猪下丘脑—垂体—甲状腺轴五个关键基因的研究
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摘要
候选基因鉴定法是分析数量性状基因的重要方法。本论文以在机体物质与能量代谢、个体生长发育调控中发挥重要作用的下丘脑-垂体-甲状腺轴五个关键调控基因：促甲状腺激素释放激素前体TRH基因、促甲状腺激素释放激素受体TRHR基因、组成促甲状腺激素的糖蛋白激素共同亚基CGA基因和促甲状腺激素β亚基TSHB基因,以及促甲状腺激素受体TSHR基因为研究对象,应用生物信息学、辐射杂交细胞系定位技术、3'RACE、实时荧光定量RT-PCR、PCR-RFLP、四引物ARMS-PCR等技术对HPT轴五个关键基因进行染色体定位、QTL分布分析、cDNA克隆、组织表达谱分析、遗传多态寻找以及与猪主要经济性状的关联分析研究,以期了解HPT轴该五个关键基因的分子生物学特性,并为猪主要经济性状遗传改良和标记辅助选择提供科学依据。实验主要得出以下一些结果：
(1)应用生物信息学和辐射杂交细胞系定位技术,HPT轴五个关键基因分别被定位于猪13、4、1、4和7号染色体。根据QTL数据库查询结果,五个基因全部位于日增重、肌肉品质和脂肪性状相关QTL内,提示猪HPT轴基因多态与个体生长速度、肉质和脂肪性状差异可能存在重要关联,为相应QTL的位置功能候选基因。
(2)本论文首次克隆获得猪TRHR基因mRNA序列,并在分子水平上进行了深入分析。猪TRHR基因与人TRHR基因进化上很接近。除TRHR基因的功能性转录本外,本论文实验中还发现了另外两种转录本类型。其中,转录本2为功能转录本1的截断型,仅含N端结构、跨膜螺旋1-5及部分胞内环3序列,缺失跨膜域6和7以及蛋白C端结构；而转录本3则恰与转录本2相反,剪切661 bp的选择性剪接内含子后,使之缺失了TRHR蛋白的N端编码序列,但保留有C端编码序列。然而选择性内含子的剪接,破坏了原阅读框,转录本3可能编码一种新的功能蛋白,也可能使用了不同的翻译起始位点。多种转录本存在的意义有待研究。
(3)采用荧光定量RT-PCR技术,检测了HPT轴五个关键基因在大脑、下丘脑、垂体、心、肝、脾、肺、’肾、甲状腺、胰、胃、小肠、大肠,以及肌肉和皮下脂肪共15个组织中的表达分布。HPT轴激素及其受体在外周组织,如皮下脂肪中的共表达,提示相应激素可能通过旁分泌或自分泌方式对局部组织进行着生长发育调控。
(4)以金华猪和皮特兰资源家系亲本个体为模板,共设计17对引物扩增HPT轴五个关键基因总长11,340 bp的DNA序列,进行PCR再测序以寻找核苷酸多态变异。分析基因测序峰图,共发现37个多态座位,其中位于TRH基因多态座位8个,TRHR基因多态座位7个,CGA基因多态座位14个,TSHB基因多态座位5个,TSHR基因多态座位3个。检测到的所有多态座位都提交到了国际SNP数据库dbSNP,并获得SNP登录号。根据多态座位彼此间距离间隔、侧翼序列特点及其潜在功能重要性,选择了其中20个座位,采用PCR-RFLP和四引物ARMS-PCR技术设计并优化了分型方法。
(5)对49头纯种金华猪和24头纯种皮特兰猪进行HPT轴20个多态座位的分型,并采用HapBlock软件进行基因单倍型块分析和标签SNP选择。除TRH基因SNP在金华猪中分布于两个单倍型块外,其他基因的SNP座位均位于同一单倍型块中。结合两个品种的单倍型区块和标签SNP集合信息,共选择了3个TRH基因标签SNP,3个TRHR基因标签SNP,5个CGA基因标签SNP,3个TSHB基因标签SNP和1个TSHR基因标签SNP,用于在金华猪与皮特兰资源家系中进行HPT轴基因多态遗传效应分析。
(6)在金华猪与皮特兰资源家系共463头个体中分析了HPT轴基因多态性与猪生长、胴体和肉质共30个主要经济性状的关联性,并在在约克夏、杜洛克、长白猪以及嘉兴黑猪中进行了一定的验证分析。分析结果显示：
1)在金皮资源家系中TRH ss325994933与个体生长发育后期,尤其是150-180日龄期间增重有显著关联,其在国内和国外猪种中的基因频率亦存在明显的对立分布差异,但在生长较慢的金华猪中占优势的插入突变却在资源家系中表现为生长优势。本研究认为TRH基因可能在中外猪种生长性状差异形成中有一定影响,是相关日增重QTL下的位置功能候选基因,但其多态座位效应仍有待进一步挖掘验证。
2) TRHR基因多态性的种群间分化较大。在金皮资源家系中,其对个体头重和胴体长有极显著效应,对眼肌的导电率、pH值、系水力、肌内水份和肌内脂肪性状有显著影响。TRHR基因与多项肉质指标存在显著关联,且在肌肉组织中有表达,本文认为有必要对TRHR基因在猪肌肉组织中的功能进行深入研究。
3)尽管本文发现CGA基因多态性与猪肌内水份含量存在显著关联,此前并未见肌内水份QTL定位于CGA基因。可能由于CGA基因内微卫星的存在,造成较频繁的基因内重组,而使基因效应表现不稳定。所有5个CGA SNP在国内外猪种中均未表现出明显对立的等位基因频率分布差异。因此本研究认为,CGA基因多态性可能在国内外猪种性状差异形成中不具有重要地位。
