鸡visfatin和PRDM16基因遗传变异及其效应与表达研究
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摘要
利用分子生物学技术在DNA水平上寻找控制鸡生产性状的主效基因或与其紧密连锁的分子标记,研究我国地方鸡优良基因的功能,进行标记辅助选择育种和转基因育种,是我国未来家禽育种的新方向。Visfatin和PRDM16基因作为新发现的与脂肪性状相关的基因,其鸡该基因遗传变异效应及功能研究在国内外尚未见报道。为此本研究以固始鸡×安卡鸡F2资源群体为实验材料,采用PCR-SSCP和DNA池测序技术检测了visfatin和PRDM16基因共28个位点的遗传变异,采用Forced-PCR-RFLP等技术对其中的9个SNPs位点进行基因分型。将其不同基因型及双倍型与849只F2代鸡的84个性状进行了关联分析。克隆了丝毛乌骨鸡visfatin基因的全编码序列,进行了生物信息学分析。运用实时定量PCR技术,研究肉鸡和丝毛乌骨鸡visfatin和PRDM16基因在肝脏、心脏、脾脏、肾脏、骨髓、胸肌、颈皮下脂肪、腿皮下脂肪、腹脂和肠周围脂肪中表达水平及1日龄,4,8,12,16周龄乌鸡visfatin和PRDM16基因的组织表达变化规律。旨在寻找与经济性状相关的DNA标记,为进行鸡经济性状标记辅助选择打下基础。另外通过揭示visfatin和PRDM16基因与鸡生长和脂肪性状的关系,可为人类肥胖症的诊治奠定基础。本研究主要得到了如下结果:
1.鸡visfatin基因遗传变异的检测及其与生产性状的关联分析
检测到了visfatin基因的12个SNPs,3个位于编码区(14404A>T,15526C>T,17873C>T),9个位于非编码区(14360C>T,15673C>G,17928T>C,24019A>G,24238T>C,24262G>T,24285A>G,24294A>G和1个9 bp Indel)。除24238T>C,24262G>T,24294A>G外,其他为新发现的SNPs。14404A>T,17873C>T,24262G>T 3个SNPs之间具有强的连锁不平衡,以此构建了8种单倍型和5种主要双倍型。
关联分析发现:14404A>T位点的突变与不同周龄生长性状达到了显著相关(P <0.05),等位基因T有利于鸡的生长发育,AA基因型有利于提高肌肉的嫩度。15526C>T位点的TT基因型个体的初生体重、4周龄体重及8周龄胸角度显著高于CC基因型(P<0.05)。17873C>T位点的突变的TT基因型为与鸡早期生长的有利基因型。24238T>C位点CC基因型个体的生长性状显著高于TT基因型(P<0.05)。24262G>T突变位点TT基因型是对鸡早期生长有利的基因型。24285A>G多态位点的突变纯合型GG基因型对初生体重、8周龄胸骨长、8周龄体重来说有正效应,AA基因型对8周龄骨盆宽和腿肌重有正效应。24294A>G多态位点的AA基因型为生长性状有利基因型,GG基因型为减少脂肪沉积有利基因型。9 bp Indel多态的等位基因I即9 bp插入对生长有正效应而9 bp的缺失对鸡的生长有负效应。单倍型组合分别与8周胸骨长、胸肌纤维密度和低密度脂蛋白显著相关(P<0.05)。关联分析结果显示,其有利于鸡生长8个SNPs位点的基因型组合为TTTTTTIICCTTGGAA。相关分析表明visfatin基因与鸡骨骼和肌肉等生长发育有密切关系,且17873C>T和24262G>T位点与鸡的早期生长性状显著相关。
2.鸡PRDM16基因遗传变异位点的检测及其与生产性状的关联分析
检测到了PRDM16基因新的6个SNPs,4个位于编码区,2个位于非编码区。其中115512G>A位于第11外显子导致了一个Bsel I酶切位点的多态。该位点多态与鸡脂肪和屠宰性状显著相关,AA基因型为降低腹脂重和血清甘油三脂的选择基因型(P<0.05)。
3.丝毛乌骨鸡visfatin基因的克隆与生物信息学分析
本研究克隆了鸡visfatin基因cDNA全长1482 bp,编码493个氨基酸序列。预测鸡Visfatin氨基酸序列有26个磷酸化位点和一个疏水性区域但没有信号肽序列,该氨基酸序列中含α-螺旋、β-折叠,β-转角及无规卷曲4种二级结构,具有NAPRTase家族保守结构域特征及6个功能基序位点。Visfatin为高度保守的蛋白。
4.不同品种和不同时期鸡visfatin基因组织表达研究
鸡visfatin基因在胸肌中表达量最高,骨髓中最低。内脏和皮下脂肪中visfatin的表达量未显著差异(P>0.05)。肉鸡骨髓,肝脏,肾脏、脂肪中visfatin的表达量均显著高于乌鸡中的相应含量。骨髓中visfatin的表达量随着机体的生长发育呈现降低的趋势(P<0.05),在鸡的快速生长时期肝脏和腿肌中visfatin表达水平较高。肝脏、心脏和骨髓visfatin基因的表达量未见性别差异
5.不同品种和不同时期鸡PRDM16基因组织表达研究
PRDM16基因心脏组织中表达量最高,肝脏组织中最低,内脏和皮下脂肪中PRDM16表达量差异不显著(P>0.05)。肉鸡胸肌、脂肪中PRDM16表达量显著高于乌鸡相应组织的表达量(P<0.05)。骨髓中PRDM16表达水平随着生长发育逐渐降低(P<0.05)。1日龄、8周龄,12周龄时骨髓中最高,4周龄肝脏中最高,16周龄心脏中最高。组织PRDM16基因的表达丰度远远低于visfatin基因的表达。肝脏、心脏和骨髓中PRDM16基因的表达量未见性别差异。
With the rapid development of molecular biology, many works on searching major genes or closely linked molecular markers of growth and production traits from DNA level and on studying the gene functions have been carried out in recent years. The approaches of marker-assisted selection and transgenic breeding have become the future trend in poultry breeding. Visfatin and PRDM16 are the newly discovered genes and they play an important role in determination of fat traits, no information on genetic variation and functional studies of chicken visfatin and PRDM16 genes is available. In this study, the genetic variations of visfatin and PRDM16 genes were detected by single stranded conformation polymorphism and DNA pool sequencing. SNPs of visfatin and PRDM16 genes were genotyped in an F2 resource population of Gushi chickens crossing with Anka broilers using forced-PCR-RFLP. Haplotypes were