黄牛生长性状选择的IRX3基因标记研究与应用
发布时间：2018-08-06 17:05
【摘要】：易洛魁族同源盒3(iroquois homeobox3,IRX3)是易洛魁族同源盒家族(IRXs)中的最具代表的一员,最新报道,公认的肥胖基因FTO(fat mass and obesity associated)基因非编码区的变异会促使基因IRX3过度表达,进而诱发肥胖,IRX3基因可有效控制褐色脂肪的形成。并且IRX3基因和FTO基因的的这种互动关系普遍存在于人类、老鼠和斑马鱼中。进而可推测IRX3基因很可能影响肉牛脂肪代谢进而影响肉牛生产,而目前IRX3基因在肉牛上未见报道,因此分析IRX3基因标记及其应用对于提高肉牛产业的经济效益有重要的理论和实践意义。本试验通过DNA混合池测序技术和PCR-RFLP技术分析研究了724个黄牛个体(晋南牛205头、秦川牛519头)间的遗传变异及其对黄牛生长性状的影响,以期找到对肉牛产业发展有高价值的分子标记,并提出该技术在肉牛选育中的具体应用方案。试验结果如下:1、黄牛IRX3基因的遗传变异研究以30个秦川牛和晋南牛个体的DNA等量混合的DNA池为模板设计了5对引物扩增IRX3基因的全长及其启动子区,发现了3个多态位点,其中g.-1941GA多态位点和g.-991GC多态位点位于启动子区,g.1941TG多态位点位于第二内含子区。这些多态位点分别采用Msp1-RFLP、KpnI-RFLP和Hinf1-RFLP的分型方法检测其在晋南牛和秦川牛的遗传变异。对IRX3基因3个多态位点进行群体遗传学分析、连锁不平衡分析、单倍型分析。群体遗传学分析结果表明两黄牛品种间存在较大差异,SNP1位点野生型的等位基因频率(0.647和0.601)均显著高于突变型的等位基因频率(0.353和0.399),SNP3位点野生型的等位基因频率(0.916和0.849)均显著高于突变型的等位基因频率(0.154和0.256),而SNP2位点的突变型的等位基因频率(0.85和0.823)较高;而且SNP3位点在晋南牛中只检测到两种基因型GG和GT,未发现纯合型的突变个体。遗传多态性指标分析表明3个位点多态信息比较丰富,育种潜力较大,除了晋南牛中SNP3位点处于低度多态(PIC0.25)以外,其他位点在群体中均处于中度多态(0.25PIC0.5)。此外卡方检验表明除了秦川牛在SNP2位点处于哈代-温伯格不平衡状态(P0.05),其它位点在两黄牛群体中均处于哈代-温伯格平衡状态(P0.05)。单倍型分析结果表明相同品种间单倍型分布频率有差异,而相同单倍型在不同品种也有差异,IRX3基因三个多态位点存在的8种单倍型,AGG单倍型的分布频率最高,在秦川牛中可以检测到全部的单倍型,而在晋南牛中只检测到6种单倍型。连锁分析结果表明不同群体间的相同两位点间的连锁程度仍不相同,晋南牛中的SNP1和SNP3位点的连锁稍强,而在秦川牛中处于弱连锁状态。2、黄牛IRX3基因的遗传变异与生长性状的关联分析IRX3基因3个多态位点与秦川牛和晋南牛的生长性状关联分析结果表明,SNP1位点对晋南牛的胸深有显著影响(P0.05),纯合子AA基因型的胸深显著高于AG基因型个体;SNP2位点对晋南牛的体高、胸深、体高和体长有显著影响(P0.05),CC基因型的个体在体高、胸深、体高和体长方面均显著高于CG基因型个体和GG基因型个体,对秦川牛的生长性状影响不显著(P0.05);SNP3位点与秦川牛的胸围直接存在显著相关(P0.05),GG基因型个体胸围显著高于GT基因型,对晋南牛的生长性状影响不显著(P0.05)。综合以上分析说明IRX3基因的3个多态位点可作为黄牛生长性状选育的重要分子遗传标记,IRX3基因可作为黄牛育种的重要候选基因。3、黄牛IRX3基因标记技术在肉牛选育中的应用方案利用IRX3基因标记技术与多阶段选择相结合的方法通过性能测定对黄牛进行有效选育。1)理论依据:找出与黄牛生长性状显著相关的SNP位点,确定显著提高黄牛生长性状的基因型及其优势性状。SNP1位点对晋南牛的胸深有显著影响(P0.05),纯合子AA基因型的胸深显著高于AG基因型个体;SNP2位点对晋南牛的体高、胸深和体长有显著影响(P0.05),CC基因型的个体在体高、胸深和体长方面均显著高于CG基因型个体和GG基因型个体,对秦川牛的生长性状影响不显著(P0.05);SNP3位点与秦川牛的胸围直接存在显著相关(P0.05),GG基因型个体胸围显著高于GT基因型,对晋南牛的生长性状影响不显著(P0.05)。2)断奶前选择:首先对犊牛编号标记,详细记录出生时间、父母代的信息以及体重等,以便以后的选育工作正常进行。由于断奶时的各种性状未表现出来,通过测定犊牛IRX3基因相关分子标记位点的基因型,如SNP1位点对应的AA优势基因型、SNP2位点对应的CC优势基因型和SNP3位点对应的GG优势基因型,对犊牛进行早期选种,也可选择能繁育具有这些优势基因型后代的亲本进行配种;3)6月龄黄牛的主要生长性状已经显现,应该作为主选阶段。通过分子测定结合对其测定优势性状如胸深、体高、体长以及胸围,筛选优势性状较为明显的黄牛个体。
[Abstract]:The Iroquois homologous box 3 (Iroquois homeobox3, IRX3) is one of the most representative members of the Iroquois homologous box family (IRXs). The latest report shows that the variation of the noncoding region of the obese gene FTO (fat mass and obesity associated) can induce the gene IRX3 overexpression and induce obesity. The IRX3 gene can effectively control the brown fat. The interaction between the IRX3 gene and the FTO gene is common in human, mice and zebrafish. Then it can be deduced that the IRX3 gene may affect beef fat metabolism and affect beef production. At present, the IRX3 gene is not reported on beef cattle. Therefore, the IRX3 based marker and its application are analyzed to improve the beef cattle industry. The economic benefit has important theoretical and practical significance. In this experiment, the genetic variation of 724 cattle (205 cattle of Jinnan cattle, 519 heads of Qinchuan cattle) and their effects on the growth traits of yellow cattle were analyzed by DNA mixing pool sequencing and PCR-RFLP technology, in order to find the molecular markers of high value for the development of beef cattle production and put forward the technique. The specific application in breeding beef cattle. The results are as follows: 1, the genetic variation of IRX3 gene in cattle was studied by using the DNA isometric DNA pool of 30 Qinchuan cattle and southern Jinnan cattle to design 5 pairs of primers to amplify the full length of the IRX3 gene and its promoter region, and 3 polymorphic loci were found, of which g.-1941GA polymorphic loci and g.-991GC were found. The polymorphic loci were located in the promoter region, and the g.1941TG polymorphic loci were located in the intron second. The polymorphic loci used Msp1-RFLP, KpnI-RFLP and Hinf1-RFLP to detect their genetic variation in the southern Jinnan and Qinchuan cattle. The 3 polymorphic loci of the IRX3 gene were analyzed by population genetic analysis, linkage disequilibrium analysis and haplotype analysis. The results of population genetics analysis showed that there were significant differences among the two yellow cattle. The allele frequencies of the wild type SNP1 loci (0.647 and 0.601) were significantly higher than those of the mutant allele frequencies (0.353 and 0.399). The frequencies of the allele (0.916 and 0.849) of the wild type SNP3 loci (0.916 and 0.849) were significantly higher than those of the mutant allele frequencies (0.154 and 0.25). 