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

doi:10.11843/j.issn.0366-6964.2022.07.006

Abstract

Abstract: The aim of this study was to investigate the polymorphism of DKK3 and CCR1 genes and their effects on backfat thickness of Beijing black pigs, so as to screen out molecular markers that can be used to improve backfat thickness traits and provide basis for directional breeding of excellent traits in Beijing black pigs. DNA extraction, PCR amplification and gene sequencing were performed on 413 healthy Beijing black pigs to screen SNPs of candidate genes. At the same time, SAS 9.2 software was used to analyze the association between different genotypes of mutation sites and backfat thickness of 6-7th ribs, backfat thickness of lumbosacral region. The results showed that a total of 10 SNPs were detected in the exons of DKK3 gene in Beijing black pig, including 1 splice region variant, 1 missense variant and 8 3'UTR variants. Among them, 4 SNPs of 3' UTR variants were significantly associated with the backfat thickness of lumbosacral region (P<0.05), which were g.47443779 T > C, g.47444258 C > T, g.47444912 G > T and g.47445304 T > C, respectively, and other SNPs had no significant correlation with backfat thickness of lumbosacral region or backfat thickness of 6-7th ribs (P>0.05). A total of 3 SNPs were detected in the exon of CCR1 gene, including 2 synonymous variant and 1 missense variant. One synonymous variant (g.29229037 G > A) was significantly associated with the backfat thickness of 6-7th ribs (P<0.05). The linkage disequilibrium analysis of 10 SNPs in DKK3 showed that g. 47443779 T > C and g. 47443783 C > T were in a completely linked state (D'=1), g. 47443783 C > T and g. 47443858 C > T were in a completely linked state (D'=1), g. 47444258 C > T and g. 47444275 C > T were in a highly linked state (D'=0.98). In summary, SNPs of DKK3 and CCR1 genes were respectively significantly associated with the backfat thickness of lumbosacral region and backfat thickness of 6-7th ribs of Beijing black pig, which could provide reference for the early molecular breeding of backfat thickness in Beijing black pig.

Key words: Beijing black pigs, DKK3, CCR1, backfat thickness

CLC Number:

S828.2

TIAN Weilong, LAN Ganqiu, ZHANG Longchao, WANG Lixian, LIANG Jing, LIU Xin. 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.