constructed based on 3 SNPs with linkage disequilibrium of visfatin gene. The associations of 9 SNPs polymorphisms with 84 parameter in 849 F2 chickens were analyzed. The coding sequence of Silky Chicken’s visfatin gene was cloned and analyzed by bioinformatics methods. Using real-time PCR techique, the mRNA of visfatin and PRDM16 gene in heart, liver, kidney, spleen, breast muscle, subcutaneous fat, viscera fat and bone marrowfrom broiler and silky fowl were analyzed. Expressions of heart, liver, bone morrow, sebum and leg muscle from silky fowl at 1-day, 4, 8, 12, 16 weeks old were also investigated. The goal of this study is to identify the sequence variations of the visfatin and PRDM16 gene, to analyze the relationship between gene variation and chicken performance, and to find molecular markers for chicken genetics and breeding programs. In addition, it would provide theoretical basis for studying visfatin and PRDM16 functions and diagnosing and treating the obesity. The main results were summarized as below:
1.Genetic variations of visfatin gene and their associations with chicken production traits
Twelve SNPs were found in visfatin gene with the location of intron 3 (14360C>T), exon 4 (14404A>T), exon 6 (15526C>T), intron 6 (15673C>G), exon 7 (17873C>T), intron 7 (17928T>C), intron 8 (24019A>G), intron 9 (4238T>C, 24262G>T, 24285A>G, 24294A>G) and intron 10 (9 bp Indel), respectively. Except for 14404A>T, 17873C>T and 24262G>T, other 9 SNPs were newly discoverd, of which eight SNPs were genotyped. Three were main haplotypes including H1(ACG), H2(ACT) and H8(TTT) and 5 main diplotypes based on three SNPs with strong linkage disequilibrium.
14404A>T polymorphisms was significantly associated with body weight and body size traits at different age (P<0.05). For the traits body weight and carcass weight with genotype TT were significantly higher than those of genotype AA. 15526C>T polymorphisms was associated with body weight at birth and at 4 weeks, and with breast angle at 8 weeks. 17873 C>T polymorphisms was associated with the early growth traits. The growth traits at 4 weeks of the individual with the genotype TT was higher than those with genotype CC (P<0.05). 24238 T>C polymorphisms was also associated with growth traits and genotype CC is a favorable genotype for chicken growth and development. The genotype TT of 24262G>T polymorphisms was a favorable gene for chicken early growth traits and breast muscle weight. 24285A>G polymorphism was associated with growth traits at 8 weeks. 24294A>G polymorphisms was associated with chest depth at 8 weeks, pelvis breadth at 4 weeks and12 weeks, skin fat thicknessand and low density lipoprotein cholesterol (P<0.05). 9 bp Indel polymorphisms was associated with growth traits and pancreas weight, allele D (9 bp deletion) of the vistafin gene had a negative effect on skeletal growth. The five main diplotypes was associated with breast angle at 8 weeks, breast muscle fiber density and low density lipoprotein cholesterol (P<0.05). The genotype combination TTTTTTIICCTTGGAA had a positivie effects on chicken growth and development. The results has affirmed that there is a close relationship between visfatin gene and chicken growth and development..