6), the mutant allele frequencies of the SNP2 loci (0.85 and 0.823) were higher, and only two genotypes GG and GT were detected in the southern Jinnan cattle, and no homozygous mutant individuals were found. The genetic polymorphism index analysis showed that the 3 loci polymorphism information was rich and the breeding potential was large, except that the SNP3 loci in the southern Shanxi cattle were low. Besides the polymorphism (PIC0.25), other loci were in moderate polymorphism (0.25PIC0.5). Besides, chi square test showed that in addition to the Hardy Weinberg imbalance (P0.05) at the SNP2 site of Qinchuan cattle (P0.05), the other loci were in the Hardy Weinberg equilibrium state in the two cattle population (P0.05). The haplotype analysis showed that the same varieties were among the same varieties. The haplotype distribution frequency is different, and the same haplotype is also different in different varieties. The distribution frequency of 8 haplotypes of the three polymorphic loci of IRX3 gene is the highest. All the haplotypes can be detected in the Qinchuan cattle, and only 6 haplotypes are detected in the southern Jinnan cattle. The linkage analysis results show that the different populations are among the different populations. The linkage between the same two loci is still different. The linkage between the SNP1 and SNP3 loci in the southern Jinnan cattle is slightly stronger, while the weak linkage.2 in the Qinchuan cattle and the association of the genetic variation with the growth traits of the Yellow Cattle IRX3 gene analysis the correlation analysis between the 3 polymorphic loci of the IRX3 gene and the growth traits of the Qinchuan cattle and the southern Jinnan cattle. The results show that the SNP1 locus is the site of the relationship between the IRX3 gene and the growth traits of the southern Jinnan cattle. The chest depth of the southern Jinnan cattle was significantly affected (P0.05). The thorax depth of the homozygote AA genotype was significantly higher than that of the AG genotype. The SNP2 locus had significant influence on body height, chest depth, body height and body length (P0.05). The CC genotype individuals were significantly higher in body height, chest depth, body height and body length than CG genotypes and GG genotypes. The growth traits of Sichuan cattle were not significantly affected (P0.05), and there was a significant correlation between the SNP3 locus and the chest circumference of Qinchuan cattle (P0.05). The GG genotype was significantly higher than that of the GT genotype, and the effect on the growth traits of the southern Jinnan cattle was not significant (P0.05). The analysis of the 3 polymorphic loci of the IRX3 base could be important for the selection of the growth traits of the cattle. Molecular genetic markers, IRX3 gene can be used as an important candidate gene.3 for cattle breeding, and the application scheme of yellow cattle IRX3 gene marker technique in breeding beef cattle is based on the combination of IRX3 gene marker technique and multi stage selection method, which can be used to select.1 effectively through performance measurement for Yellow Cattle: to find out the significant correlation with the growth traits of yellow cattle. The SNP loci confirmed that the genotype and.SNP1 locus of the dominant traits significantly affected the chest depth of the southern Shanxi cattle (P0.05). The thorax depth of the homozygote AA genotype was significantly higher than that of the AG genotype, and the SNP2 locus had a significant influence on the body height, the chest depth and the body length of the southern Shanxi cattle (P0.05), and the individuals of the CC genotypes were in body height and chest depth. And the length of body length was significantly higher than that of CG genotype and GG genotype, which had no significant influence on the growth traits of Qinchuan cattle (P0.05). The SNP3 locus had a significant correlation with the chest circumference of Qinchuan cattle (P0.05), and the individual chest circumference of GG genotype was significantly higher than that of the GT genotypes, which had no significant effect on the growth traits of the southern Shanxi cattle (P0.05) before weaning. First, the number of calves was numbered to record the birth time, the information of the parent generation and the weight, so that the future breeding work was carried out normally. The genotype of the IRX3 gene related marker loci of calves, such as the AA dominant genotype at the SNP1 site, and the CC best of the SNP2 locus, were not shown in the weaning. The GG dominant genotype of the potential genotypes and SNP3 loci can be selected early and can also be selected to breed the parent of the offspring with these dominant genotypes; 3) the main growth traits of the 6 month old yellow cattle have already appeared and should be selected as the main selection stage. Long and chest circumference were used to screen yellow cattle individuals with superior traits.
【学位授予单位】：西北农林科技大学
【学位级别】：硕士
【学位授予年份】：2015
【分类号】：S823.81
本文编号：2168385
[Abstract]:The Iroquois homologous box 3 (Iroquois homeobox3, IRX3) is one of the most representative members of the Iroquois homologous box family (IRXs). The latest report shows that the variation of the noncoding region of the obese gene FTO (fat mass and obesity associated) can induce the gene IRX3 overexpression and induce obesity. The IRX3 gene can effectively control the brown fat. The interaction between the IRX3 gene and the FTO gene is common in human, mice and zebrafish. Then it can be deduced that the IRX3 gene may affect beef fat metabolism and affect beef production. At present, the IRX3 gene is not reported on beef cattle. Therefore, the IRX3 based marker and its application are analyzed to improve the beef cattle industry. The economic benefit has important theoretical and practical significance. In this experiment, the genetic variation of 724 cattle (205 cattle of Jinnan cattle, 519 heads of Qinchuan cattle) and their effects on the growth traits of yellow cattle were analyzed by DNA mixing pool sequencing and PCR-RFLP technology, in order to find the molecular markers of high value for the development of beef cattle production and put forward the technique. The specific application in breeding beef cattle. The results are as follows: 1, the genetic variation of IRX3 gene in cattle was studied by using the DNA isometric DNA pool of 30 Qinchuan cattle and southern Jinnan cattle to design 5 pairs of primers to amplify the full length of the IRX3 gene and its promoter region, and 3 polymorphic loci were found, of which g.-1941GA polymorphic loci and g.-991GC were found. The polymorphic loci were located in the promoter region, and the g.1941TG polymorphic loci were located in the intron second. The polymorphic loci used Msp1-RFLP, KpnI-RFLP and Hinf1-RFLP to detect their genetic variation in the southern Jinnan and Qinchuan cattle. The 3 polymorphic loci of the IRX3 gene were analyzed by population genetic analysis, linkage disequilibrium analysis and haplotype analysis. The results of population genetics analysis showed that there were significant differences among the two yellow cattle. The allele frequencies of the wild type SNP1 loci (0.647 and 0.601) were significantly higher than those of the mutant allele frequencies (0.353 and 0.399). The frequencies of the allele (0.916 and 0.849) of the wild type SNP3 loci (0.916 and 0.849) were significantly higher than those of the mutant allele frequencies (0.154 and 0.25). 6), the mutant allele frequencies of the SNP2 loci (0.85 and 0.823) were higher, and only two genotypes GG and GT were detected in the southern Jinnan cattle, and no homozygous mutant individuals were found. The genetic polymorphism index analysis showed that the 3 loci polymorphism information was rich and the breeding potential was large, except that the SNP3 loci in the southern Shanxi cattle were low. Besides the polymorphism (PIC0.25), other loci were in moderate polymorphism (0.25PIC0.5). Besides, chi square test showed that in addition to the Hardy Weinberg imbalance (P0.05) at the SNP2 site of Qinchuan cattle (P0.05), the other loci were in the Hardy Weinberg equilibrium state in the two cattle population (P0.05). The haplotype analysis showed that the same varieties