北京黑猪FABP3和SCD基因多态性与肉品质性状关联分析

doi:10.11843/j.issn.0366-6964.2023.03.011

摘要/Abstract

摘要： 旨在研究脂肪酸结合蛋白-3(fatty acid binding protein 3，FABP3)和硬脂酰基辅酶A脱氢酶(stearoyl-CoA desaturase，SCD)基因的多态性及其与肉品质性状的关联，从而能够在分子水平上指导北京黑猪的育种工作。本研究以413头北京黑猪为材料，收集肉品质性状数据并提取DNA和RNA，根据FABP3和SCD基因序列设计20对引物进行PCR扩增及测序，运用DNAStar软件分析测序结果，对FABP3和SCD基因进行不同基因型与北京黑猪肌内脂肪(intramuscular fat，IMF)含量的关联分析并运用荧光定量PCR对其进行基因表达差异分析。结果发现，FABP3基因存在1个错义突变(c.681A>G)，SCD基因存在1个错义突变、2个同义突变以及2个3'UTR区突变。使用Duncan’s多重检验统计分析发现，SCD基因内的SNPs与肉品质性状关联均不显著；FABP3基因错义突变位点c.681A>G与肉色L^*和IMF含量显著关联(P<0.05)。该错义突变导致FABP3蛋白第51位氨基酸残基由异亮氨酸(I)突变为苏氨酸(T)。利用qPCR开展FABP3 c.681A>G两种纯合基因型(AA和GG)个体表达量差异分析，发现该突变位点两种纯合基因型个体间基因表达量差异不显著，说明FABP3 c.681A>G错义突变位点可能通过影响蛋白功能来调控肌内脂肪含量和肉色L^*性状。上述两个基因中只有1个位点与肉色L^*和IMF含量关联显著，可以作为北京黑猪肉品质性状的候选基因功能位点，也能为北京黑猪肉品质育种提供了新的分子标记。

关键词: 北京黑猪, FABP3, SCD, 肉品质, 关联分析

Abstract: The study aimed to investigate the polymorphism of fatty acid binding protein 3 (FABP3) and stearoyl-CoA desaturase (SCD) genes and their association with meat quality traits. It can guide the breeding of Beijing black pigs at molecular level. In this study, meat quality and trait data of 413 Beijing black pigs were collected, DNA and RNA was extracted. According to FABP3 and SCD gene sequences, 20 pairs of primers were designed for PCR amplification and sequencing. DNAStar software was used to analyze the sequencing results. The correlation between FABP3 and SCD genotypes and intramuscular fat content of Beijing black pigs was analyzed and the gene expression difference was analyzed by fluorescence quantitative PCR. FABP3 gene was identified a missense mutation (c. 681 A>G), SCD gene was identified a missense mutation, two synonymous mutations and two 3'UTR region mutations. Duncan’s multiple test statistical analysis showed that all SNPs in SCD gene were not significantly associated with meat quality traits. FABP3 missense mutant c.681A>G was significantly associated with carnation L^* and intramuscular fat (IMF) content (P<0.05). The missense mutation resulted in the mutation of amino acid residue 51 of FABP3 from isoleucine (I) to threonine (T). qPCR was used to analyze the differences in individual expression levels of two homozygous genotypes of c.681A>G (AA and GG) of FABP3, and it was found that there was no significant difference in gene expression levels between the individuals with two homozygous genotypes at the mutation site. These results suggested that the missense mutation site of FABP3 c.681A>G may regulate the intramuscular fat content and carnation L^* traits by affecting the protein function. Only one locus of the FABP3 and SCD genes was significantly associated with carnation L^* and intramuscular fat content, which could be used as a candidate gene functional locus for meat quality traits of Beijing black pigs and also provide a new molecular marker for meat quality breeding of Beijing black pigs.

Key words: Beijing black pigs, FABP3, SCD, meat quality, association analysis

中图分类号:

S828.2

苏艳芳, 杨曼, 牛乃琪, 侯欣华, 张龙超. 北京黑猪FABP3和SCD基因多态性与肉品质性状关联分析[J]. 畜牧兽医学报, 2023, 54(3): 966-975.

SU Yanfang, YANG Man, NIU Naiqi, HOU Xinhua, ZHANG Longchao. Association Analysis of FABP3 and SCD Gene Polymorphisms with Meat Quality Traits in Beijing Black Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 966-975.