2.Genetic variations of PRDM16 gene and associations with production traits
Six novel SNPs of the PRDM16 gene were found and 92188G>A and 115305C>T was located at non-cording region, 102872C>T, 102944C>T, 103144G>A and 115512G>A located at cording region. The polymorphism of the 115512G>A was significantly associated with the fatness and carcass traits and the genotype AA is an optional genotype for decreasing abdominal fat weight and triglyceride (P<0.05). On the other hand, the genotype GG is an optional genotype for enhancing evisceration weight and meat quality. The results indicated that the polymorphism of PRDM16 gene in chicken may influence the carcass and fat traits, but no association with the growth traits.
3. Clone and bioinformatics analysis of visfatin gene of Silky fowl
The 1482 bp full coding region sequence of visfatin gene in Silky fowl were obtained and it coded 493 amino acid sequence. It has 26 phosphorylation sites and a conserved domain of NAPRTase family but no signal peptide sequence. There is a hydrophobic region in 140-160aa of the visfatin. The amino acid sequence contains four kinds of secondary structure:α-helix,β-fold,β-angle and random coil. It has six function motifs including an amidation site. The visfatin is a highly conserved protein.
4. Study of the expression of chicken visfatin gene in different tissue and developmental stages
The highest expression of visfatin was found in breast muscle and the lowest in bone marrow. There was no difference of the expression in visceral fat and subcutaneous fat. However, the expressions of visfatin in bone marrow, liver, kidney, subcutaneous and visceral fat in broiler were significantly higher than in silky fowl (P< 0.05). Visfatin mRNA levels decreased in the bone marrow with the body development (P< 0.05) but increased in the liver and leg muscle.
4. Study of the expression of chicken PRDM16 gene in different tissue and developmental stages
The highest expression of PRDM16 was found in heart and the lowest in liver. There was no difference of the expression in visceral fat and abdominal fat. The expressions of PRDM16 in breast muscle, abdominal fat, subcutaneous fat and visceral fat in broiler were significantly higher than in silky fowl (P<0.05).The expressions of PRDM16 decreased in the bone marrow with the growth and development (P<0.05). The highest expression in the bone marrow was found at the age of 1 day, 8 weeks and 12 weeks, and the highest expression in the liver was found at the age of 4 weeks, the highest expression in the liver was found at the age of 16 weeks. The mRNA levels of ten tissues were much lower in PRDM16 than in visfatin (P<0.05). The visfatin and PRDM16 gene expression in the liver, heart and bone marrow has no gender difference in silky fowl.
1.鸡visfatin基因遗传变异的检测及其与生产性状的关联分析
检测到了visfatin基因的12个SNPs,3个位于编码区(14404A>T,15526C>T,17873C>T),9个位于非编码区(14360C>T,15673C>G,17928T>C,24019A>G,24238T>C,24262G>T,24285A>G,24294A>G和1个9 bp Indel)。除24238T>C,24262G>T,24294A>G外,其他为新发现的SNPs。14404A>T,17873C>T,24262G>T 3个SNPs之间具有强的连锁不平衡,以此构建了8种单倍型和5种主要双倍型。
关联分析发现:14404A>T位点的突变与不同周龄生长性状达到了显著相关(P <0.05),等位基因T有利于鸡的生长发育,AA基因型有利于提高肌肉的嫩度。15526C>T位点的TT基因型个体的初生体重、4周龄体重及8周龄胸角度显著高于CC基因型(P<0.05)。17873C>T位点的突变的TT基因型为与鸡早期生长的有利基因型。24238T>C位点CC基因型个体的生长性状显著高于TT基因型(P<0.05)。24262G>T突变位点TT基因型是对鸡早期生长有利的基因型。24285A>G多态位点的突变纯合型GG基因型对初生体重、8周龄胸骨长、8周龄体重来说有正效应,AA基因型对8周龄骨盆宽和腿肌重有正效应。24294A>G多态位点的AA基因型为生长性状有利基因型,GG基因型为减少脂肪沉积有利基因型。9 bp Indel多态的等位基因I即9 bp插入对生长有正效应而9 bp的缺失对鸡的生长有负效应。单倍型组合分别与8周胸骨长、胸肌纤维密度和低密度脂蛋白显著相关(P<0.05)。关联分析结果显示,其有利于鸡生长8个SNPs位点的基因型组合为TTTTTTIICCTTGGAA。相关分析表明visfatin基因与鸡骨骼和肌肉等生长发育有密切关系,且17873C>T和24262G>T位点与鸡的早期生长性状显著相关。