were among the same varieties. The haplotype distribution frequency is different, and the same haplotype is also different in different varieties. The distribution frequency of 8 haplotypes of the three polymorphic loci of IRX3 gene is the highest. All the haplotypes can be detected in the Qinchuan cattle, and only 6 haplotypes are detected in the southern Jinnan cattle. The linkage analysis results show that the different populations are among the different populations. The linkage between the same two loci is still different. The linkage between the SNP1 and SNP3 loci in the southern Jinnan cattle is slightly stronger, while the weak linkage.2 in the Qinchuan cattle and the association of the genetic variation with the growth traits of the Yellow Cattle IRX3 gene analysis the correlation analysis between the 3 polymorphic loci of the IRX3 gene and the growth traits of the Qinchuan cattle and the southern Jinnan cattle. The results show that the SNP1 locus is the site of the relationship between the IRX3 gene and the growth traits of the southern Jinnan cattle. The chest depth of the southern Jinnan cattle was significantly affected (P0.05). The thorax depth of the homozygote AA genotype was significantly higher than that of the AG genotype. The SNP2 locus had significant influence on body height, chest depth, body height and body length (P0.05). The CC genotype individuals were significantly higher in body height, chest depth, body height and body length than CG genotypes and GG genotypes. The growth traits of Sichuan cattle were not significantly affected (P0.05), and there was a significant correlation between the SNP3 locus and the chest circumference of Qinchuan cattle (P0.05). The GG genotype was significantly higher than that of the GT genotype, and the effect on the growth traits of the southern Jinnan cattle was not significant (P0.05). The analysis of the 3 polymorphic loci of the IRX3 base could be important for the selection of the growth traits of the cattle. Molecular genetic markers, IRX3 gene can be used as an important candidate gene.3 for cattle breeding, and the application scheme of yellow cattle IRX3 gene marker technique in breeding beef cattle is based on the combination of IRX3 gene marker technique and multi stage selection method, which can be used to select.1 effectively through performance measurement for Yellow Cattle: to find out the significant correlation with the growth traits of yellow cattle. The SNP loci confirmed that the genotype and.SNP1 locus of the dominant traits significantly affected the chest depth of the southern Shanxi cattle (P0.05). The thorax depth of the homozygote AA genotype was significantly higher than that of the AG genotype, and the SNP2 locus had a significant influence on the body height, the chest depth and the body length of the southern Shanxi cattle (P0.05), and the individuals of the CC genotypes were in body height and chest depth. And the length of body length was significantly higher than that of CG genotype and GG genotype, which had no significant influence on the growth traits of Qinchuan cattle (P0.05). The SNP3 locus had a significant correlation with the chest circumference of Qinchuan cattle (P0.05), and the individual chest circumference of GG genotype was significantly higher than that of the GT genotypes, which had no significant effect on the growth traits of the southern Shanxi cattle (P0.05) before weaning. First, the number of calves was numbered to record the birth time, the information of the parent generation and the weight, so that the future breeding work was carried out normally. The genotype of the IRX3 gene related marker loci of calves, such as the AA dominant genotype at the SNP1 site, and the CC best of the SNP2 locus, were not shown in the weaning. The GG dominant genotype of the potential genotypes and SNP3 loci can be selected early and can also be selected to breed the parent of the offspring with these dominant genotypes; 3) the main growth traits of the 6 month old yellow cattle have already appeared and should be selected as the main selection stage. Long and chest circumference were used to screen yellow cattle individuals with superior traits.
【学位授予单位】：西北农林科技大学
【学位级别】：硕士
【学位授予年份】：2015
【分类号】：S823.81
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