References 41

[1]	GIUFFRA E,KIJAS J M H,AMARGER V,et al.The origin of the domestic pig:Independent domestication and subsequent introgression[J].Genetics,2000,154(4):1785-1791.
[2]	HE Y A,YANG X G,XIA J,et al.Consumption of meat and dairy products in China:A review[J].Proc Natr Soc,2016,75(3):385-391.
[3]	MEURENS F,SUMMERFIELD A,NAUWYNCK H,et al.The pig:A model for human infectious diseases[J].Trends Microbiol,2012,20(1):50-57.
[4]	BERTHO N,MEURENS F.The pig as a medical model for acquired respiratory diseases and dysfunctions:an immunological perspective[J].Mol Immunol,2021,135:254-267.
[5]	BERGEN W G.Pigs (Sus Scrofa) in biomedical research[M]//WU G Y.Recent Advances in Animal Nutrition and Metabolism.Cham:Springer,2022:335-343.
[6]	SUZUKI K,KATOH K,ADOWAKI H K,et al.Genetic correlations among carcass cross-sectional fat area ratios,production traits,intramuscular fat,and serum leptin concentration in Duroc pigs[J].J Anim Sci,2009,87(7):2209-2215.
[7]	YANG Q,WU P X,WANG K,et al.SNPs associated with body weight and backfat thickness in two pig breeds identified by a genome-wide association study[J].Genomics,2019,111(6):1583-1589.
[8]	GOZALO-MARCILLA M,BUNTJER J,JOHNSSON M,et al.Genetic architecture and major genes for backfat thickness in pig lines of diverse genetic backgrounds[J].Genet Sel Evol,2021,53(1):76.
[9]	WHITE G E,IQBAL A J,GREAVES D R.CC chemokine receptors and chronic inflammation-therapeutic opportunities and pharmacological challenges[J].Pharmacol Rev,2013,65(1):47-89.
[10]	CHENG J F,JACK R.CCR1 antagonists[J].Mol Divers,2008,12(1):17-23.
[11]	ZHAO K S,DONG R,YU Y F,et al.Cigarette smoke-induced lung inflammation in COPD mediated via CCR1/JAK/STAT/NF-κB pathway[J].Aging,2020,12(10):9125-9138.
[12]	KHOLODNYUK I,RIVKINA A,HIPPE L,et al.Chemokine receptors CCR1 and CCR2 on peripheral blood mononuclear cells of newly diagnosed patients with the CD38-positive chronic lymphocytic leukemia[J].J Clin Med,2020,9(7):2312.
[13]	YANG Y F,ZHANG X M,ZHOU C Y,et al.Elevated immunoreactivity of RANTES and CCR1 correlate with the severity of stages and dysmenorrhea in women with deep infiltrating endometriosis[J].Acta Histochem,2013,115(5):434-439.
[14]	柴继田.基于猪CCR1和CCR5受体高通量细胞筛选模型的构建及其条件优化[D].扬州:扬州大学,2015.CHAI J T.The construction and optimization of porcine CCR1 and CCR5 receptor of high-throughput cell screening model[D].Yangzhou:Yangzhou University,2015.(in Chinese)
[15]	KOGELMAN L J A,CIRERA S,ZHERNAKOVA D V,et al.Identification of co-expression gene networks,regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model[J].BMC Med Genomics,2014,7:57.
[16]	VEECK J,DAHL E.Targeting the Wnt pathway in cancer:the emerging role of Dickkopf-3[J].Biochim Biophys Acta,2012,1825(1):18-28.
[17]	LIU Q W,LI J Y,ZHANG X C,et al.Human amniotic mesenchymal stem cells inhibit hepatocellular carcinoma in tumour-bearing mice[J].J Cell Mol Med,2020,24(18):10525-10541.
[18]	CAO Q,ZHANG J X,GAO L,et al.Dickkopf-3 upregulation mediates the cardioprotective effects of curcumin on chronic heart failure[J].Mol Med Rep,2018,17(5):7249-7257.
[19]	LI H X,LUO X,LIU R X,et al.Roles of Wnt/β-catenin signaling in adipogenic differentiation potential of adipose-derived mesenchymal stem cells[J].Mol Cell Endocrinol,2008,291(1-2):116-124.
[20]	LIU X,GONG J F,WANG L G,et al.Genome-wide profiling of the microrna transcriptome regulatory network to identify putative candidate genes associated with backfat deposition in pigs[J].Animals (Basel),2019,9(6):313.
[21]	EUSEBI P G,GONZÁLEZ-PRENDES R,QUINTANILLA R,et al.A genome-wide association analysis for carcass traits in a commercial Duroc pig population[J].Anim Genet,2017,48(4):466-469.
[22]	DING R R,ZHUANG Z W,QIU Y B,et al.Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis[J].J Anim Sci,2022,100(2):skac012.
[23]	FABBRI M C,ZAPPATERRA M,DAVOLI R,et al.Genome-wide association study identifies markers associated with carcass and meat quality traits in Italian Large White pigs[J].Anim Genet,2020,51(6):950-952.
[24]	CHEN D J,WU P X,YANG Q,et al.Genome-wide association study for backfat thickness at 100 kg and loin muscle thickness in domestic pigs based on genotyping by sequencing[J].Physiol Genomics,2019,51(7):261-266.
[25]	武群清.北京黑猪肉质性状的研究及其背最长肌转录组差异分析[D].长沙:湖南农业大学,2017.WU Q Q.The study on pork quality and transcriptional profiling of longissimus dorsi muscle on Beijing black pig[D].Changsha:Hunan Agricultural University,2017.(in Chinese)
[26]	GUO Y M,QIU H Q,XIAO S J,et al.A genome-wide association study identifies genomic loci associated with backfat thickness,carcass weight,and body weight in two commercial pig populations[J].J Appl Genet,2017,58(4):499-508.
[27]	TOYODA H,MIYAGAWA T,KOIKE A,et al.A polymorphism in CCR1/CCR3 is associated with narcolepsy[J].Brain Behav Immun,2015,49:148-155.
[28]	KIRINO Y,BERTSIAS G,ISHIGATSUBO Y,et al.Genome-wide association analysis identifies new susceptibility loci for Behçet's disease and epistasis between HLA-B*51 and ERAP1[J].Nat Genet,2013,45(2):202-207.
[29]	HAAS B E,HORVATH S,PIETILÄINEN K H,et al.Adipose co-expression networks across Finns and Mexicans identify novel triglyceride-associated genes[J].BMC Med Genomics,2012,5:61.
[30]	ALEXANDER T,NOLTE C,KRUMLAUF R.Hox genes and segmentation of the hindbrain and axial skeleton[J].Annu Rev Cell Dev Biol,2009,25:431-456.
[31]	ROSS S E,HEMATI N,LONGO K A,et al.Inhibition of adipogenesis by wnt signaling[J].Science,2000,289(5481):950-953.
[32]	ZANG L,WANG Y D,SUN B X,et al.Identification of a 13 bp indel polymorphism in the 3'-UTR of DGAT2 gene associated with backfat thickness and lean percentage in pigs[J].Gene,2016,576(2):729-733.
[33]	BARTEL D P.MicroRNAs:target recognition and regulatory functions[J].Cell,2009,136(2):215-233.
[34]	DJURANOVIC S,NAHVI A,GREEN R.miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay[J].Science,2012,336(6078):237-240.
[35]	BARTEL D P.MicroRNAs[J].Cell,2004,116(2):281-297.
[36]	WANG G,ZOU H B,LAI C Y,et al.Repression of MicroRNA-124-3p alleviates high-fat diet-induced hepatosteatosis by targeting pref-1[J].Front Endocrinol (Lausanne),2020,11:589994.
[37]	WANG J K,WANG Z,LI G D.MicroRNA-125 in immunity and cancer[J].Cancer Lett,2019,454:134-145.
[38]	何春,张琦悦,孙浩伟,等.miRNA和lncRNA在动物脂肪沉积中的研究进展[J].生物工程学报,2020,36(8):1504-1514.HE C,ZHANG Q Y,SUN H W,et al.Role of miRNA and lncRNA in animal fat deposition-a review[J].Chinese Journal of Biotechnology,2020,36(8):1504-1514.(in Chinese)
[39]	LIU F T,LIU Y L,DU Y Q,et al.MiRNA-130a promotes inflammation to accelerate atherosclerosis via the regulation of proliferator-activated receptor γ(PPARγ) expression[J].Anatol J Cardiol,2021,25(9):630-637.
[40]	XU P Z,VERNOOY S Y,GUO M,et al.The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism[J].Curr Biol,2003,13(9):790-795.
[41]	李常红,张明国,胡玮宜,等.不同猪种IGF1R基因扩增及SNPs的筛选[J].吉林农业大学学报,2018,40(6):734-739.LI C H,ZHANG M G,HU W Y,et al.Study on amplification of IGF1R gene and SNPs screening in different pig breeds[J].Journal of Jilin Agricultural University,2018,40(6):734-739.(in Chinese)