2.鸡PRDM16基因遗传变异位点的检测及其与生产性状的关联分析
检测到了PRDM16基因新的6个SNPs,4个位于编码区,2个位于非编码区。其中115512G>A位于第11外显子导致了一个Bsel I酶切位点的多态。该位点多态与鸡脂肪和屠宰性状显著相关,AA基因型为降低腹脂重和血清甘油三脂的选择基因型(P<0.05)。
3.丝毛乌骨鸡visfatin基因的克隆与生物信息学分析
本研究克隆了鸡visfatin基因cDNA全长1482 bp,编码493个氨基酸序列。预测鸡Visfatin氨基酸序列有26个磷酸化位点和一个疏水性区域但没有信号肽序列,该氨基酸序列中含α-螺旋、β-折叠,β-转角及无规卷曲4种二级结构,具有NAPRTase家族保守结构域特征及6个功能基序位点。Visfatin为高度保守的蛋白。
4.不同品种和不同时期鸡visfatin基因组织表达研究
鸡visfatin基因在胸肌中表达量最高,骨髓中最低。内脏和皮下脂肪中visfatin的表达量未显著差异(P>0.05)。肉鸡骨髓,肝脏,肾脏、脂肪中visfatin的表达量均显著高于乌鸡中的相应含量。骨髓中visfatin的表达量随着机体的生长发育呈现降低的趋势(P<0.05),在鸡的快速生长时期肝脏和腿肌中visfatin表达水平较高。肝脏、心脏和骨髓visfatin基因的表达量未见性别差异
5.不同品种和不同时期鸡PRDM16基因组织表达研究
PRDM16基因心脏组织中表达量最高,肝脏组织中最低,内脏和皮下脂肪中PRDM16表达量差异不显著(P>0.05)。肉鸡胸肌、脂肪中PRDM16表达量显著高于乌鸡相应组织的表达量(P<0.05)。骨髓中PRDM16表达水平随着生长发育逐渐降低(P<0.05)。1日龄、8周龄,12周龄时骨髓中最高,4周龄肝脏中最高,16周龄心脏中最高。组织PRDM16基因的表达丰度远远低于visfatin基因的表达。肝脏、心脏和骨髓中PRDM16基因的表达量未见性别差异。
With the rapid development of molecular biology, many works on searching major genes or closely linked molecular markers of growth and production traits from DNA level and on studying the gene functions have been carried out in recent years. The approaches of marker-assisted selection and transgenic breeding have become the future trend in poultry breeding. Visfatin and PRDM16 are the newly discovered genes and they play an important role in determination of fat traits, no information on genetic variation and functional studies of chicken visfatin and PRDM16 genes is available. In this study, the genetic variations of visfatin and PRDM16 genes were detected by single stranded conformation polymorphism and DNA pool sequencing. SNPs of visfatin and PRDM16 genes were genotyped in an F2 resource population of Gushi chickens crossing with Anka broilers using forced-PCR-RFLP. Haplotypes were constructed based on 3 SNPs with linkage disequilibrium of visfatin gene. The associations of 9 SNPs polymorphisms with 84 parameter in 849 F2 chickens were analyzed. The coding sequence of Silky Chicken’s visfatin gene was cloned and analyzed by bioinformatics methods. Using real-time PCR techique, the mRNA of visfatin and PRDM16 gene in heart, liver, kidney, spleen, breast muscle, subcutaneous fat, viscera fat and bone marrowfrom broiler and silky fowl were analyzed. Expressions of heart, liver, bone morrow, sebum and leg muscle from silky fowl at 1-day, 4, 8, 12, 16 weeks old were also investigated. The goal of this study is to identify the sequence variations of the visfatin and PRDM16 gene, to analyze the relationship between gene variation and chicken performance, and to find molecular markers for chicken genetics and breeding programs. In addition, it would provide theoretical basis for studying visfatin and PRDM16 functions and diagnosing and treating the obesity. The main results were summarized as below:
1.Genetic variations of visfatin gene and their associations with chicken production traits
Twelve SNPs were found in visfatin gene with the location of intron 3 (14360C>T), exon 4 (14404A>T), exon 6 (15526C>T), intron 6 (15673C>G), exon 7 (17873C>T), intron 7 (17928T>C), intron 8 (24019A>G), intron 9 (4238T>C, 24262G>T, 24285A>G, 24294A>G) and intron 10 (9 bp Indel), respectively. Except for 14404A>T, 17873C>T and 24262G>T, other 9 SNPs were newly discoverd, of which eight SNPs were genotyped. Three were main haplotypes including H1(ACG), H2(ACT) and H8(TTT) and 5 main diplotypes based on three SNPs with strong linkage disequilibrium.