4)TSHB基因的种群间分化也较大。在金皮资源家系中,TSHB基因多态性对猪90-120日龄期间增重、后腿肌肉重有统计显著效应,对猪胴体重、胴体长和平均背膘厚有极显著效应。含金华猪单倍型G-G-A纯合子个体较皮特兰单倍型A-G-G纯合子个体增重显著慢,与一般认为的金华猪生长速度慢相一致。并且含皮特兰单倍型A-G-G个体背膘厚显著小于含金华猪单倍型G-G-A个体。此外,在杜洛克群体中,TSHB SNP座位ss181129015与背膘厚也存在显著关联,在国外猪种中占优势的等位基因A有降低背膘厚的效应,验证了在金皮资源家系中的分析结果。因此本研究认为,TSHB基因,尤其是其SNP ss181129015且有作为遗传分子标记应用于猪背膘厚性状改良育种中的价值。
5) TSHR基因多态性座位的等位基因A在所有猪种中均以低频出现。金皮资源家系中,TSHR基因多态性对个体生长发育后期120日龄至180日龄期间增重以及眼肌pH值有显著影响。在长白猪群体中的关联分析,进一步确证了TSHR与日增重的关联性。然而,在金皮资源家系中表现出生长优势的等位基因A,在长白猪群体中却表现为生长劣势。
Candidate gene approach is one of the important methods in quantitative trait analysis. In the present study, five candidate genes of hypothalamo-pituitary-thyroid axis which plays important roles in the regulation of animals' growth, development and many metabolic and physical processes:thyrotropin releasing hormone gene (TRH), thyrotropin releasing hormone receptor gene (TRHR), thyrotropin alpha subunit gene (CGA) and beta subunit gene (TSHB), and thyrotropin receptor gene (TSHR) were investigated using bioinformatis, radiation hybrid mapping,3'RACE, real-time quantitative RT-PCR, PCR-RFLP, tetra-primers ARMS-PCR technolgies and so on to map the genes, analyse the QTLs located on them, clone the cDNA, study the genes' tissue expression profile, seach for the genetic polymorphisms and investigate their associations with porcine economical important traits. The objectives of these studies were to characterize the five porcine key genes of HPT axis, develop and evaluate new effective genetic markers for the improvements of porcine economical important traits. The results obtained were as follows:
(1) With bioinformatics method and Radiation Hybrid mapping technology, the five key genes of HPT axis were mapped to Sus Scorfa chormosome 13,4,1,1 and 7, respectively. According to the information from pig QTL datebase, all the five genes lie in the daily gain, meat quality and fat related QTLs, which suggesting that genetic polymorphisms of HPT asis might associate with individuals' growth rate, meat quality and fat traits' variation, and could be the positional and functional candidate genes of respective QTLs.
