Haplotype analysis of genomic prediction by incorporating genomic pathway information based on high-density SNP marker in Chinese yellow-feathered chicken
文献类型： 外文期刊
作者： Ye, Haoqiang 1 ; Xu, Zhenqiang 3 ; Bello, Semiu Folaniyi 1 ; Zhu, Qianghui 1 ; Kong, Shaofen 1 ; Zheng, Ming 1 ; Fang, Xiang 1 ; Jia, Xinzheng 3 ; Xu, Haiping 1 ; Zhang, Xiquan 1 ; Nie, Qinghua 1 ;
作者机构： 1.South China Agr Univ, Coll Anim Sci, Dept Anim Genet Breeding & Reprod, Guangzhou 510642, Peoples R China
2.Minist Agr, Guangdong Prov Key Lab Agroanim Genom & Mol Breedi, Guangzhou 510642, Peoples R China
3.Minist Agr, Key Lab Chicken Genet Breeding & Reprod, Guangzhou 510642, Peoples R China
4.Wens Nanfang Poultry Breeding Co Ltd, Yunfu 527400, Guangdong, Peoples R China
5.Foshan Univ, Guangdong Prov Key Lab Anim Mol Design & Precise B, Foshan 528225, Peoples R China
关键词： genomic prediction; haplotype; genomic annotation information; linkage disequilibrium; chicken
期刊名称：POULTRY SCIENCE （ 影响因子：4.4； 五年影响因子：4.4 ）
ISSN： 0032-5791
年卷期： 2023 年 102 卷 5 期
页码：
收录情况： SCI
摘要： Genomic selection using single nucleo-tide polymorphism (SNP) markers is now intensively investigated in breeding and has been widely utilized for genetic improvement. Currently, several studies have used haplotype (consisting of multiallelic SNPs) for genomic prediction and revealed its performance advan-tage. In this study, we comprehensively evaluated the performance of haplotype models for genomic prediction in 15 traits, including 6 growth, 5 carcass, and 4 feeding traits in a Chinese yellow-feathered chicken population. We adopted 3 methods to define haplotypes from high -density SNP panels, and our strategy included combin-ing Kyoto Encyclopedia of Genes and Genomes pathway information and considering linkage disequilibrium (LD) information. Our results showed an increase in prediction accuracy due to haplotypes ranging from -0.04 >> 27.16% in all traits, where the significant improvements were found in 12 traits. The estimates of haplotype epistasis heritability were strongly correlated with the accuracy increase by haplotype models. In addi-tion, incorporating genomic annotation information could further increase the accuracy of the haplotype model, where the further increase in accuracy is signifi-cantly relative to the increase of relative haplotype epis-tasis heritability. The genomic prediction using LD information for constructing haplotypes has the best prediction performance among the 4 traits. These results uncovered that haplotype methods were beneficial for genomic prediction, and the accuracy could be further increased by incorporating genomic annotation informa-tion. Moreover, using LD information would potentially improve the performance of genomic prediction.
- 相关文献
作者其他论文 更多>>
-
Exploring variances in meat quality between Qingyuan partridge chicken and Cobb broiler: Insights from combined multi-omics analysis
作者：Yang, Xin;Cai, Bolin;Zhang, Zhaofeng;Mo, Yu;Zhou, Zhen;Wu, Ruiquan;Kong, Shaofen;Cai, Danfeng;Zhang, Ruitong;Li, Zhenhui;Nie, Qinghua;Yang, Xin;Cai, Bolin;Zhang, Zhaofeng;Mo, Yu;Zhou, Zhen;Wu, Ruiquan;Kong, Shaofen;Cai, Danfeng;Li, Zhenhui;Nie, Qinghua
关键词：Qingyuan partridge chicken; Commercial broiler; Meat quality; Multi-omics analysis
-
Application of mRNA-Seq and Metagenomic Sequencing to Study Salmonella pullorum Infections in Chickens
作者：Chao, Xiaohuan;Fan, Zhexia;Wu, Jiongwen;Ye, Chutian;Wang, Xiaomeng;Li, Ruina;Chen, Shuya;Zhang, Xiquan;Fang, Cheng;Luo, Qingbin;Fan, Zhexia;Wu, Jiongwen;Ye, Chutian;Wang, Xiaomeng;Li, Ruina;Chen, Shuya;Zhang, Xiquan;Fang, Cheng;Luo, Qingbin
关键词：
Salmonella pullorum ; chicken; DEGs; DEASs; microbial community -
EGR1 mRNA expression levels and polymorphisms are associated with slaughter performance in chickens
作者：Ye, Mao;Ye, Chutian;Guo, Lijin;Fan, Zhexia;Ma, Xuerong;Liu, Aijun;Liang, Weiming;Chen, Shuya;Fang, Cheng;Zhang, Xiquan;Luo, Qingbin;Ye, Mao;Chao, Xiaohuan;Ye, Chutian;Guo, Lijin;Fan, Zhexia;Ma, Xuerong;Liu, Aijun;Liang, Weiming;Chen, Shuya;Fang, Cheng;Zhang, Xiquan;Luo, Qingbin;Ye, Mao;Chao, Xiaohuan;Ye, Chutian;Guo, Lijin;Fan, Zhexia;Ma, Xuerong;Liu, Aijun;Liang, Weiming;Chen, Shuya;Fang, Cheng;Zhang, Xiquan;Luo, Qingbin;Ye, Mao;Chao, Xiaohuan;Ye, Chutian;Guo, Lijin;Fan, Zhexia;Ma, Xuerong;Liu, Aijun;Liang, Weiming;Chen, Shuya;Fang, Cheng;Zhang, Xiquan;Luo, Qingbin
关键词：Early growth response protein 1 ( EGR1 ); Polymorphism; Slaughter performance; Association analysis; Skeletal muscle
-
METTL3-dependent m6A modification of GHR mRNA regulates mitochondrial function through mitochondrial biogenesis during myoblast differentiation
作者：Zhao, Changbin;Hu, Bowen;Wang, Zhijun;Zhang, Ze;Luo, Wen;Li, Hongmei;Zhang, Xiquan;Zhao, Changbin;Hu, Bowen;Wang, Zhijun;Zhang, Ze;Luo, Wen;Li, Hongmei;Zhang, Xiquan;Zhao, Changbin;Hu, Bowen;Wang, Zhijun;Zhang, Ze;Luo, Wen;Li, Hongmei;Zhang, Xiquan
关键词：GHR; METTL3; m6A; Mitochondrial biogenesis; Mitochondrial function
-
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
-
G-Quadruplexes in Gene Regulation and Cellular Function
作者：Guo, Lijin;Nie, Qinghua
关键词：diseases; function; G-quadruplex; structure
-
Skeletal muscle myopathies and cardiovascular diseases in poultry: challenges for meat production
作者：Bordbar, Farhad;Wadood, Armughan Ahmed;Nie, Qinghua;Guo, Wei
关键词：Poultry; muscle growth; meat quality; muscle myopathy; cardiomyopathy
