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Journal of Integrative Agriculture  2022, Vol. 21 Issue (7): 2065-2075    DOI: 10.1016/S2095-3119(21)63805-4
Special Issue: 动物科学合辑Animal Science
Animal Science · Veterinary Medicine Advanced Online Publication | Current Issue | Archive | Adv Search |
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
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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FST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KPNA3FOXO1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 (FST (fixation index) and θπ (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.

Keywords:  chicken       muscle growth and development       GWAS       selection signature  
Received: 06 June 2021   Accepted: 20 July 2021
Fund: 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).
About author:  LI Yu-dong, E-mail:,; Correspondence WANG Shou-zhi, Tel: +86-451-55191495, E-mail:

Cite this article: 

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. 2022. Integration of genome-wide association study and selection signatures reveals genetic determinants for skeletal muscle production traits in an F2 chicken population. Journal of Integrative Agriculture, 21(7): 2065-2075.

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