JIA-2021-0958 整合全基因组关联分析和选择信号分析揭示鸡F2群体骨骼肌产肉性状的遗传因子

doi:10.1016/S2095-3119(21)63805-4

Journal of Integrative Agriculture ›› 2022, Vol. 21 ›› Issue (7): 2065-2075.DOI: 10.1016/S2095-3119(21)63805-4

所属专题：动物科学合辑Animal Science

JIA-2021-0958 整合全基因组关联分析和选择信号分析揭示鸡F₂群体骨骼肌产肉性状的遗传因子

收稿日期:2021-06-06 接受日期:2021-07-20 出版日期:2022-07-01 发布日期:2021-07-20

Integration of genome-wide association study and selection signatures reveals genetic determinants for skeletal muscle production traits in an F₂ chicken population

LI Yu-dong¹^{, 2, 3}, BAI Xue¹^{, 2, 3}, LIU Xin¹^{, 2, 3}, WANG Wei-jia¹^{, 2, 3}, LI Zi-wei¹^{, 2, 3}, WANG Ning¹^{, 2, 3}, XIAO Fan⁴, GAO Hai-he⁴, GUO Huai-shun⁴, LI Hui¹^{, 2, 3}, WANG Shou-zhi¹^{, 2, 3}

¹ Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, P.R.China ² Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, P.R.China ³ School of Animal Sciences and Technology, Northeast Agricultural University, Harbin 150030, P.R.China ⁴ Fujian Sunnzer Biotechnology Development Co., Ltd., Guangze 354100, P.R.China

Received:2021-06-06 Accepted:2021-07-20 Online:2022-07-01 Published:2021-07-20
About author:LI Yu-dong, E-mail: 710827104@qq.com, liyudong886@163.com; Correspondence WANG Shou-zhi, Tel: +86-451-55191495, E-mail: shouzhiwang@neau.edu.cn
Supported by:
This work was supported by the National Natural Science Foundation of China (31572394), the China Agriculture Research System of MOF and MARA (CARS-41), and the White Feather Broiler Breeding Joint Project of the Ministry of Agriculture and Rural Affairs of China (19190526).

摘要/Abstract

摘要：

本研究以东北农业大学鸡F₂资源群体（NEAURP）为材料，利用 Illumina HiSeq PE150平台进行全基因组测序（26个F₀个体进行10×重测序，519个F₂个体进行3×重测序）。使用SAMtools进行SNP calling，BEAGLE 4.0在默认参数设置下进行基因型填充。经过质量控制和基因型填充后，共有7,890,258个SNPs用于分析。根据GRCg6a参考基因组，使用ANNOVAR软件进行SNP注释。基于混合线性模型（MLM），使用GEMMA软件进行全基因组关联分析。使用F_ST和π两种选择信号方法评估F₂群体的遗传分化和遗传多样性。 GWAS与选择信号的整合分析表明，控制鸡骨骼肌产肉性状的遗传因子主要位于第1染色体（168.95Mb-172.43Mb）和第4染色体（74.37Mb-75.23Mb）上，共鉴定出17个可能影响目标性状的位置候选基因（ LRCH1、CDADC1、CAB39L、LOC112531568、LOC112531569、FAM124A、FOXO1、NBEA、GPALPP1、RUBCNL、ARL11、KPNA3、LHFP、GBA3、LOC112532426、KCNIP4、SLIT2），其中KPNA3和FOXO1是与鸡产肉性状相关的强烈候选基因。本研究的主要创新点是结合GWAS和选择信号分析方法解析鸡骨骼肌产肉性状的遗传结构，发现了一些新的影响鸡产肉性状的基因组区域和候选基因。

Abstract: Improving the production of broiler chicken meat has been a goal of broiler breeding programs worldwide for many years. However, the genetic architectures of skeletal muscle production traits in chickens have not yet been fully elucidated. In the present study, a total of 519 F₂ birds, derived from a cross of Arbor Acres broiler and Baier layer, were re-sequenced (26 F₀ individuals were re-sequenced at a 10-fold depth; 519 F₂ individuals were re-sequenced at a 3-fold depth) and the coupling of genome-wide association study (GWAS) and selection signatures (F_ST (fixation index) and θ_π (nucleotide diversity)) was carried out to pinpoint the associated loci and genes that contribute to pectoral muscle weight (PMW) and thigh muscle weight (TMW). A total of 7 890 258 single nucleotide polymorphisms (SNPs) remained to be analyzed after quality control and imputation. The integration of GWAS and selection signature analyses revealed that genetic determinants responsible for skeletal muscle production traits were mainly localized on chromosomes 1 (168.95–172.43 Mb) and 4 (74.37–75.23 Mb). A total of 17 positional candidate genes (PCGs) (LRCH1, CDADC1, CAB39L, LOC112531568, LOC112531569, FAM124A, FOXO1, NBEA, GPALPP1, RUBCNL, ARL11, KPNA3, LHFP, GBA3, LOC112532426, KCNIP4, and SLIT2) were identified in these regions. In particular, KPNA3 and FOXO1 were the most promising candidates for meat production in chickens. These findings will help enhance our understanding of the genetic architecture of chicken muscle production traits, and the significant SNPs identified could be promising candidates for integration into practical breeding programs such as genome-wide selection (GS) to improve the meat yield of chickens.

Key words: chicken , muscle growth and development , GWAS , selection signature

. JIA-2021-0958 整合全基因组关联分析和选择信号分析揭示鸡F₂群体骨骼肌产肉性状的遗传因子[J]. Journal of Integrative Agriculture, 2022, 21(7): 2065-2075.

LI Yu-dong, BAI Xue, LIU Xin , WANG Wei-jia, LI Zi-wei, WANG Ning, XIAO Fan, GAO Hai-he, GUO Huai-shun, LI Hui, WANG Shou-zhi. Integration of genome-wide association study and selection signatures reveals genetic determinants for skeletal muscle production traits in an F₂ chicken population[J]. Journal of Integrative Agriculture, 2022, 21(7): 2065-2075.

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JIA-2021-0958 整合全基因组关联分析和选择信号分析揭示鸡F₂群体骨骼肌产肉性状的遗传因子

Integration of genome-wide association study and selection signatures reveals genetic determinants for skeletal muscle production traits in an F₂ chicken population

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