(2) mRNA sequence of porcine TRHR gene was obtained at the first time. Porcine TRHR gene was near to the human TRHR gene in the evolution. Except the functional transcript variant (TV1), two additional transcript variants (TV2 and TV3) were also found in this study. TV2 was truncated in the nucleotide sequence that encodes the putative third intracellular loop and retained a part of the intron, while TV3 was the purduct of a 661-bp alternative spliced intron existed in the 2nd exon. The splicing of the alternative spliced intron interrupts the open reading frame, thus TV3 might code a new protein or use a different translation start site. The meaning of the existence of more than one transcript variant remains investigation.
(3) Using real-time quantitative RT-PCR technology, tissue distributions of the five genes in brain, hypothalamus, pituitary, heart, liver, spleen, lung, kidney, thyroid, pancreas, stomach, small intestine, large intestine, muscle and fat were investigated. Co-expression of the hormones and their receptors in the same tissues, e.g. in fat tissue, indicating that regulations of the respective hormones on the tissues might partly via paracrine or autocrine effects.
(4) To scan for the nucleotide polymorphisms in the genes of HPT axis, re-sequencing 11,340 bp DNA sequence of each founder animal of the Jinhua and Pietrain resource family with 17 pairs of primers were performed.37 polymorphisms in total were identified, among which 8 loci in TRH gene,7 loci in TRHR gene,14 loci in CGA gene,5 loci in TSHB gene, and 3 loci in TSHR gene. All the polymorphisms identified in this study has been submitted to the international SNP database (dbSNP) and gotten the SNP accession number (ss#). Based on the distance between each locus,the flanking sequence, and their potential functions,20 loci were selected and genotyping methods using PCR-RFLP or tetra-primers ARMS PCR technology were designed and verified.
(5) The 20 SNP loci of HTP axis were genotyped in 49 Jinhua pigs and 24 Pieterain pigs, and the haplotype block analysis and Tag SNP selection were performed with HapBlock software. All the loci of the same gene located in one block, except the TRH gene in Jinhua population which were separated into two blocks. In combination of the haploblock and Tag SNP information in the two breeds, 3 TRH tag SNP,3 TRHR tag SNP,5 CGA tag SNP,3 TSHB tag SNP and 1 TSHR tag SNP were selected to genotype in Jinhua and Pietrain resource family to analyze the genetic effects of HPT axis.
(6) Association analysis between the genetic polymorphisms of HPT axis and 30 porcine growth, carcass and meat quality traits were carried out in the Jinhua and Pietrain resource family (463 individuals in total), and verified in purebreds Yorkshire, Duroc, Landrace and Jiaxing Black pigs. The results showed that:
1) TRH ss325994933 had effects on the growth in later stage, especially significant (P<0.05) on the weight gain between 150 to 180 days old. And opposite dominant alleles appeared in the Chinese and Western breeds. However, the insertion allele which was dominant in the slowly growing Jinhua pigs showed growth advatage in the resource family. The results suggested that TRH might play important roles in the growth rate difference between breeds and could be the candidate gene of daily gain, though its genetic effects remains further investigation.
2) Considerable population diversity of TRHR gene existed. TRHR polymorphisms had high significant effects on heat weight and carcass length, and significant effects on the conductivity, pH value, water holding capacity, and intramuscular water and fat content of loin muscle. Both TRHR's expression in muscle and its associations with the meat quality traits suggested that further investigation on roles of TRHR in musle tissue was necessary.
3) CGA polymorphisms had significant effect on intramuscular water content, however no such QTL had been located on the CGA gene previously. The existence of intragenic microsatellite in CGA gene might be the reasons of its instable genetic effects. Allele distributions of all the five CGA SNPs showed no apparent differences in the pig breeds. Thus, CGA gene might do not play important roles in the forming of breed specific characteristics.
4) Considerable population diversity of TSHB gene was also observed. TSHB polymorphisms had significant effects on weight gain between 90-120 days old and ham muscle weight, and high significant effects on carcass weight, carcass length and average backfat thickness. In the resource family, homozygotes of G-G-A which was from the Jinhua pigs significantly grew slower than the homozygotes of A-G-G which was from the Pietrain, in accordance with the truth that Jinhua pigs had slower growth rate. And BFT of individuals with A-G-G was significantly thinner than those with G-G-A. Futher, TSHB ss181129015 showed significant association with BFT in Duroc and its allele A which was mainly observed in Western breeds was associated with thinner BFT, supporting the results obtained from the resource family. TSHB gene, especially the ss181129015, could be utilized as genetic marker for BFT improvement in pig breeding.
