杜洛克猪生长性状全基因组关联分析及候选基因鉴定

doi:10.11843/j.issn.0366-6964.2023.05.010

摘要/Abstract

摘要： 旨在对杜洛克猪生长性状进行全基因组关联分析及候选基因鉴定。本研究选用361头杜洛克种公猪作为试验群体,对达100 kg体重日龄、达100 kg平均日增重、达100 kg活体背膘厚和达100 kg眼肌面积性状进行测定,基因型信息使用50K单核苷酸多态性阵列进行分型,质控后得到31 618个SNPs。使用GCTA软件利用基因组信息对各生长性状进行遗传参数估计,使用R软件rMVP包FarmCPU模型进行全基因组关联分析,鉴定与生长性状相关的基因组区域和候选基因。结果表明,达100 kg体重日龄、达100 kg平均日增重、达100 kg活体背膘厚和达100 kg眼肌面积性状的遗传力分别为0.27、0.29、0.16和0.11,属于中等遗传力性状,达100 kg体重日龄和达100 kg平均日增重的遗传相关和表型相关值均为-0.99,为强负相关关系。全基因关联分析结果表明,在达100 kg体重日龄和达100 kg平均日增重性状上共检测到3个显著SNPs,均位于10号染色体上。使用最小显著差数检验法对显著SNPs的等位基因型进行多重比较,显著SNPs rs81237156、rs81424502和rs81313018的优势等位基因分别为G、T和A。候选基因HACD1和BAMBI在显著SNPs附近的候选区域内被鉴定与猪生长性状相关。本研究新发现的候选基因将促进对生长性状的理解,而新变异的识别可为猪育种的潜在标记提供新的思路。

关键词: 猪, 生长性状, 全基因组关联分析, 候选基因, FarmCPU

Abstract: This study aimed to perform genome-wide association study for candidate gene identification of growth traits in Duroc pigs. In this study, 361 Duroc boars were selected as the experimental population, the days to 100 kg, average daily gain to 100 kg, average backfat thickness to 100 kg and loin muscle area to 100 kg traits were measured. The genotype information was typed by 50K single nucleotide polymorphism array, and 31 618 SNPs were obtained after quality control. The genetic parameters of growth traits were estimated using genome information by GCTA software, and candidate genes related to growth traits were identified by GWAS using R software rMVP package FarmCPU model. The results showed that the heritabilities of the days to 100 kg, average daily gain to 100 kg, average backfat thickness to 100 kg and loin muscle area to 100 kg were 0.27, 0.29, 0.16 and 0.11, respectively, which were moderate heritability traits. The genetic correlation and phenotypic correlation of days to 100 kg and average daily gain to 100 kg were -0.99, indicating the strong negative correlation. The results of GWAS showed that 3 significant SNPs were detected on the days to 100 kg and average daily gain to 100 kg traits, located on chromosome 10. Multiple comparison of allelic genotypes of significant SNPs was performed by Least significant difference test. The dominant alleles of significant SNPs rs81237156, rs81424502 and rs81313018 were G, T, and A, respectively. Candidate genes HACD1 and BAMB were identified to be associated with pig growth traits in the candidate region near significant SNPs. In this study, the newly discovered candidate genes will promote the understanding of growth traits, and the identification of new variants can provide new insights for potential markers in pig breeding.

Key words: pig, growth traits, GWAS, candidate genes, FarmCPU

中图分类号:

S828.2

张笑科, 廖伟莉, 陈信佑, 李婷婷, 袁晓龙, 李加琪, 黄翔, 张豪. 杜洛克猪生长性状全基因组关联分析及候选基因鉴定[J]. 畜牧兽医学报, 2023, 54(5): 1868-1876.

ZHANG Xiaoke, LIAO Weili, CHEN Xinyou, LI Tingting, YUAN Xiaolong, LI Jiaqi, HUANG Xiang, ZHANG Hao. Genome-wide Association Study for Identifying Candidate Genes of Growth Traits in Duroc Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1868-1876.