Detection of DKK3 and CCR1 Genes Polymorphisms and Their Association with Backfat Thickness in Beijing Black Pigs

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References 41

Related Articles 11

Recommended Articles

Metrics

Comments

[1]	ZHU Xueli, ZHANG Longchao, WANG Lixian, PU Lei, LIU Xin. Association Analysis of AQP9 and RPS10 Gene Polymorphisms with Backfat Thickness in Beijing Black Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 87-98.
[2]	NIU Naiqi, ZHAO Runze, ZONG Wencheng, LIU Xiance, LIU Hai, SHI Guohua, JING Xitao, ZHANG Longchao. Association of Polymorphisms of GREB1L and MIB1 Genes with Rib Number and Carcass Traits in Beijing Black Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 79-86.
[3]	WU Jun, CAI Xiaodian, LIN Qing, ZHONG Zhanming, YE Haoqiang, WEI Chen, XU Zhiting, WU Xibo, SI Jinglei, ZHANG Zhe, LI Jiaqi. Weighted Single-step GWAS of Eye Muscle Area, Predicted Lean Meat Percentage and Average Backfat Thickness in A Yorkshire Pig Population [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1403-1414.
[4]	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.
[5]	NIU Naiqi, SU Yanfang, YANG Man, HOU Xinhua, WANG Ligang, ZHANG Longchao. Association Analysis of Polymorphisms of HoxB Cluster Genes with Vertebral Number and Carcass Traits in Beijing Black Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(1): 113-121.
[6]	NIU Naiqi, LIU Qian, HOU Xinhua, LIU Xin, WANG Ligang, ZHAO Fuping, GAO Hongmei, SHI Lijun, WANG Lixian, ZHANG Longchao. Association of Polymorphisms of NR6A1, VSX2, VRTN, LTBP2 Genes with Vertebral Number and Carcass Traits in Beijing Black Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(6): 2005-2014.
[7]	HOU Renda, ZHANG Run, NIU Naiqi, YANG Man, HUANG Xiaoyu, LI Huihui, ZHANG Longchao. Association of FUBP3 and USP43 Gene Polymorphisms with Loin Muscle Area in Beijing Black Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(12): 4197-4206.
[8]	GONG Jianfei, YUE Jingwei, ZHAO Lingling, LIU Yunpeng, WANG Lixian, LIU Xin, SUN Jinhai. Tissue Expression Profiles of HMGA1 Gene in Pigs and Its Association with Backfat Thickness [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(7): 1340-1346.
[9]	WANG Ji-ying, WANG Yan-ping, XU Yun-hua, WANG Cheng, LIN Hai-chao, HU Hong-mei, WU Ying, GUO Jian-feng. Analyses of Intramuscular Fat Content, Fatty Acid Composition and the Related Traits in Lulai Black Pigs [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2017, 48(4): 585-594.
[10]	LI Jian-hua;CHU Xiao-hong;ZHAO Xiao-feng;XU Ningying. Study on the Single Nucleotide Polymorphism in Porcine SHP Gene Exon 1 [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2007, 38(11): 1253-1256.
[11]	YANG Hai-ling;ZENG Yong-qing;WEI Shu-dong;WU Ying;CAO Hong-fang;LIU Chan-juan;WANG Gang;BAO Xin-jian. Studies on the Development Changes of Fatty Enzymatic Activities and TheirAssociation with Intramuscular Fat in Laiwu Pig [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2005, 36(11): 1150-1154.