5) Allele A of TSHR had low frequencies in all pig breeds. TSHR polymorphism had significant effects on weight gain between 120-180 days old and intramuscular pH value. Association between TSHR and ADG was also observed in Landrace. However, Allele A was associated with faster growth rate in the resource family but with slower growth rate in the Lancrace.
(1)应用生物信息学和辐射杂交细胞系定位技术,HPT轴五个关键基因分别被定位于猪13、4、1、4和7号染色体。根据QTL数据库查询结果,五个基因全部位于日增重、肌肉品质和脂肪性状相关QTL内,提示猪HPT轴基因多态与个体生长速度、肉质和脂肪性状差异可能存在重要关联,为相应QTL的位置功能候选基因。
(2)本论文首次克隆获得猪TRHR基因mRNA序列,并在分子水平上进行了深入分析。猪TRHR基因与人TRHR基因进化上很接近。除TRHR基因的功能性转录本外,本论文实验中还发现了另外两种转录本类型。其中,转录本2为功能转录本1的截断型,仅含N端结构、跨膜螺旋1-5及部分胞内环3序列,缺失跨膜域6和7以及蛋白C端结构；而转录本3则恰与转录本2相反,剪切661 bp的选择性剪接内含子后,使之缺失了TRHR蛋白的N端编码序列,但保留有C端编码序列。然而选择性内含子的剪接,破坏了原阅读框,转录本3可能编码一种新的功能蛋白,也可能使用了不同的翻译起始位点。多种转录本存在的意义有待研究。
(3)采用荧光定量RT-PCR技术,检测了HPT轴五个关键基因在大脑、下丘脑、垂体、心、肝、脾、肺、’肾、甲状腺、胰、胃、小肠、大肠,以及肌肉和皮下脂肪共15个组织中的表达分布。HPT轴激素及其受体在外周组织,如皮下脂肪中的共表达,提示相应激素可能通过旁分泌或自分泌方式对局部组织进行着生长发育调控。
(4)以金华猪和皮特兰资源家系亲本个体为模板,共设计17对引物扩增HPT轴五个关键基因总长11,340 bp的DNA序列,进行PCR再测序以寻找核苷酸多态变异。分析基因测序峰图,共发现37个多态座位,其中位于TRH基因多态座位8个,TRHR基因多态座位7个,CGA基因多态座位14个,TSHB基因多态座位5个,TSHR基因多态座位3个。检测到的所有多态座位都提交到了国际SNP数据库dbSNP,并获得SNP登录号。根据多态座位彼此间距离间隔、侧翼序列特点及其潜在功能重要性,选择了其中20个座位,采用PCR-RFLP和四引物ARMS-PCR技术设计并优化了分型方法。
(5)对49头纯种金华猪和24头纯种皮特兰猪进行HPT轴20个多态座位的分型,并采用HapBlock软件进行基因单倍型块分析和标签SNP选择。除TRH基因SNP在金华猪中分布于两个单倍型块外,其他基因的SNP座位均位于同一单倍型块中。结合两个品种的单倍型区块和标签SNP集合信息,共选择了3个TRH基因标签SNP,3个TRHR基因标签SNP,5个CGA基因标签SNP,3个TSHB基因标签SNP和1个TSHR基因标签SNP,用于在金华猪与皮特兰资源家系中进行HPT轴基因多态遗传效应分析。
(6)在金华猪与皮特兰资源家系共463头个体中分析了HPT轴基因多态性与猪生长、胴体和肉质共30个主要经济性状的关联性,并在在约克夏、杜洛克、长白猪以及嘉兴黑猪中进行了一定的验证分析。分析结果显示：
1)在金皮资源家系中TRH ss325994933与个体生长发育后期,尤其是150-180日龄期间增重有显著关联,其在国内和国外猪种中的基因频率亦存在明显的对立分布差异,但在生长较慢的金华猪中占优势的插入突变却在资源家系中表现为生长优势。本研究认为TRH基因可能在中外猪种生长性状差异形成中有一定影响,是相关日增重QTL下的位置功能候选基因,但其多态座位效应仍有待进一步挖掘验证。
2) TRHR基因多态性的种群间分化较大。在金皮资源家系中,其对个体头重和胴体长有极显著效应,对眼肌的导电率、pH值、系水力、肌内水份和肌内脂肪性状有显著影响。TRHR基因与多项肉质指标存在显著关联,且在肌肉组织中有表达,本文认为有必要对TRHR基因在猪肌肉组织中的功能进行深入研究。
3)尽管本文发现CGA基因多态性与猪肌内水份含量存在显著关联,此前并未见肌内水份QTL定位于CGA基因。可能由于CGA基因内微卫星的存在,造成较频繁的基因内重组,而使基因效应表现不稳定。所有5个CGA SNP在国内外猪种中均未表现出明显对立的等位基因频率分布差异。因此本研究认为,CGA基因多态性可能在国内外猪种性状差异形成中不具有重要地位。
4)TSHB基因的种群间分化也较大。在金皮资源家系中,TSHB基因多态性对猪90-120日龄期间增重、后腿肌肉重有统计显著效应,对猪胴体重、胴体长和平均背膘厚有极显著效应。含金华猪单倍型G-G-A纯合子个体较皮特兰单倍型A-G-G纯合子个体增重显著慢,与一般认为的金华猪生长速度慢相一致。并且含皮特兰单倍型A-G-G个体背膘厚显著小于含金华猪单倍型G-G-A个体。此外,在杜洛克群体中,TSHB SNP座位ss181129015与背膘厚也存在显著关联,在国外猪种中占优势的等位基因A有降低背膘厚的效应,验证了在金皮资源家系中的分析结果。因此本研究认为,TSHB基因,尤其是其SNP ss181129015且有作为遗传分子标记应用于猪背膘厚性状改良育种中的价值。
