您好,欢迎访问广东省农业科学院 机构知识库!

Evaluation of the selection of key individuals for genotype imputation in Chinese yellow-feathered chicken

文献类型: 外文期刊

作者: Zheng, Ming 1 ; Liao, Jiahao 1 ; Li, Zhuohang 1 ; Xu, Zhenqiang 4 ; Jiang, Ziqin 4 ; Tan, Liangtian 1 ; Fu, Rong 1 ; Xu, Haiping 1 ; Li, Zhenhui 1 ; Zhang, Xiquan 1 ; Nie, Qinghua 1 ;

作者机构: 1.South China Agr Univ, Coll Anim Sci, Lingnan Guangdong Lab Modern Agr, Guangzhou 510642, Guangdong, Peoples R China

2.Minist Agr, Guangdong Prov Key Lab Agroanim Genom & Mol Breedi, Guangzhou 510642, Guangdong, Peoples R China

3.Minist Agr, Key Lab Chicken Genet Breeding & Reprod, Guangzhou 510642, Guangdong, Peoples R China

4.South China Agr Univ, State Key Lab Livestock & Poultry Breeding, Guangzhou 510642, Guangdong, Peoples R China

5.Guangdong Wens Nanfang Poultry Breeding Co Ltd, Xinxing 527439, Peoples R China

关键词: chicken; selection approach; imputation reference panel

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 10 期

页码:

收录情况: SCI

摘要: Genotype imputation is a powerful technique employed by next-generation sequencing (NGS) and genotyping arrays, which can significantly enhance the cost-effectiveness and efficiency of geno-mic selection. The accuracy of imputation is largely determined by the choice of reference panel, with pre-vious studies generally demonstrating that a closely related population as a reference panel leads to greater accuracy than a more distantly related population. Various strategies have been proposed for selecting desirable individuals via targeted resequencing, but their efficiencies need further improvement. In this study, we present a practical broiler selection method-ology for a local Chinese chicken line that integrates established methods based on pedigree, genomics, and random sampling, and leverages genotype and pedi-gree information from the yellow-plumage dwarf chicken line. The efficacy of these selection strategies was assessed by evaluating their ability to accurately impute masked genotypes from data obtained using a 600K chip. Our findings reveal that the pedigree-based method yields superior accuracy in genotype imputa-tion, whereas the haplotype-based method exhibits greater stability. Nonetheless, the impact of these tar-geted methods for selecting key individuals is slightly different when initiating a new sequencing project in a production context. Overall, this study highlights the advantages of using the pedigree-based approach as the preferred method for optimizing genotype imputa-tion in broiler chickens.

  • 相关文献
作者其他论文 更多>>
  • The transmembrane protein TMEM182 promotes fat deposition and alters metabolomics and lipidomics

    作者:Chen, Genghua;Lin, Zetong;Peng, Haoqi;Zhang, Shuai;Zhang, Zihao;Zhang, Xiquan;Nie, Qinghua;Luo, Wen;Chen, Genghua;Lin, Zetong;Peng, Haoqi;Zhang, Shuai;Zhang, Zihao;Zhang, Xiquan;Nie, Qinghua;Chen, Genghua;Lin, Zetong;Peng, Haoqi;Zhang, Shuai;Zhang, Zihao;Zhang, Xiquan;Nie, Qinghua

    关键词:TMEM182; Fat formation; Metabolomics; Lipidomics

  • Using multiomics to explore the weight differences between genders in Muscovy ducks

    作者:Tian, Jinghong;Tan, Liangtian;Wei, Shenghua;Yao, Zipei;Xu, Yibin;Nie, Qinghua;Tian, Jinghong;Tan, Liangtian;Wei, Shenghua;Yao, Zipei;Xu, Yibin;Nie, Qinghua;Tian, Jinghong;Tan, Liangtian;Wei, Shenghua;Yao, Zipei;Xu, Yibin;Nie, Qinghua;Tian, Jinghong;Tan, Liangtian;Wei, Shenghua;Yao, Zipei;Xu, Yibin;Nie, Qinghua;Zhu, Weijian;Ji, Congliang

    关键词:Muscovy duck; sexual dimorphism; growth and development; RNA-seq; 16S rRNA sequencing technology

