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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.

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