, Xiaoyu;Chen, Xifan;Du, Jinshi;Li, Jiaqi;Yuan, Xiaolong;Zhang, Zhe;Zhao, Fuping;Zhao, Yunxiang;Ballester, Maria;Crespo-Piazuelo, Daniel;Amills, Marcel;Clop, Alex;Amills, Marcel;Clop, Alex;Karlskov-Mortensen, Peter;Fredholm, Merete;Li, Pinghua;Huang, Ruihua;Li, Pinghua;Huang, Ruihua;Tang, Guoqing;Li, Mingzhou;Liu, Xiaohong;Chen, Yaosheng;Zhang, Qin;Ding, Xiangdong;Fang, Lingzhao
关键词：
-
A novel trans-acting lncRNA of ACTG1 that induces the remodeling of ovarian follicles
作者：Li, Nian;Zhou, Yinqi;Cai, Jiali;Wang, Yifei;Zhou, Xiaofeng;Hu, Mengting;Zhang, Hao;Li, Jiaqi;Yuan, Xiaolong;Li, Yubin;Cai, Bing
关键词：Trans-acting lncRNAs; Granulosa cells; Follicular remodeling
