大白猪生长性状的全基因组关联分析

doi:10.11843/j.issn.0366-6964.2025.12.014

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (12): 6094-6103.doi: 10.11843/j.issn.0366-6964.2025.12.014

大白猪生长性状的全基因组关联分析

石焱煌¹^,²^,³(), 赵真坚¹^,²^,³, 陈栋¹^,²^,³, 崔晟頔¹^,²^,³, 王俊戈¹^,²^,³, 陈子旸¹^,²^,³, 禹世欣¹^,²^,³, 陈佳苗¹^,²^,³, 周垚茜¹^,²^,³, 黄润杰¹^,²^,³, 唐国庆¹^,²^,³^,*()

1. 四川农业大学动物科技学院, 猪禽种业全国重点实验室, 成都 611130
2. 四川农业大学动物科技学院, 农业农村部畜禽生物组学重点实验室, 成都 611130
3. 四川农业大学“畜禽遗传资源发掘与创新利用四川省重点实验室”, 成都 611130

收稿日期:2025-05-12 出版日期:2025-12-23 发布日期:2025-12-24
通讯作者: 唐国庆 E-mail:shiyanhuanghhh@163.com;tyq003@163.com
作者简介:石焱煌(2002-)，男，四川泸州人，硕士生，主要从事饲料资源开发与利用研究，E-mail：shiyanhuanghhh@163.com
基金资助:
国家生猪技术创新中心先导科技项目(NCTIP-XD/B01)；四川省科技厅项目(2020YFN0024;2021ZDZX0008;2021YFYZ0030)；四川省猪创新团队(sccxtd-2022-08)

Genome-wide Association Study of Growth Traits in Large White Pigs

SHI Yanhuang¹^,²^,³(), ZHAO Zhenjian¹^,²^,³, CHEN Dong¹^,²^,³, CUI Shengdi¹^,²^,³, WANG Junge¹^,²^,³, CHEN Ziyang¹^,²^,³, YU Shixin¹^,²^,³, CHEN Jiamiao¹^,²^,³, ZHOU Yaoxi¹^,²^,³, HUANG Runjie¹^,²^,³, TANG Guoqing¹^,²^,³^,*()

1. State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
2. Key Laboratory of Livestock and Poultry Multi-omics of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
3. Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China

Received:2025-05-12 Online:2025-12-23 Published:2025-12-24
Contact: TANG Guoqing E-mail:shiyanhuanghhh@163.com;tyq003@163.com

摘要/Abstract

摘要：

旨在通过全基因组关联分析(GWAS)解析大白猪关键生长性状的遗传机制，为分子标记辅助育种提供理论依据。本研究以5 701头大白猪为研究对象，采集猪达100kg体重日龄(AGE)、达100 kg体重背膘厚(BF)及达100 kg体重眼肌面积(LMA)的表型数据，结合Illumina 50K SNP芯片基因分型数据，采用混合线性模型进行全基因组关联分析，鉴定与猪生长性状相关的SNPs与候选基因。结果表明：AGE、BF和LMA遗传力分别为0.50、0.45和0.43，均属中高遗传力性状，AGE与BF的遗传相关系数为-0.13，表型相关系数为-0.20；AGE与LMA的遗传相关系数为-0.09，表型相关系数为-0.31；BF与LMA的遗传相关系数为0.22，表型相关系数为0.06；GWAS分析共鉴定出13个显著SNPs，其中AGE鉴定出8个显著SNPs，关联到PIK3CG等11个候选基因；BF鉴定出3个显著SNPs，关联到IFN-ALPHA-15等6个候选基因；LMA鉴定出2个显著SNPs，关联到ALDH6A1基因。本研究通过长白猪生长性状的GWAS鉴定了PIK3CG、ELOVL2、IFN-ALPHA-15和ALDH6A1等20个与猪生长性状相关的候选基因。研究结果为猪生长性状的分子标记辅助选择育种提供了重要参考。

关键词: 大白猪, 全基因组关联分析, 生长性状, 遗传力, 候选基因

Abstract:

This study aimed to analyze the genetic mechanism of key growth traits in Large White pigs through genome-wide association study (GWAS) and provide a theoretical basis for molecular marker-assisted breeding. A total of 5 701 Large White pigs were used in this study. Phenotypic data on age at 100 kg body weight (AGE), backfat thickness at 100 kg body weight (BF), and loin muscle area at 100 kg body weight (LMA) were collected. Combined with genotyping data from the Illumina 50K SNP chip, GWAS was performed using a mixed linear model to identify SNPs and candidate genes associated with pig growth traits. The heritability values of AGE, BF, and LMA were 0.50, 0.45, and 0.43, respectively, all of which were medium to high heritability traits. The genetic correlation coefficient between AGE and BF was -0.13, and the phenotypic correlation coefficient was -0.20; between AGE and LMA, the genetic correlation coefficient was -0.09, and the phenotypic correlation coefficient was -0.31; between BF and LMA, the genetic correlation coefficient was 0.22, and the phenotypic correlation coefficient was 0.06. A total of 13 significant SNPs were identified through GWAS, including 8 significant SNPs for AGE, which were associated with 11 candidate genes including PIK3CG; 3 significant SNPs for BF, which were associated with 6 candidate genes including IFN-ALPHA-15; and 2 significant SNPs for LMA, which were associated with ALDH6A1. This study identified 20 candidate genes related to growth traits in Large White pigs, including PIK3CG, ELOVL2, IFN-ALPHA-15, and ALDH6A1, through GWAS. The results provide an important reference for molecular marker-assisted selection in pig breeding.

Key words: Large White pig, genome-wide association study, growth traits, heritability, candidate genes

中图分类号:

S828.2

石焱煌, 赵真坚, 陈栋, 崔晟頔, 王俊戈, 陈子旸, 禹世欣, 陈佳苗, 周垚茜, 黄润杰, 唐国庆. 大白猪生长性状的全基因组关联分析[J]. 畜牧兽医学报, 2025, 56(12): 6094-6103.

SHI Yanhuang, ZHAO Zhenjian, CHEN Dong, CUI Shengdi, WANG Junge, CHEN Ziyang, YU Shixin, CHEN Jiamiao, ZHOU Yaoxi, HUANG Runjie, TANG Guoqing. Genome-wide Association Study of Growth Traits in Large White Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(12): 6094-6103.

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性状 Trait	样本数 Number of samples	平均值 Mean	标准差 Standard deviation	最小值 Minimum	最大值 Maximum	变异系数/% Coefficient of variation
AGE/d	5 701	177.15	16.51	139.07	269.99	9.32
BF/mm	5 701	9.28	1.94	4.47	19.22	20.95
LMA/cm²	5 701	36.39	4.53	21.61	60.97	12.43

性状 Trait	遗传方差 Genetic variance	残差方差 Residual variance	表型方差 Phenotypic variance	遗传力 Heritability
AGE	130.89	132.93	263.82	0.50
BF	1.80	2.18	3.98	0.45
LMA	7.02	9.15	16.16	0.43

性状 Trait	染色体 Chromosome	SNP名称 SNP name	SNP位置/bp Position	P值 P-value	基因 Gene
AGE	2	WU_10.2_2_15144119	192 608	3.366 33×10^-9	B4GALNT4、PKP3、SIGIRR、ANO9
	1	WU_10.2_1_310475592	127 704 276	1.107 87×10^-7	WDR76、MFAP1
	6	MARC0087863	41 972 632	3.275 84×10^-7	\
	12	ALGA0066694	23 815 963	3.218 12×10^-6	MRPL45、NPEPPS
	9	WU_10.2_9_117626730	106 791 438	4.467 56×10^-6	PIK3CG
	7	WU_10.2_7_8030810	7 705 554	5.876 06×10^-6	ELOVL2
	15	WU_10.2_15_33168294	28 530 053	1.021 85×10^-5	\
	13	WU_10.2_13_3310140	3 174 384	1.981 95×10^-5	ANKRD28
BF	1	Affx-115316901	201 711 021	8.239 71×10^-11	IFN-DELTA-9、IFN-ALPHA-15、IFN-DELTA-10、IFN-OMEGA-6、IFN-DELTA-11、IFN-DELTA-4
	6	ALGA0109178	10 727	6.981 98×10^-6	\
	2	WU_10.2_2_25835060	23 617 127	1.109 92×10^-5	\
LMA	6	ALGA0109178	10 727	6.951 56×10^-6	\
LMA	7	WU_10.2_7_103148794	97 394 296	1.868 86×10^-5	BBOF1、ALDH6A1、LIN52

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大白猪生长性状的全基因组关联分析

Genome-wide Association Study of Growth Traits in Large White Pigs

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性状Trait	AGE	BF	LMA
AGE	1.00	-0.13	-0.09
BF	-0.20	1.00	0.22
LMA	-0.31	0.06	1.00