5) TSHR基因多态性座位的等位基因A在所有猪种中均以低频出现。金皮资源家系中,TSHR基因多态性对个体生长发育后期120日龄至180日龄期间增重以及眼肌pH值有显著影响。在长白猪群体中的关联分析,进一步确证了TSHR与日增重的关联性。然而,在金皮资源家系中表现出生长优势的等位基因A,在长白猪群体中却表现为生长劣势。
Candidate gene approach is one of the important methods in quantitative trait analysis. In the present study, five candidate genes of hypothalamo-pituitary-thyroid axis which plays important roles in the regulation of animals' growth, development and many metabolic and physical processes:thyrotropin releasing hormone gene (TRH), thyrotropin releasing hormone receptor gene (TRHR), thyrotropin alpha subunit gene (CGA) and beta subunit gene (TSHB), and thyrotropin receptor gene (TSHR) were investigated using bioinformatis, radiation hybrid mapping,3'RACE, real-time quantitative RT-PCR, PCR-RFLP, tetra-primers ARMS-PCR technolgies and so on to map the genes, analyse the QTLs located on them, clone the cDNA, study the genes' tissue expression profile, seach for the genetic polymorphisms and investigate their associations with porcine economical important traits. The objectives of these studies were to characterize the five porcine key genes of HPT axis, develop and evaluate new effective genetic markers for the improvements of porcine economical important traits. The results obtained were as follows:
(1) With bioinformatics method and Radiation Hybrid mapping technology, the five key genes of HPT axis were mapped to Sus Scorfa chormosome 13,4,1,1 and 7, respectively. According to the information from pig QTL datebase, all the five genes lie in the daily gain, meat quality and fat related QTLs, which suggesting that genetic polymorphisms of HPT asis might associate with individuals' growth rate, meat quality and fat traits' variation, and could be the positional and functional candidate genes of respective QTLs.
(2) mRNA sequence of porcine TRHR gene was obtained at the first time. Porcine TRHR gene was near to the human TRHR gene in the evolution. Except the functional transcript variant (TV1), two additional transcript variants (TV2 and TV3) were also found in this study. TV2 was truncated in the nucleotide sequence that encodes the putative third intracellular loop and retained a part of the intron, while TV3 was the purduct of a 661-bp alternative spliced intron existed in the 2nd exon. The splicing of the alternative spliced intron interrupts the open reading frame, thus TV3 might code a new protein or use a different translation start site. The meaning of the existence of more than one transcript variant remains investigation.
