陕北白绒山羊POU1F1基因3'-UTR多态性及其与生长性状的相关分析
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摘要
垂体特异性转录因子1 (pituitary specific transcription factor 1, POU1F1)是POU家族(垂体特异性转录因子Pit-1,八聚体结合蛋白Oct-1和Oct-2及美丽新小杆线虫神经Unc-86)成员之一,对哺乳动物生长发育起着重要作用。为了探究POU1F1基因侧翼序列多态性对陕北白绒山羊(Shaanbei white cashmere goats, SBWC goats)(Capra hircus)生长性状的遗传效应,本研究以621只陕北白绒山羊为研究对象,利用DNA直接测序法检测POU1F1基因3'-非翻译区(3'-untranslated region, 3'-UTR)的多态位点并对其进行基因分型,同时分析多态位点不同基因型与陕北白绒山羊生长性状之间的关联性。结果表明,在POU1F1基因3'-UTR检测到一个单核苷酸多态性(single nucleotide polymorphism, SNP)(NC_030808.1:g.34235967T>C),其位于3'-UTR第164位(c.876+164A>G)。该位点等位基因A和G的频率分别为0.894和0.106,有效等位基因数(number of effective alleles, Ne)为1.235,基因纯合度(homozygosity, Ho)为0.810,基因杂合度(heterozygosity, He)为0.190,多态信息含量(polymorphism information content, PIC)为0.172,属于低度多态;该位点处于Hardy-Weinberg平衡状态(P>0.05)。进一步的相关性分析表明,c.876+164A>G位点与山羊的体长和管围性状显著相关(P<0.05),且AG型个体在体长及管围方面显著优于其他基因型个体,而对其他体尺指标在统计学上无显著影响(P>0.05)。此外,通过生物信息学分析发现,当该位点突变时,可能会影响转录因子—骨髓增生异常综合征1/亲嗜性病毒整合位点-1样基因1 (myelodysplasia syndrome 1/ecotropic viral integration site1-like gene 1, MEL1)与POU1F1基因的正常结合,从而解除对POU1F1基因的抑制,促进该基因表达,进而影响个体生长发育。综上,POU1F1基因c.876+164A>G位点对陕北白绒山羊体长和管围等生长性状有显著影响,可以作为陕北白绒山羊生长性状分子标记辅助选择的候选标记,为陕北白绒山羊的选育改良提供科学资料。
Pituitary specific transcription factor 1(POU1 F1) is a member of the POU family(pituitary specific transcription factor, Pit-1; octameric binding protein, Oct-1 and Oct-2; caenorhabedit Ⅰ nematode nerve Unc-86), who is a positive transcription factor regulating pituitary hormone-related genes and plays an important role in the growth and development of mammals. Thus, POU1 F1 gene is extensively considered as a candidate gene for growth performance in goats(Capra hircus). In order to verify the genetic effects of flanking region of POU1 F1 gene on the growth traits in Shaanbei white cashmere(SBWC) goats, the genetic polymorphisms of 3'-untranslated region(3'-UTR) within POU1 F1 gene was detected in all adult SBWC goats(n=621) by direct DNA sequencing method, and the associations of different genotypes of polymorphisms and9 kinds of growth traits in SBWC goats were analyzed. Sequencing results showed that a single nucleotide polymorphism(SNP), named NC_030808.1:g.34235967 T>C and located at position 164 of the 3'-UTR within POU1 F1 gene(c.876+164 A>G), was identified in these SBWC population. The frequencies of alleles A and G of this locus were 0.894 and 0.106, respectively; the number of effective alleles(Ne) was 1.235; the homozygosity(Ho) was 0.810; the heterozygosity(He) was 0.190; and the polymorphism information content(PIC) was 0.172 and the loci was low polymorphisms. The values of these genetic polymorphism indexes reflect the inferior degree of genetic variation in this population, and the value of PIC belongs to the low PIC(PIC<0.25). In addition, the c. 876 + 164 A>G locus conformed to Hardy-Weinberg equilibrium(P>0.05) in the SBWC goat population. The further association analysis results demonstrated that the c. 876 + 164 A>G locus was significantly associated with the body length and cannon circumference in SBWC goats(P<0.05).However, there were no significant effects from the SNP for other growth traits, including body weight, body height, height at hip cross, chest circumference, chest depth, chest width and hip width. The individuals with AG genotype were significantly superior to other genotypes in both body length(P=0.047) and cannon circumference(P=0.035) in this population. Thus, the AG genotype could be considered as a positive genotype for this SNP in SBWC goats. In addition, the mutation in 3'-UTR could not only affect its binding to target miRNA, but also change transcription factor binding sites. Here, bioinformatics prediction of transcription factors on this SNP was performed by Genomatix MatInspector software v3.11, and analysis result indicated that the binding of the transcription factor MEL1(myelodysplasia syndrome 1/ecotropic viral integration site1-like gene 1) with POU1 F1 gene was affected when this locus mutated. MEL1, also called PRDM16, could simultaneously activate and inhibit gene transcription, which might be related to multiple transcriptional domains in gene structure. Therefore, when the A allele was replaced by G allele at the c.876+164 A>G locus,the binding of the MEL1 with POU1 F1 gene was hampered and the inhibition of POU1 F1 gene was discharged, which might affect growth and development of individuals by facilitating the expression level of POU1 F1 gene. These research results unveiled that the c.876+164 A>G had strong effects on body length and cannon circumference of SBWC goats, which could be used as a candidate marker for marker assisted selection of greater growth performance and would provide scientific information for the genetic breeding and improvement in goat industry.
