大规模群体解析猪日增重及达百千克体重日龄的潜在因果基因

doi:10.11843/j.issn.0366-6964.2025.03.012

摘要/Abstract

摘要：

旨在探究影响猪达100 kg体重日龄(age at 100 kg，AGE)和达100 kg体重平均日增重(average daily gain at 100 kg，ADG)的候选基因。本研究采集了来自大白、长白和杜洛克3个品种的共计4 593头健康成年猪的耳组织作为试验材料，其中公猪2 563头，母猪2 030头。通过记录猪只的日龄和体重，计算校正AGE和ADG。通过酚氯仿法提取样品DNA，利用“中芯一号”50K SNP芯片对样本进行基因分型，并对质控后的SNPs进行基因型填充，将SNPs位点数从4万填充至800万。随后，利用GEMMA混合线性模型对AGE和ADG性状进行填充前后的全基因组关联分析，使用BEDTools在显著位点上、下游1 Mb范围查找候选基因。同时，结合PigGTEx中的34个组织的表达量数量性状位点数据，使用R软件进行共定位分析，挖掘与GWAS信号共享同一因果变异的基因，通过GWAS和共定位分析，确定AGE和ADG性状的候选基因。GWAS分析结果显示，AGE与ADG性状的显著SNP为1号染色体上的1_270827213。在该位点上、下游1 Mb范围内，共鉴定到32个基因。共定位分析结果显示，对于AGE性状，有10个基因的eQTL信号与GWAS信号共定位。对于ADG性状，有11个基因的eQTL信号与GWAS信号共定位。最终，确定了CRAT、GPR107和USP20这3个基因作为AGE的候选基因，确定了CRAT、GPR107、USP20、FNBP1、PTGES和HMCN2这6个基因作为ADG的候选基因。本研究为猪品种改良提供了分子标记，对猪生长相关性状功能基因挖掘奠定基础。

关键词: 猪, AGE, ADG, 全基因组关联分析, 候选基因

Abstract:

The aim of this study was to explore candidate genes influencing age at 100 kg (AGE) and average daily weight gain at 100 kg (ADG) in pigs. Ear tissue samples were collected from 4 593 healthy adult pigs, including 2 563 boars and 2 030 sows, representing three breeds: Large White, Landrace, and Duroc. The age and body weight of the pigs were recorded, and the corrected AGE and ADG were calculated accordingly. The DNA from the samples was extracted using the phenol-chloroform method. Genotyping was performed using the "CC-1" 50K SNP chip, and SNP markers were imputed from 40 000 to 8 million after quality control. Subsequently, genome-wide association study was performed using the GEMMA mixed linear model on AGE and ADG traits. Candidate genes were identified by searching within a 1 Mb window upstream and downstream of significant SNP loci using BEDTools. Additionally, the study integrated expression quantitative trait locus data from 34 tissues in the PigGTEx, and colocalization analysis was conducted using R software to identify genes that shared causal variants with the GWAS signals. Through GWAS and colocalization analysis, candidate genes for AGE and ADG traits were identified. The significant SNP associated with both AGE and ADG traits is 1_270827213 on chromosome 1. Within a 1 Mb region upstream and downstream of this SNP, 32 candidate genes were identified. Colocalization analysis showed that, there were 10 genes had eQTL signals that colocalized with the GWAS signal for AGE, while 11 genes had eQTL signals colocalizing with the GWAS signal for ADG. Ultimately, the genes CRAT, GPR107 and USP20 were identified as candidate genes for AGE, and CRAT, GPR107, USP20, FNBP1, PTGES and HMCN2 were identified as candidate genes for ADG. This study provides molecular markers for pig breed improvement and lays the foundation for the functional gene discovery related to growth traits in pigs.

Key words: pigs, AGE, ADG, genome-wide association analysis, candidate genes

中图分类号:

S828.2

黄雅妮, 唐熹, 李井泉, 魏嘉诚, 吴珍芳, 李新云, 肖石军, 张志燕. 大规模群体解析猪日增重及达百千克体重日龄的潜在因果基因[J]. 畜牧兽医学报, 2025, 56(3): 1100-1109.

HUANG Yani, TANG Xi, LI Jingquan, WEI Jiacheng, WU Zhenfang, LI Xinyun, XIAO Shijun, ZHANG Zhiyan. Large-scale Population Analysis of Potential Causal Genes for Daily Weight Gain and Age at 100 kg in Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(3): 1100-1109.