(3) Using real-time quantitative RT-PCR technology, tissue distributions of the five genes in brain, hypothalamus, pituitary, heart, liver, spleen, lung, kidney, thyroid, pancreas, stomach, small intestine, large intestine, muscle and fat were investigated. Co-expression of the hormones and their receptors in the same tissues, e.g. in fat tissue, indicating that regulations of the respective hormones on the tissues might partly via paracrine or autocrine effects.
(4) To scan for the nucleotide polymorphisms in the genes of HPT axis, re-sequencing 11,340 bp DNA sequence of each founder animal of the Jinhua and Pietrain resource family with 17 pairs of primers were performed.37 polymorphisms in total were identified, among which 8 loci in TRH gene,7 loci in TRHR gene,14 loci in CGA gene,5 loci in TSHB gene, and 3 loci in TSHR gene. All the polymorphisms identified in this study has been submitted to the international SNP database (dbSNP) and gotten the SNP accession number (ss#). Based on the distance between each locus,the flanking sequence, and their potential functions,20 loci were selected and genotyping methods using PCR-RFLP or tetra-primers ARMS PCR technology were designed and verified.
(5) The 20 SNP loci of HTP axis were genotyped in 49 Jinhua pigs and 24 Pieterain pigs, and the haplotype block analysis and Tag SNP selection were performed with HapBlock software. All the loci of the same gene located in one block, except the TRH gene in Jinhua population which were separated into two blocks. In combination of the haploblock and Tag SNP information in the two breeds, 3 TRH tag SNP,3 TRHR tag SNP,5 CGA tag SNP,3 TSHB tag SNP and 1 TSHR tag SNP were selected to genotype in Jinhua and Pietrain resource family to analyze the genetic effects of HPT axis.
(6) Association analysis between the genetic polymorphisms of HPT axis and 30 porcine growth, carcass and meat quality traits were carried out in the Jinhua and Pietrain resource family (463 individuals in total), and verified in purebreds Yorkshire, Duroc, Landrace and Jiaxing Black pigs. The results showed that:
1) TRH ss325994933 had effects on the growth in later stage, especially significant (P<0.05) on the weight gain between 150 to 180 days old. And opposite dominant alleles appeared in the Chinese and Western breeds. However, the insertion allele which was dominant in the slowly growing Jinhua pigs showed growth advatage in the resource family. The results suggested that TRH might play important roles in the growth rate difference between breeds and could be the candidate gene of daily gain, though its genetic effects remains further investigation.
2) Considerable population diversity of TRHR gene existed. TRHR polymorphisms had high significant effects on heat weight and carcass length, and significant effects on the conductivity, pH value, water holding capacity, and intramuscular water and fat content of loin muscle. Both TRHR's expression in muscle and its associations with the meat quality traits suggested that further investigation on roles of TRHR in musle tissue was necessary.
3) CGA polymorphisms had significant effect on intramuscular water content, however no such QTL had been located on the CGA gene previously. The existence of intragenic microsatellite in CGA gene might be the reasons of its instable genetic effects. Allele distributions of all the five CGA SNPs showed no apparent differences in the pig breeds. Thus, CGA gene might do not play important roles in the forming of breed specific characteristics.
4) Considerable population diversity of TSHB gene was also observed. TSHB polymorphisms had significant effects on weight gain between 90-120 days old and ham muscle weight, and high significant effects on carcass weight, carcass length and average backfat thickness. In the resource family, homozygotes of G-G-A which was from the Jinhua pigs significantly grew slower than the homozygotes of A-G-G which was from the Pietrain, in accordance with the truth that Jinhua pigs had slower growth rate. And BFT of individuals with A-G-G was significantly thinner than those with G-G-A. Futher, TSHB ss181129015 showed significant association with BFT in Duroc and its allele A which was mainly observed in Western breeds was associated with thinner BFT, supporting the results obtained from the resource family. TSHB gene, especially the ss181129015, could be utilized as genetic marker for BFT improvement in pig breeding.
5) Allele A of TSHR had low frequencies in all pig breeds. TSHR polymorphism had significant effects on weight gain between 120-180 days old and intramuscular pH value. Association between TSHR and ADG was also observed in Landrace. However, Allele A was associated with faster growth rate in the resource family but with slower growth rate in the Lancrace.
引文
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