Pituitary specific transcription factor 1(POU1 F1) is a member of the POU family(pituitary specific transcription factor, Pit-1; octameric binding protein, Oct-1 and Oct-2; caenorhabedit Ⅰ nematode nerve Unc-86), who is a positive transcription factor regulating pituitary hormone-related genes and plays an important role in the growth and development of mammals. Thus, POU1 F1 gene is extensively considered as a candidate gene for growth performance in goats(Capra hircus). In order to verify the genetic effects of flanking region of POU1 F1 gene on the growth traits in Shaanbei white cashmere(SBWC) goats, the genetic polymorphisms of 3'-untranslated region(3'-UTR) within POU1 F1 gene was detected in all adult SBWC goats(n=621) by direct DNA sequencing method, and the associations of different genotypes of polymorphisms and9 kinds of growth traits in SBWC goats were analyzed. Sequencing results showed that a single nucleotide polymorphism(SNP), named NC_030808.1:g.34235967 T>C and located at position 164 of the 3'-UTR within POU1 F1 gene(c.876+164 A>G), was identified in these SBWC population. The frequencies of alleles A and G of this locus were 0.894 and 0.106, respectively; the number of effective alleles(Ne) was 1.235; the homozygosity(Ho) was 0.810; the heterozygosity(He) was 0.190; and the polymorphism information content(PIC) was 0.172 and the loci was low polymorphisms. The values of these genetic polymorphism indexes reflect the inferior degree of genetic variation in this population, and the value of PIC belongs to the low PIC(PIC<0.25). In addition, the c. 876 + 164 A>G locus conformed to Hardy-Weinberg equilibrium(P>0.05) in the SBWC goat population. The further association analysis results demonstrated that the c. 876 + 164 A>G locus was significantly associated with the body length and cannon circumference in SBWC goats(P<0.05).However, there were no significant effects from the SNP for other growth traits, including body weight, body height, height at hip cross, chest circumference, chest depth, chest width and hip width. The individuals with AG genotype were significantly superior to other genotypes in both body length(P=0.047) and cannon circumference(P=0.035) in this population. Thus, the AG genotype could be considered as a positive genotype for this SNP in SBWC goats. In addition, the mutation in 3'-UTR could not only affect its binding to target miRNA, but also change transcription factor binding sites. Here, bioinformatics prediction of transcription factors on this SNP was performed by Genomatix MatInspector software v3.11, and analysis result indicated that the binding of the transcription factor MEL1(myelodysplasia syndrome 1/ecotropic viral integration site1-like gene 1) with POU1 F1 gene was affected when this locus mutated. MEL1, also called PRDM16, could simultaneously activate and inhibit gene transcription, which might be related to multiple transcriptional domains in gene structure. Therefore, when the A allele was replaced by G allele at the c.876+164 A>G locus,the binding of the MEL1 with POU1 F1 gene was hampered and the inhibition of POU1 F1 gene was discharged, which might affect growth and development of individuals by facilitating the expression level of POU1 F1 gene. These research results unveiled that the c.876+164 A>G had strong effects on body length and cannon circumference of SBWC goats, which could be used as a candidate marker for marker assisted selection of greater growth performance and would provide scientific information for the genetic breeding and improvement in goat industry.
