秦川牛PSMC3基因的SNP檢測及與體尺、胴體性狀的關(guān)聯(lián)性分析
發(fā)布時間：2018-08-31 18:15
【摘要】：PSMC3基因(ATP酶亞基3)定位于牛9號染色體上,全長約8059bp,共有12個外顯子。目前對PSMC3基因的研究主要集中在人類以及小鼠上,而在秦川牛上則未見相關(guān)報道,以PSMC3基因作為影響秦川牛體尺及胴體性狀的候選基因,探索其與秦川牛體尺及胴體性狀的相關(guān)性,具有重要的研究價值。本文以秦川牛PSMC3基因為候選基因,首先利用軟件DNAman、ProtScale、Netphos、TMHMM、Predictprotein對牛PSMC3基因進(jìn)行生物信息學(xué)分析。然后選取167頭在同等條件下飼養(yǎng)的24月齡健康秦川牛為研究對象,通過混合DNA池、測序、PCR-RFLP等技術(shù),檢測了PSMC3基因的SNPs位點(diǎn),并將檢測到的位點(diǎn)與秦川牛的體尺性狀進(jìn)行關(guān)聯(lián)分析。研究結(jié)果如下:1.PSMC3基因生物信息學(xué)分析牛PSMC3基因CDS區(qū)共8059bp;親水性氨基酸占多數(shù)為親水性蛋白;潛在磷酸化位點(diǎn)絲氨酸11個、蘇氨酸5個、絡(luò)氨酸4個;蛋白沒有跨膜結(jié)構(gòu)區(qū)域;蛋白質(zhì)二級結(jié)構(gòu)有α-螺旋占44.77%,β-折疊占12.05%,無規(guī)則卷曲占43.18%。2.PSMC3基因的遺傳變異檢測利用測序及PCR-RFLP技術(shù),找出了秦川牛PSMC3基因的4個突變,包含第一內(nèi)含子位點(diǎn)g.2672、第一內(nèi)含子位點(diǎn)g.3017、第五外顯子位點(diǎn)g.4012、第七外顯子位點(diǎn)g.4893,分別命名為T56C、G324A、T140C和G134A。其中突變T56C、T140C處T為優(yōu)勢等位基因;突變G324A處A為優(yōu)勢等位基因,G134A處G為優(yōu)勢等位基因。3.PSMC3基因的群體遺傳學(xué)分析4個突變位點(diǎn)均為中度多態(tài)性(0.25P0.5)。位點(diǎn)T56C、T140C處于HardyWeinberg平衡狀態(tài);突變位點(diǎn)G324A、G134A處于HardyWeinberg極度不平衡狀態(tài)。4.PSMC3基因多態(tài)性與體尺、胴體性狀的關(guān)聯(lián)性分析關(guān)聯(lián)分析表明PSMC3基因突變位點(diǎn)T56C與體高和屠宰率差異顯著(P0.05),與腰角寬性狀差異極顯著(P0.01);突變位點(diǎn)G324A與體長性狀差異顯著(P0.05);突變位點(diǎn)T140C與腰角寬性狀差異極顯著(P0.01),與體高、屠宰率性狀差異顯著(P0.05);突變位點(diǎn)G134A與體高性狀差異顯著(P0.05)。綜上所述,秦川牛PSMC3基因內(nèi)含子與外顯子中存在多態(tài)位點(diǎn)且與部分體尺和胴體性狀顯著相關(guān),顯示牛PSMC3基因可考慮作為候選基因加強(qiáng)研究以促進(jìn)為秦川肉牛的育種工作。
[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 偽 -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.
【學(xué)位授予單位】：西北農(nóng)林科技大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2015
【分類號】：S823
本文編號：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 偽 -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.
【學(xué)位授予單位】：西北農(nóng)林科技大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2015
【分類號】：S823
【參考文獻(xiàn)】
相關(guān)期刊論文 前1條
1 黃磊;昝林森;王洪寶;劉洪瑜;;秦川牛LXRα基因第二外顯子多態(tài)性及其與部分胴體、肉用性狀關(guān)聯(lián)性研究[J];畜牧獸醫(yī)學(xué)報;2010年05期
，本文編號：2215767
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