  • PMAIP1 promotes J subgroup avian leukosis virus replication by regulating mitochondrial function

    作者:Zhao, Yongxia;Zhao, Changbin;Pan, Ming;Mo, Guodong;Liao, Zhiying;Zhang, Xiquan;Zhang, Dexiang;Li, Hongmei;Zhao, Yongxia;Zhao, Changbin;Deng, Yuelin;Pan, Ming;Mo, Guodong;Liao, Zhiying;Zhang, Xiquan;Zhang, Dexiang;Li, Hongmei;Zhao, Yongxia;Zhao, Changbin;Deng, Yuelin;Pan, Ming;Mo, Guodong;Liao, Zhiying;Zhang, Xiquan;Zhang, Dexiang;Li, Hongmei;Zhao, Yongxia;Zhao, Changbin;Deng, Yuelin;Pan, Ming;Mo, Guodong;Liao, Zhiying;Zhang, Xiquan;Zhang, Dexiang;Li, Hongmei;Deng, Yuelin

    关键词:ALV-J; PMAIP1; mitochondrial function; immune; DF-1

  • Live chicken body fat measurement technology based on bio-electrical impedance

    作者:Liang, Jinping;Li, Zhenhui;Nie, Qinghua;Zhang, Dexiang;Zhang, Xiquan;Li, Hongmei;Zuo, Jiaming;Cheng, Shangshang;Li, Zhen;Zuo, Jiaming;Cheng, Shangshang;Li, Zhen;Liang, Jinping;Li, Zhenhui;Nie, Qinghua;Zhang, Dexiang;Zhang, Xiquan;Li, Hongmei;Liang, Jinping;Li, Zhenhui;Nie, Qinghua;Zhang, Dexiang;Zhang, Xiquan;Li, Hongmei;Liang, Jinping;Li, Zhenhui;Nie, Qinghua;Zhang, Dexiang;Zhang, Xiquan;Li, Hongmei;Deng, Yuelin

    关键词:BIA; Electrical impedance; Fat content; Broilers

  • Whole-transcriptome sequencing revealed the ceRNA regulatory network during the proliferation and differentiation of goose myoblast

    作者:Zhang, Xiquan;Luo, Wen;Zhang, Xiquan;Luo, Wen;Xiao, Liangchao;Chen, Jiahui;He, Xueying;Zhang, Xiquan;Luo, Wen;Xiao, Liangchao;Chen, Jiahui;He, Xueying;Zhang, Xiquan;Luo, Wen;Xiao, Liangchao;Chen, Jiahui;He, Xueying;Zhang, Xiquan;Luo, Wen

    关键词:Shitou goose; skeletal muscle; whole-transcriptome sequencing; lncRNA; ceRNA network

  • LncEDCH1 g.1703613 T>C regulates chicken carcass traits by targeting miR-196-2-3p

    作者:Yuan, Rongshuai;Cai, Bolin;Ma, Manting;Zhao, Changbin;Xian, Yuanrong;Nie, Qinghua;Zhang, Xiquan;Zhang, Dexiang;Zhang, Dexiang

    关键词:LncEDCH1; miR-196-2-3p; single nucleotide polymorphism; carcass trait; chicken

  • Weighted single-step GWAS identified candidate genes associated with carcass traits in a Chinese yellow-feathered chicken population

    作者:Pan, Rongyang;Qi, Lin;Xu, Zhenqiang;Zhang, Dexiang;Nie, Qinghua;Zhang, Xiquan;Luo, Wen;Pan, Rongyang;Qi, Lin;Xu, Zhenqiang;Zhang, Dexiang;Nie, Qinghua;Zhang, Xiquan;Luo, Wen;Pan, Rongyang;Pan, Rongyang;Qi, Lin;Zhang, Dexiang;Nie, Qinghua;Zhang, Xiquan;Luo, Wen;Pan, Rongyang;Qi, Lin;Xu, Zhenqiang;Zhang, Dexiang;Nie, Qinghua;Zhang, Xiquan;Luo, Wen;Pan, Rongyang;Qi, Lin;Xu, Zhenqiang;Zhang, Dexiang;Nie, Qinghua;Zhang, Xiquan;Luo, Wen

    关键词:Chinese yellow-feathered chicken; weighted single-step GWAS; carcass traits; SNP