引文
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An X,Song Y,Hou J,et al.2016.Identification of a functional SNP in the 3'-UTR of caprine MTHFR gene that is associated with milk protein levels[J].Animal Genetics,47(4):499-503.
Ba?F,Abal?ZY,Toksoy G,et al.2018.Precocious or early puberty in patients with combined pituitary hormone deficiency due to POU1F1 gene mutation:Case report and review of possible mechanisms[J].Hormones(Athens),17(4):581-588.
Cartharius K,Frech K,Grote K,et al.2005.MatInspector and beyond:Promoter analysis based on transcription factor binding sites[J].Bioinformatics,21(13):2933-2942.
Cui Y,Yan H,Wang K,et al.2018.Insertion/deletion within the KDM6A gene is significantly associated with litter size in goat[J].Frontiers in Genetics,9:91.
Daga C,Paludo M,Luridiana S,et al.2013.Identification of novel SNPs in the Sarda breed goats POU1F1 gene and their association with milk productive performance[J].Molecular Biology Reports,40(4):2829-2835.
Fei L R,Huang W J,Wang Y,et al.2019.PRDM16 functions as a suppressor of lung adenocarcinoma metastasis[J].Journal of Experimental&Clinical Cancer Research,38(1):35.
Feng T,Chu M X,Cao G L,et al.2012.Polymorphisms of caprine POU1F1 gene and their association with litter size in Jining Grey goats[J].Molecular Biology Reports,39(4):4029-4038.
Frühbeck G,Sesma P,Burrell MA.2009.PRDM16:The interconvertible adipo-myocyte switch[J].Trends in Cell Biology,19(4):141-146.
Hou J,An X,Song Y,et al.2015.Two mutations in the caprine MTHFR 3'UTR regulated by microRNAs are associated with milk production traits[J].PLoS ONE,10(7):e0133015.
Iannaccone M,Cosenza G,Pauciullo A,et al.2018.The SNPg.4667G>A at 3'-UTR of IFNG gene is associated with susceptibility to bovine tuberculosis in Mediterranean water buffalo(Bubalus bubalis)[J].Animal Genetics,49(5):496-497.
Kajimura S,Seale P,Tomaru T,et al.2008.Regulation of the brown and white fat gene programs through a PRDM16/CtBP transcriptional complex[J].Genes&Development,22(10):1397-1409.
Lan X Y,Pan C Y,Chen H,et al.2007a.An AluⅠPCR-RFLPdetecting a silent allele at the goat POU1F1 locus and its association with production traits[J].Small Ruminant Research,73(1-3):8-12.
Lan X Y,Pan C Y,Chen H,et al.2007b.DdeⅠpolymorphism in coding region of goat POU1F1 gene and its association with production traits[J].Asian Australasian Journal of Animal Sciences,20(9):1342-1348.
Lan X Y,Shu J H,Chen H,et al.2009.A PstⅠpolymorphism at 3'UTR of goat POU1F1 gene and its effect on cashmere production[J].Molecular Biology Reports,36(6):1371-1374.
Li S,Crenshaw E B,Rawson E J,et al.1990.Dwarf locus mutants lacking three pituitary cell types result from mutations in the POU-domain gene PIT-1[J].Nature,347(6293):528-533.
Mayr C.2018.What Are 3'UTRs Doing?[J].Cold Spring Harbor Perspectives in Biology,a034728.
Miltiadou D,Hager-Theodorides A L,Symeou S,et al.2017.Variants in the 3'untranslated region of the ovine acetylcoenzyme A acyltransferase 2 gene are associated with dairy traits and exhibit differential allelic expression[J].Journal of Dairy Science,100(8):6285-6297.
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