秦川牛PSMC3基因的SNP检测及与体尺、胴体性状的关联性分析
发布时间：2018-08-31 18:15
【摘要】：PSMC3基因(ATP酶亚基3)定位于牛9号染色体上,全长约8059bp,共有12个外显子。目前对PSMC3基因的研究主要集中在人类以及小鼠上,而在秦川牛上则未见相关报道,以PSMC3基因作为影响秦川牛体尺及胴体性状的候选基因,探索其与秦川牛体尺及胴体性状的相关性,具有重要的研究价值。本文以秦川牛PSMC3基因为候选基因,首先利用软件DNAman、ProtScale、Netphos、TMHMM、Predictprotein对牛PSMC3基因进行生物信息学分析。然后选取167头在同等条件下饲养的24月龄健康秦川牛为研究对象,通过混合DNA池、测序、PCR-RFLP等技术,检测了PSMC3基因的SNPs位点,并将检测到的位点与秦川牛的体尺性状进行关联分析。研究结果如下:1.PSMC3基因生物信息学分析牛PSMC3基因CDS区共8059bp;亲水性氨基酸占多数为亲水性蛋白;潜在磷酸化位点丝氨酸11个、苏氨酸5个、络氨酸4个;蛋白没有跨膜结构区域;蛋白质二级结构有α-螺旋占44.77%,β-折叠占12.05%,无规则卷曲占43.18%。2.PSMC3基因的遗传变异检测利用测序及PCR-RFLP技术,找出了秦川牛PSMC3基因的4个突变,包含第一内含子位点g.2672、第一内含子位点g.3017、第五外显子位点g.4012、第七外显子位点g.4893,分别命名为T56C、G324A、T140C和G134A。其中突变T56C、T140C处T为优势等位基因;突变G324A处A为优势等位基因,G134A处G为优势等位基因。3.PSMC3基因的群体遗传学分析4个突变位点均为中度多态性(0.25P0.5)。位点T56C、T140C处于HardyWeinberg平衡状态;突变位点G324A、G134A处于HardyWeinberg极度不平衡状态。4.PSMC3基因多态性与体尺、胴体性状的关联性分析关联分析表明PSMC3基因突变位点T56C与体高和屠宰率差异显著(P0.05),与腰角宽性状差异极显著(P0.01);突变位点G324A与体长性状差异显著(P0.05);突变位点T140C与腰角宽性状差异极显著(P0.01),与体高、屠宰率性状差异显著(P0.05);突变位点G134A与体高性状差异显著(P0.05)。综上所述,秦川牛PSMC3基因内含子与外显子中存在多态位点且与部分体尺和胴体性状显著相关,显示牛PSMC3基因可考虑作为候选基因加强研究以促进为秦川肉牛的育种工作。
[Abstract]:The PSMC3 gene (ATP subunit 3) is located on bovine chromosome 9, with a total length of 8059bp and 12 exons. At present, the study of PSMC3 gene is mainly focused on human and mice, but not on Qinchuan cattle. The PSMC3 gene is used as candidate gene to affect the body size and carcass traits of Qinchuan cattle. It is of great value to explore the correlation between the body size and carcass traits of Qinchuan cattle. In this paper, the PSMC3 gene of Qinchuan cattle was used as candidate gene. Firstly, the bioinformatics analysis of bovine PSMC3 gene was carried out by software DNAman,ProtScale,Netphos,TMHMM,Predictprotein. The SNPs loci of the PSMC3 gene were detected by using mixed DNA pool and sequencing PCR-RFLP from 167 healthy 24 month old Qinchuan cattle raised under the same conditions. The detected loci were correlated with the body size traits of Qinchuan cattle. The results were as follows: 1. The CDS region of bovine PSMC3 gene was analyzed by bioinformatics. The hydrophilic amino acids were mostly hydrophilic proteins, the potential phosphorylation sites were serine (11), threonine (5) and complex amino acid (4). The secondary structure of protein consists of 伪 -helix (44.77) and 尾 -folding (12.05). The genetic variation of 43.18%.2.PSMC3 gene was detected by random curling. Four mutations of PSMC3 gene in Qinchuan cattle were identified by sequencing and PCR-RFLP techniques. It contains the first intron locus g.2672, the first intron locus g.3017, the fifth exon locus g.4012 and the seventh exon locus g.4893. The dominant alleles were T at T56CnT140C and A at G324A and G at G134A. 3. The four mutation loci of PSMC3 gene were moderately polymorphic (0.25P0.5). The mutation locus G324AfG134A was in the extremely unbalanced state of HardyWeinberg. 4. PSMC3 gene polymorphism and body size. Correlation analysis of carcass traits: PSMC3 gene mutation site T56C was significantly different from body height and slaughter rate (P0.05), and significantly different from waist angle width trait (P0.01), mutation locus G324A was significantly different from body length trait (P0.05), mutation locus T140C was significantly different from waist trait (P0.05). The difference between angle width and body height was significant (P0.01). There were significant differences in slaughter rate (P0.05), mutation locus (G134A) and body height (P0.05). In conclusion, there were polymorphic loci in the intron and exon of the PSMC3 gene of Qinchuan cattle and significant correlation with some body size and carcass traits, indicating that the PSMC3 gene of cattle could be considered as a candidate gene to enhance the research for the breeding of Qinchuan beef cattle.