参考文献 32

[1]	ROS-FREIXEDES R,GOL S,PENA R N,et al.Genome-wide association study singles out SCD and LEPR as the two main loci influencing intramuscular fat content and fatty acid composition in Duroc pigs[J].PLoS One,2016,11(3):e0152496.
[2]	SOLÉ E,ROS-FREIXEDES R,TOR M,et al.A sequence variant in the diacylglycerol O-acyltransferase 2 gene influences palmitoleic acid content in pig muscle[J].Sci Rep,2021,11(1):14797.
[3]	WANG L Y,ZHANG Y W,ZHANG B,et al.Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs[J].BMC Genom,2021,22(1):441.
[4]	WON S,JUNG J,PARK E,et al.Identification of genes related to intramuscular fat content of pigs using genome-wide association study[J].Asian-Australas J Anim Sci,2018,31(2):157-162.
[5]	LI X P,KIM S W,CHOI J S,et al.Investigation of porcine FABP3 and LEPR gene polymorphisms and mRNA expression for variation in intramuscular fat content[J].Mol Biol Rep,2010,37(8):3931-3939.
[6]	WANG Z X,LI Q G,CHAMBA Y,et al.Identification of genes related to growth and lipid deposition from transcriptome profiles of pig muscle tissue[J].PLoS One,2015,10(10):e0141138.
[7]	呼红梅,王继英,郭建凤,等.莱芜猪和杜洛克猪肌肉H-FABP基因表达量与肌内脂肪和脂肪酸含量关联分析[J].华北农学报,2010,25(4):64-68.HU H M,WANG J Y,GUO J F,et al.Correlation of H-FABP gene expression with IMF and fatty acid content in Laiwu pigs and Duroc[J].Acta Agriculturae Boreali-Sinica,2010,25(4):64-68.(in Chinese)
[8]	韦克林,胡天龙,李坤.肌内脂肪、脂肪酸与猪肉肉质三者关系研究进展[J].中国畜牧兽医文摘,2012,28(11):50-51,66.WEI K L,HU T L,LI K.Research progress on the relationship between intramuscular fat,fatty acid and pork meat quality[J].Chinese Animal Husbandry and Veterinary Abstracts,2012,28(11):50-51,66.(in Chinese)
[9]	BLECHA I M Z,SIQUEIRA F,FERREIRA A B R,et al.Identification and evaluation of polymorphisms in FABP3 and FABP4 in beef cattle[J].Genet Mol Res,2015,14(4):16353-16363.
[10]	刘顺德,李娜,高小艳,等.动物FABP家族基因与脂肪沉积关联研究进展[J].农业科学研究,2010,31(3):44-48.LIU S D,LI N,GAO X Y,et al.Progress of animal FABP family genes and their association with fat deposition[J].Journal of Agricultural Sciences,2010,31(3):44-48.(in Chinese)
[11]	艾锦新,龙安炬,罗卫星,等.黔北麻羊不同组织中FABP1、FABP3基因表达水平的研究[J].中国畜牧杂志,2020, 56(11):63-67,73.AI J X,LONG A J,LUO W X,et al.Expression levels of FABP1 and FABP3 genes in different tissues of Qianbei Ma goat[J].Chinese Journal of Animal Science,2020,56(11):63-67,73.(in Chinese)
[12]	VILLAPLANA-VELASCO A,NOGUERA J L,PENA R N,et al.Comparative transcriptome profile between Iberian Pig varieties provides new insights into their distinct fat deposition and fatty acids content[J].Animals (Basel),2021,11(3):627
[13]	SHANG P,ZHANG B,ZHANG J,et al.Expression and single-nucleotide polymorphisms of the H-FABP gene in pigs[J].Gene,2019,710:156-160.
[14]	胡江,曹健,张丽,等.牦牛FABP3基因组织表达、多态性及其对胴体和肉质性状的影响[J].农业生物技术学报,2019,27(6):1025-1033.HU J,CAO J,ZHANG L,et al.Tissue expression,polymorphisms of FABP3 gene and its effect on carcass and meat quality traits in yak (Bos grunniens)[J].Journal of Agricultural Biotechnology,2019,27(6):1025-1033.(in Chinese)
[15]	CHEN J N,JIANG Y Z,CEN W M,et al.Distribution of H-FABP and ACSL4 gene polymorphisms and their associations with intramuscular fat content and backfat thickness in different pig populations[J].Genet Mol Res,2014,13(3):6759-6772.
[16]	UEMOTO Y,NAKANO H,KIKUCHI T,et al.Fine mapping of porcine SSC14 QTL and SCD gene effects on fatty acid composition and melting point of fat in a Duroc purebred population[J].Anim Genet,2012,43(2):225-228.
