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

Abstract

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

CLC Number:

S828.2

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.

References

[1] ZENG M, WANG B H, LIU L, et al. Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs[J]. J Integr Agric, 2024, 23(1):217-227.
[2] GUO Y M, HUANG Y X, HOU L, et al. Genome-wide detection of genetic markers associated with growth and fatness in four pig populations using four approaches[J]. Genet Sel Evol, 2017, 49(1):21.
[3] 窦腾飞,吴姿仪,白利瑶, 等. 全基因组关联分析鉴定大白猪生长性状遗传变异及候选基因[J]. 中国畜牧杂志, 2023, 59(8):264-272.
DOU T F, WU Z Y, BAI L Y, et al. Genome-wide association analysis identifies genetic variants and candidate genes for growth traits in Large White pigs[J]. Chinese Journal of Animal Science, 2023, 59(8):264-272. (in Chinese)
[4] TANG Z, XU J, YIN L, et al. Genome-wide association study reveals candidate genes for growth relevant traits in pigs[J]. Front Genet, 2019, 10:302.
[5] RUAN D L, ZHUANG Z W, DING R R, et al. Weighted single-step gwas identified candidate genes associated with growth traits in a Duroc pig population[J]. Genes (Basel), 2021, 12(1):117.
[6] WANG K J, LIU Y F, XU Q, et al. A post-GWAS confirming GPAT3 gene associated with pig growth and a significant SNP influencing its promoter activity[J]. Anim Genet, 2017, 48(4):478-482.
[7] KORTE A, FARLOW A. The advantages and limitations of trait analysis with GWAS: a review[J]. Plant Methods, 2013, 9:29.
[8] ZHOU P, YIN C, WANG Y W, et al. Genomic association analysis of growth and backfat traits in Large White Pigs[J]. Genes (Basel), 2023, 14(6):1258.
[9] JUNG J H, LEE S M, OH S H. A genome-wide association study on growth traits of Korean commercial pig breeds using Bayesian methods[J]. Anim Biosci, 2024, 37(5):807-816.
[10] XU P, LI D S, WU Z P, et al. An imputation-based genome-wide association study for growth and fatness traits in Sujiang pigs[J]. Animal, 2022, 16(8):100591.
[11] QIAO J K, LI K B, MIAO N, et al. Additive and dominance genome-wide association studies reveal the genetic basis of heterosis related to growth traits of Duhua Hybrid Pigs[J]. Animals (Basel), 2024, 14(13):1944.
[12] PURCELL S, NEALE B, TODD-BROWN K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses[J]. Am J Hum Genet, 2007, 81(3):559-575.
[13] YANG J, LEE S H, GODDARD M E, et al. GCTA: a tool for genome-wide complex trait analysis[J]. Am J Hum Genet, 2011, 88(1):76-82.
[14] ZHOU X, STEPHENS M. Genome-wide efficient mixed-model analysis for association studies[J]. Nat Genet, 2012, 44(7):821-824.
[15] YU J M, PRESSOIR G, BRIGGS W H, et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness[J]. Nat Genet, 2006, 38(2):203-208.
[16] NICODEMUS K K, LIU W L, CHASE G A, et al. Comparison of type I error for multiple test corrections in large single-nucleotide polymorphism studies using principal components versus haplotype blocking algorithms[J]. BMC Genet, 2005, 6(S1):S78.
[17] 尹剑. 大白猪生长和繁殖性状的全基因组关联分析[D]. 广州：华南农业大学, 2020.
YIN J. Genome-wide association analysis of growth and reproductive traits in Large White pigs[D]. Guangzhou: South China Agricultural University, 2020. (in Chinese)
[18] CHO K H, KIM M J, JEON G J, et al. Association of genetic variants for FABP3 gene with back fat thickness and intramuscular fat content in pig[J]. Mol Biol Rep, 2011, 38(3):2161-2166.
[19] 叶健,胡晓湘,边成, 等. 大白猪主要生长性状的遗传参数估计及育种中存在问题的探讨[J]. 华南农业大学学报, 2017, 38(1):1-4.
YE J, HU X X, BIAN C, et al. Estimation of genetic parameters for major growth traits in Large White pigs and discussion of breeding issues[J]. Journal of South China Agricultural University, 2017, 38(1):1-4. (in Chinese)
[20] 黄叶. 大白猪胴体性状全基因组关联分析及遗传参数估计[D]. 广州：华南农业大学, 2020.
HUANG Y. Genome-wide association analysis and estimation of genetic parameters for carcass traits in Large White pigs[D]. Guangzhou: South China Agricultural University, 2020. (in Chinese)
[21] 张蕾. 种猪繁殖与生长性状的遗传参数估计及影响因素分析[D].杨凌：西北农林科技大学,2021.
ZHANG L. Estimation of genetic parameters and analysis of factors influencing reproduction and growth traits in breeding pigs[D]. Yangling: Northwest A&F University, 2021. (in Chinese)