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品种 Breed	公猪 Boar	母猪 Sow
大白Large white	50.775	46.415
长白Landrace	48.441	51.014
杜洛克Duroc	55.289	49.361

表型 Trait	平均值±标准差 Mean±SD	最大值 Maximum	最小值 Minimum	值域 Range	方差 Variance	变异系数/% CV
AGE/d	160.07±7.27	188.59	138.15	50.44	52.81	0.05
ADG/(g·d^-1)	615.70±27.50	709.43	516.56	192.87	756.33	0.04

性状 Trait	染色体 Chromosome	SNP名称 SNP name	位置 Position	效应值 Beta	标准误 SE	P值 P-value
AGE	1	1_270827213	270827213	－1.246	0.218	1.23×10^-8
ADG	1	1_270827213	270827213	4.839	0.827	5.29×10^-9

组织 Tissue	基因 Gene	SNP数量 SNP number	PP.H0.abf	PP.H1.abf	PP.H2.abf	PP.H3.abf	PP.H4.abf
血液Blood	SPTAN1	49	0.036 909 816	0.010 126 732	0.101 001 093	0.026 886 008	0.825 076 351
血液Blood	DYNC212	27	0.097 667 167	0.017 861 012	0.108 656 142	0.019 113 934	0.756 701 746
大脑Brain	GLE1	69	5.87×10^-5	1.43×10^-5	0.058 270 568	0.013 224 164	0.928 432 334
大脑Brain	CRAT	75	0.002 547 613	0.001 575 547	0.059 611 937	0.035 966 132	0.900 298 771
大脑Brain	TORA1	48	0.000 407 217	0.000 101 622	0.006 065 363	0.000 520 716	0.992 905 082
大脑Brain	GPR107	15	0.153 769 887	0.034 532 902	0.033 007 367	0.006 640 586	0.772 049 258
肝Liver	EXOSC2	55	0.068 160 145	0.051 873 945	0.050 815 144	0.037 882 094	0.791 268 673
肌肉Muscle	ENDOG	25	0.000 221 142	0.000 108 116	0.016 117 346	0.006 903 087	0.976 650 309
肌肉Muscle	NUP188	3	0.090 167 323	0.000 845 334	0.143 226 173	0.000 577 585	0.765 183 585
脾Spleen	USP20	142	7.18×10^-5	0.006 173 712	0.001 301 539	0.111 076 123	0.881 376 855
睾丸Testis	DYNC212	82	0.000 440 394	0.000 372 687	0.102 408 901	0.085 853 531	0.810 924 486

组织 Tissue	基因 Gene	SNP数量 SNP number	PP.H0.abf	PP.H1.abf	PP.H2.abf	PP.H3.abf	PP.H4.abf
大脑Brain	CRAT	75	0.007 236 723	0.002 530 961	0.169 333 086	0.058 459 875	0.762 439 354
大脑Brain	TOR1A	48	0.000 187 523	0.000 111 277	0.002 793 096	0.000 661 182	0.996 246 923
大脑Brain	GPR107	15	0.068 069 088	0.037 270 208	0.014 611 322	0.007 127 288	0.872 922 094
肝Liver	EXOSC2	55	0.054 799 403	0.074 246 459	0.040 854 366	0.054 577 125	0.775 522 646
肌肉Muscle	TMEFF1	393	1.24×10^-12	1.43×10^-12	0.105 640 671	0.120 898 331	0.773 460 997
肌肉Muscle	ENDOG	25	0.000 349 317	0.000 102 806	0.025 459 119	0.006 525 219	0.967 563 539
肌肉Muscle	PTGES	82	4.09×10^-7	7.29×10^-8	0.161 141 799	0.027 926 643	0.810 931 076
肌肉Muscle	HMCN2	23	0.042 582 626	0.021 305 938	0.080 703 68	0.039 563 714	0.815 844 042
肌肉Muscle	ASS1	1	0.061 347 848	0.040 059 076	0.001 374 032	0	0.897 219 043
小肠 Small intestine	FNBP1	8	0.151 455 241	0.054 482 732	0.019 121 876	0.006 109 849	0.768 830 301
脾Spleen	USP20	142	0.000 256 969	0.006 037 688	0.004 660 025	0.108 610 336	0.880 434 982