参考文献 39

[1]	WANG K J,LIU Y F,XU Q,et al.A post-GWAS confirming GPAT 3 gene associated with pig growth and a significant SNP influencing its promoter activity[J]. Anim Genet,2017,48(4):478-482.
[2]	GUO Y M,HUANG Y X,HOU L J,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]	DING R R,YANG M,WANG X W,et al.Genetic architecture of feeding behavior and feed efficiency in a Duroc pig population[J]. Front Genet,2018,9:220.
[4]	TANG Z S,XU J Y,YIN L L,et al.Genome-wide association study reveals candidate genes for growth relevant traits in pigs[J]. Front Genet,2019,10:302.
[5]	HOQUE M A,SUZUKI K,KADOWAKI H,et al.Genetic parameters for feed efficiency traits and their relationships with growth and carcass traits in Duroc pigs[J]. J Anim Breed Genet,2007,124(3):108-116.
[6]	DO D N,STRATHE A B,OSTERSEN T,et al.Genome-wide association and pathway analysis of feed efficiency in pigs reveal candidate genes and pathways for residual feed intake[J]. Front Genet,2014,5:307.
[7]	ONTERU S K,GORBACH D M,YOUNG J M,et al.Whole genome association studies of residual feed intake and related traits in the pig[J]. PLoS One,2013,8(6):e61756.
[8]	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.
[9]	MENG Q L,WANG K J,LIU X L,et al.Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies[J]. Asian-Australas J Anim Sci,2017,30(4):462-469.
[10]	VAN LAERE A S,NGUYEN M,BRAUNSCHWEIG M,et al.A regulatory mutation in IGF 2 causes a major QTL effect on muscle growth in the pig[J]. Nature,2003,425(6960):832-836.
[11]	FONTANESI L,SCHIAVO G,GALIMBERTI G,et al.A genomewide association study for average daily gain in Italian large white pigs[J]. J Anim Sci,2014,92(4):1385-1394.
[12]	LI L Y,XIAO S J,TU J M,et al.A further survey of the quantitative trait loci affecting swine body size and carcass traits in five related pig populations[J]. Anim Genet,2021,52(5):621-632.
[13]	CHO K H,KIM M J,JEON G J,et al.Association of genetic variants for FABP 3 gene with back fat thickness and intramuscular fat content in pig[J]. Mol Biol Rep,2011,38(3):2161-2166.
[14]	KORTE A,FARLOW A.The advantages and limitations of trait analysis with GWAS:a review[J]. Plant Methods,2013,9:29.
[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]	LIU X L,HUANG M,FAN B,et al.Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies[J]. PLoS Genet,2016,12(2):e1005767.
[17]	KUSMEC A,SRINIVASAN S,NETTLETON D,et al.Distinct genetic architectures for phenotype means and plasticities in Zea mays[J]. Nat Plants,2017,3(9):715-723.
[18]	KALER A S,RAY J D,SCHAPAUGH W T,et al.Genome-wide association mapping of canopy wilting in diverse soybean genotypes[J]. Theor Appl Genet,2017,130(10):2203-2217.
[19]	WANG Y Y,LI Y Q,WU H Y,et al.Genotyping of soybean cultivars with medium-density array reveals the population structure and QTNs underlying maturity and seed traits[J]. Front Plant Sci,2018,9:610.
[20]	MENG Q L,WANG K J,LIU X L,et al.Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies[J]. Asian-Australas J Anim Sci,2017,30(4):462-469.
[21]	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.
[22]	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.
[23]	张笑科,李瑶,林清,等.华南地区公猪精液性状遗传参数估计[J].中国畜牧杂志,2022,58(8):50-55,60.ZHANG X K,LI Y,LIN Q,et al.Estimation of genetic parameters for semen traits of boars in South China[J]. Chinese Journal of Animal Science,2022,58(8):50-55,60.(in Chinese)
[24]	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.
[25]	HERING D M,OLENSKI K,KAMINSKI S.Genome-wide association study for poor sperm motility in Holstein-Friesian bulls[J]. Anim Reprod Sci,2014,146(3-4):89-97.
[26]	邢文凯.杜洛克生长性状全基因组选择早期效果及关联分析研究[D].武汉:华中农业大学,2021.XING W K.Early effect and association analysis of genomic selection for growth traits in Duroc[D].Wuhan:Huazhong Agricultural University,2021.(in Chinese)
[27]	XUE Y,LI C,DUAN D,et al.Genome-wide association studies for growth-related traits in a crossbreed pig population[J]. Anim Genet, 2021,52(2):217-222.
[28]	贺婕妤,王斌虎,廖柱,等.长白和大白猪主要生长性状的遗传参数估计[J].畜牧兽医学报,2021,52(8):2115-2123.HE J Y,WANG B H,LIAO Z,et al.Estimation of genetic parameters of main growth traits in landrace and large white pigs[J]. Acta Veterinaria et Zootechnica Sinica,2021,52(8):2115-2123.(in Chinese)
[29]	HOU L,ZHAO H.A review of post-GWAS prioritization approaches[J]. Front Genet,2013,4:280.
[30]	GODDARD M E,HAYES B J.Mapping genes for complex traits in domestic animals and their use in breeding programmes[J]. Nat Rev Genet,2009,10(6):381-391.
[31]	ZHANG H,WANG Z P,WANG S Z,et al.Progress of genome wide association study in domestic animals[J]. J Anim Sci Biotechnol,2012,3(1):26.
[32]	WANG Y,DING X D,TAN Z,et al.Genome-wide association study of piglet uniformity and farrowing interval[J]. Front Genet,2017,8:194.
[33]	XU P,NI L,TAO Y,et al.Genome-wide association study for growth and fatness traits in Chinese Sujiang pigs[J]. Anim Genet, 2020,51(2):314-318.
[34]	TANG Z S,XU J Y,YIN L L,et al.Genome-wide association study reveals candidate genes for growth relevant traits in pigs[J]. Front Genet,2019,10:302.
[35]	JAHUEY-MARTÍNEZ F J,PARRA-BRACAMONTE G M,SIFUENTES-RINCÓN A M,et al.Genomewide association analysis of growth traits in Charolais beef cattle[J]. J Anim Sci,2016,94(11):4570-4582.
[36]	BLONDELLE J,OHNO Y,GACHE V,et al. HACD 1,a regulator of membrane composition and fluidity,promotes myoblast fusion and skeletal muscle growth[J]. J Mol Cell Biol,2015,7(5):429-440.
[37]	CHEN G S,SU Y Y,CAI Y,et al.Comparative transcriptomic analysis reveals beneficial effect of dietary mulberry leaves on the muscle quality of finishing pigs[J]. Vet Med Sci,2019,5(4):526-535.
[38]	YAO X P,YU T Y,XI F X,et al.BAMBI shuttling between cytosol and membrane is required for skeletal muscle development and regeneration[J]. Biochem Biophys Res Commun,2019,509(1):125-132.
[39]	YANG X R,NING Y,MEI C G,et al.The role of BAMBI in regulating adipogenesis and myogenesis and the association between its polymorphisms and growth traits in cattle[J]. Mol Biol Rep,2020,47(8):5963-5974.