14404A>T polymorphisms was significantly associated with body weight and body size traits at different age (P<0.05). For the traits body weight and carcass weight with genotype TT were significantly higher than those of genotype AA. 15526C>T polymorphisms was associated with body weight at birth and at 4 weeks, and with breast angle at 8 weeks. 17873 C>T polymorphisms was associated with the early growth traits. The growth traits at 4 weeks of the individual with the genotype TT was higher than those with genotype CC (P<0.05). 24238 T>C polymorphisms was also associated with growth traits and genotype CC is a favorable genotype for chicken growth and development. The genotype TT of 24262G>T polymorphisms was a favorable gene for chicken early growth traits and breast muscle weight. 24285A>G polymorphism was associated with growth traits at 8 weeks. 24294A>G polymorphisms was associated with chest depth at 8 weeks, pelvis breadth at 4 weeks and12 weeks, skin fat thicknessand and low density lipoprotein cholesterol (P<0.05). 9 bp Indel polymorphisms was associated with growth traits and pancreas weight, allele D (9 bp deletion) of the vistafin gene had a negative effect on skeletal growth. The five main diplotypes was associated with breast angle at 8 weeks, breast muscle fiber density and low density lipoprotein cholesterol (P<0.05). The genotype combination TTTTTTIICCTTGGAA had a positivie effects on chicken growth and development. The results has affirmed that there is a close relationship between visfatin gene and chicken growth and development..
2.Genetic variations of PRDM16 gene and associations with production traits
Six novel SNPs of the PRDM16 gene were found and 92188G>A and 115305C>T was located at non-cording region, 102872C>T, 102944C>T, 103144G>A and 115512G>A located at cording region. The polymorphism of the 115512G>A was significantly associated with the fatness and carcass traits and the genotype AA is an optional genotype for decreasing abdominal fat weight and triglyceride (P<0.05). On the other hand, the genotype GG is an optional genotype for enhancing evisceration weight and meat quality. The results indicated that the polymorphism of PRDM16 gene in chicken may influence the carcass and fat traits, but no association with the growth traits.
3. Clone and bioinformatics analysis of visfatin gene of Silky fowl
The 1482 bp full coding region sequence of visfatin gene in Silky fowl were obtained and it coded 493 amino acid sequence. It has 26 phosphorylation sites and a conserved domain of NAPRTase family but no signal peptide sequence. There is a hydrophobic region in 140-160aa of the visfatin. The amino acid sequence contains four kinds of secondary structure:α-helix,β-fold,β-angle and random coil. It has six function motifs including an amidation site. The visfatin is a highly conserved protein.
4. Study of the expression of chicken visfatin gene in different tissue and developmental stages
The highest expression of visfatin was found in breast muscle and the lowest in bone marrow. There was no difference of the expression in visceral fat and subcutaneous fat. However, the expressions of visfatin in bone marrow, liver, kidney, subcutaneous and visceral fat in broiler were significantly higher than in silky fowl (P< 0.05). Visfatin mRNA levels decreased in the bone marrow with the body development (P< 0.05) but increased in the liver and leg muscle.
4. Study of the expression of chicken PRDM16 gene in different tissue and developmental stages
The highest expression of PRDM16 was found in heart and the lowest in liver. There was no difference of the expression in visceral fat and abdominal fat. The expressions of PRDM16 in breast muscle, abdominal fat, subcutaneous fat and visceral fat in broiler were significantly higher than in silky fowl (P<0.05).The expressions of PRDM16 decreased in the bone marrow with the growth and development (P<0.05). The highest expression in the bone marrow was found at the age of 1 day, 8 weeks and 12 weeks, and the highest expression in the liver was found at the age of 4 weeks, the highest expression in the liver was found at the age of 16 weeks. The mRNA levels of ten tissues were much lower in PRDM16 than in visfatin (P<0.05). The visfatin and PRDM16 gene expression in the liver, heart and bone marrow has no gender difference in silky fowl.
引文
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