[17]	MAHARANI D,PARK H B,LEE J B,et al.Association of the gene encoding stearoyl-CoA desaturase (SCD) with fatty acid composition in an intercross population between Landrace and Korean native pigs[J].Mol Biol Rep,2013,40(1):73-80.
[18]	VITERBO V S,LOPEZ B I M,KANG H,et al.Genome wide association study of fatty acid composition in Duroc swine[J].Asian-Australas J Anim Sci,2018,31(8):1127-1133.
[19]	WANG B B,LI P H,ZHOU W D,et al.Association of twelve candidate gene polymorphisms with the intramuscular fat content and average backfat thickness of Chinese Suhuai pigs[J].Animals (Basel),2019,9(11):858.
[20]	CRESPO-PIAZUELO D,CRIADO-MESAS L,REVILLA M,et al.Identification of strong candidate genes for backfat and intramuscular fatty acid composition in three crosses based on the Iberian pig[J].Sci Rep,2020,10(1):13962.
[21]	PIÓRKOWSKA K,MAȽOPOLSKA M,ROPKA-MOLIK K,et al.Evaluation of SCD,ACACA and FASN mutations:effects on pork quality and other production traits in pigs selected based on RNA-Seq results[J].Animals (Basel),2020,10(1):123.
[22]	LIU L L,WANG Y,LIANG X J,et al.Stearoyl-CoA desaturase is essential for porcine adipocyte differentiation[J].Int J Mol Sci,2020,21(7):2446.
[23]	ZHANG L C,WANG L G,LI Y,et al.A substitution within erythropoietin receptor gene D1 domain associated with litter size in Beijing Black pig,Sus scrofa[J].Anim Sci J,2011,82(5):627-632.
[24]	张润,刘海,杨曼,等.北京黑猪肌内脂肪含量高、低组间脂质组差异分析[J].畜牧兽医学报,2022,53(9):3262-3271.ZHANG R,LIU H,YANG M,et al.Analysis of Lipidome difference between high and low intramuscular fat content groups in Beijing black pigs[J].Acta Veterinaria et Zootechnica Sinica,2022,53(9):3262-3271.(in Chinese)
[25]	田威龙,兰干球,张龙超,等.北京黑猪DKK3和CCR1基因多态性检测及其与背膘厚的关联分析[J].畜牧兽医学报,2022,53(7):2083-2093.TIAN W L,LAN G Q,ZHANG L C,et al.Detection of DKK3 and CCR1 genes polymorphisms and their association with backfat thickness in Beijing black pigs[J].Acta Veterinaria et Zootechnica Sinica,2022,53(7):2083-2093.(in Chinese)
[26]	LIM K S,KIM J M,LEE E A,et al.A candidate single nucleotide polymorphism in the 3'Untranslated region of Stearoyl-CoA Desaturase gene for fatness quality and the gene expression in Berkshire pigs[J].Asian-Australas J Anim Sci,2015, 28(2):151-157.
[27]	GERBENS F,DE KONING D J,HARDERS F L,et al.The effect of adipocyte and heart fatty acid-binding protein genes on intramuscular fat and backfat content in Meishan crossbred pigs[J].J Anim Sci,2000,78(3):552-559.
[28]	庞卫军,杨公社,赵春平,等.猪肌内脂肪和H-FABP基因多态型研究进展[J].陕西农业科学,2002(6):14-16,33.PANG W J,YANG G S,ZHAO C P,et al.Advances in porcine intramuscular fat and H-FABP gene polymorphisms[J].Shaanxi Journal of Agricultural Sciences,2002(6):14-16,33.(in Chinese)
[29]	GERBENS F,VAN ERP A J M,HARDERS F L,et al.Effect of genetic variants of the heart fatty acid-binding protein gene on intramuscular fat and performance traits in pigs[J].J Anim Sci,1999,77(4):846-852.
[30]	GERBENS F,RETTENBERGER G,LENSTRA J A,et al.Characterization,chromosomal localization,and genetic variation of the porcine heart fatty acid-binding protein gene[J].Mamm Genome,1997,8(5):328-332.
[31]	SWEENEY T,O'HALLORAN A M,HAMILL R M,et al.Novel variation in the FABP3 promoter and its association with fatness traits in pigs[J].Meat Sci,2015,100:32-40.
[32]	GERBENS F,VERBURG F J,VAN MOERKERK H T B,et al.Associations of heart and adipocyte fatty acid-binding protein gene expression with intramuscular fat content in pigs[J].J Anim Sci,2001,79(2):347-354.