【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
本文编号：2215767
[Abstract]:The PSMC3 gene (ATP subunit 3) is located on bovine chromosome 9, with a total length of 8059bp and 12 exons. At present, the study of PSMC3 gene is mainly focused on human and mice, but not on Qinchuan cattle. The PSMC3 gene is used as candidate gene to affect the body size and carcass traits of Qinchuan cattle. It is of great value to explore the correlation between the body size and carcass traits of Qinchuan cattle. In this paper, the PSMC3 gene of Qinchuan cattle was used as candidate gene. Firstly, the bioinformatics analysis of bovine PSMC3 gene was carried out by software DNAman,ProtScale,Netphos,TMHMM,Predictprotein. The SNPs loci of the PSMC3 gene were detected by using mixed DNA pool and sequencing PCR-RFLP from 167 healthy 24 month old Qinchuan cattle raised under the same conditions. The detected loci were correlated with the body size traits of Qinchuan cattle. The results were as follows: 1. The CDS region of bovine PSMC3 gene was analyzed by bioinformatics. The hydrophilic amino acids were mostly hydrophilic proteins, the potential phosphorylation sites were serine (11), threonine (5) and complex amino acid (4). The secondary structure of protein consists of 伪 -helix (44.77) and 尾 -folding (12.05). The genetic variation of 43.18%.2.PSMC3 gene was detected by random curling. Four mutations of PSMC3 gene in Qinchuan cattle were identified by sequencing and PCR-RFLP techniques. It contains the first intron locus g.2672, the first intron locus g.3017, the fifth exon locus g.4012 and the seventh exon locus g.4893. The dominant alleles were T at T56CnT140C and A at G324A and G at G134A. 3. The four mutation loci of PSMC3 gene were moderately polymorphic (0.25P0.5). The mutation locus G324AfG134A was in the extremely unbalanced state of HardyWeinberg. 4. PSMC3 gene polymorphism and body size. Correlation analysis of carcass traits: PSMC3 gene mutation site T56C was significantly different from body height and slaughter rate (P0.05), and significantly different from waist angle width trait (P0.01), mutation locus G324A was significantly different from body length trait (P0.05), mutation locus T140C was significantly different from waist trait (P0.05). The difference between angle width and body height was significant (P0.01). There were significant differences in slaughter rate (P0.05), mutation locus (G134A) and body height (P0.05). In conclusion, there were polymorphic loci in the intron and exon of the PSMC3 gene of Qinchuan cattle and significant correlation with some body size and carcass traits, indicating that the PSMC3 gene of cattle could be considered as a candidate gene to enhance the research for the breeding of Qinchuan beef cattle.
【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
【参考文献】
相关期刊论文 前1条
1 黄磊;昝林森;王洪宝;刘洪瑜;;秦川牛LXRα基因第二外显子多态性及其与部分胴体、肉用性状关联性研究[J];畜牧兽医学报;2010年05期
，本文编号：2215767
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