[22] DONG L S, TAN C, CAI G Y, et al. Estimates of variance components and heritability using different animal models for growth, backfat, litter size, and healthy birth ratio in Large White pigs[J]. Can J Anim Sci, 2019, 100(2):330-336.
[23] 曹建新,齐莹莹,王钰龙, 等. 基于多性状动物模型估计大白猪、长白猪生长性状的遗传参数[J]. 畜牧与兽医, 2017, 49(11):154-156.
CAO J X, QI Y Y, WANG Y L, et al. Estimation of genetic parameters for growth traits in large white and long white pigs based on a multi-trait animal model[J]. Journal of Animal Science and Veterinary Medicine, 2017, 49(11):154-156. (in Chinese)
[24] 许迪,颜港,张帅, 等. 大白猪生长性状影响因素分析及遗传参数估计[J]. 中国畜牧兽医, 2024, 51(1):193-202.
XU D, YAN G, ZHANG S, et al. Analysis of factors influencing growth traits and estimation of genetic parameters in Large White pigs[J]. Chinese Journal of Animal Science and Veterinary Medicine, 2024, 51(1):193-202. (in Chinese)
[25] ORENGE J S, ILATSIA E D, KOSGEY I S, et al. Genetic and phenotypic parameters and annual trends for growth and fertility traits of Charolais and Hereford beef cattle breeds in Kenya[J]. Trop Anim Health Prod, 2009, 41(5):767-774.
[26] 李聪,段栋栋,李梦雨, 等. 豫农黑猪体尺性状遗传参数估计的模型研究[J]. 河南农业大学学报, 2022, 56(1):88-95.
LI C, DUAN D D, LI M Y, et al. A modeling study on the estimation of genetic parameters of body size traits in Yunong black pigs[J]. Journal of Henan Agricultural University, 2022, 56(1):88-95. (in Chinese)
[27] XIE Y, SHI X, SHENG K, et al. PI3K/Akt signaling transduction pathway, erythropoiesis and glycolysis in hypoxia (Review)[J]. Mol Med Rep, 2019, 19(2):783-791.
[28] 孙冠聪,焦丹,谢忠奎, 等. PI3K/AKT通路在动物葡萄糖代谢中的研究进展[J]. 生命科学, 2021, 33(5):653-666.
SUN G C, JIAO D, XIE Z K, et al. Research advances on the PI3K/AKT pathway in animal glucose metabolism[J]. Chinese Bulletin of Life Sciences, 2021, 33(5):653-666. (in Chinese)
[29] KOREN S, DIPILATO L M, EMMETT M J, et al. The role of mouse Akt2 in insulin-dependent suppression of adipocyte lipolysis in vivo[J]. Diabetologia, 2015, 58(5):1063-1070.
[30] HUANG X, LIU G, GUO J, et al. The PI3K/AKT pathway in obesity and type 2 diabetes[J]. Int J Biol Sci, 2018, 14(11):1483-1496.
[31] KARADOǦAN A H, ARIKOGLU H, GÖKTüRK F, et al. PIK3R1 gene polymorphisms are associated with type 2 diabetes and related features in the Turkish population[J]. Adv Clin Exp Med, 2018, 27(7):921-927.
[32] KIM J H, CHOI B H, LIM H T, et al. Characterization of phosphoinositide-3-kinase, class 3 (PIK3C3) gene and association tests with quantitative traits in pigs[J]. Asian-Australas J Anim Sci, 2005, 18(12):1701-1707.
[33] 邢月腾. 绿原酸对宁乡猪肉质和脂肪代谢的影响[D]. 长沙：湖南农业大学, 2020.
XING Y T. Effect of chlorogenic acid on meat quality and fat metabolism in Ningxiang pigs[D]. Changsha: Hunan Agricultural University, 2020. (in Chinese)
[34] ZHANG J, ZHANG Y, GONG H, et al. Genetic mapping using 1.4M SNP array refined loci for fatty acid composition traits in Chinese Erhualian and Bamaxiang pigs[J]. J Anim Breed Genet, 2017, 134(6):472-483.
[35] QIN Z, WANG P, CHEN W, et al. Hepatic ELOVL3 is dispensable for lipid metabolism in mice[J]. Biochem Biophys Res Commun, 2023, 658:128-135.
[36] 徐钰芳,孙洁,韩琪, 等. 鸡Elovl2基因组织表达谱及脂代谢功能研究[J]. 中国家禽, 2022, 44(3):9-16.
XU Y F, SUN J, HAN Q, et al. Tissue expression profile and lipid metabolism function of the Elovl2 gene in chickens[J]. Chinese Poultry Science, 2022, 44(3):9-16. (in Chinese)
[37] WU L, LI Z, GAO N, et al. Interferon-α could induce liver steatosis to promote HBsAg loss by increasing triglyceride level[J]. Heliyon, 2024, 10(12):e32730.
[38] 岑路,岑伟建,刘键强, 等. 猪α-干扰素临床促仔猪生长及疾病预防试验[J]. 中国畜牧兽医, 2010, 37(2):141-143.
CEN L, CEN W J, LIU J Q, et al. Clinical trial of porcine α-interferon in promoting piglet growth and disease prevention[J]. Chinese Journal of Animal Science and Veterinary Medicine, 2010, 37(2):141-143. (in Chinese)
[39] 郭思武,刘玉芳,储明星. 绵羊HERC1和ALDH6A1多态性与胴体性状的关联分析[J]. 特产研究, 2022, 44(3):18-26.
GUO S W, LIU Y F, CHU M X. Association analysis of polymorphisms in HERC1 and ALDH6A1 genes with carcass traits in sheep[J]. Special Product Research, 2022, 44(3):18-26. (in Chinese)
[40] SU G, JU K, XU Y, et al. Structural and biochemical basis of methylmalonate semialdehyde dehydrogenase ALDH6A1[J]. Med Plus, 2024, 1(1):100008.

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

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