猪肌内脂肪沉积相关基因的筛选鉴定及其特征分析
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摘要
肌内脂肪（intramuscular fat，IMF）是影响肉质的一个重要指标，其含量与肉的风味、嫩度等优良肉质性状呈正相关。由于IMF含量在活体和早期难以测定，常规育种较难进行。目前，人们从营养和遗传角度对猪IMF沉积进行了大量研究，但营养调控只能改善IMF的沉积，影响IMF沉积的主效基因又尚未确定。因此，为筛选影响猪IMF沉积的相关基因，以进一步揭示IMF沉积的分子机理，本研究以IMF含量丰富的莱芜猪和IMF贫乏的大白猪为研究材料，运用抑制性消减杂交（suppressionsubtractive hybridization，SSH）技术构建高、低IMF莱芜猪和莱芜猪与大白猪的正反抑制性消减杂交文库，筛查和鉴别差异表达基因，并对其中的部分基因进行real-timePCR验证；另外，在候选基因的研究上，我们对猪NDUFS4基因进行了克隆和表达分析。主要结果如下：
一、应用SSH技术构建了高IMF莱芜猪与低IMF莱芜猪正反消减杂交文库。正反向文库扩增后分别得到631和486个阳性克隆，PCR鉴定结果表明插入片段主要分布在0.1-1.0kb之间。使用反Northen斑点杂交技术对以高IMF莱芜猪为Tester，低IMF莱芜猪为Driver的正向文库进行筛选，得到97个阳性差异克隆，进行测序、聚类拼接后得到35条单一ESTs序列。将这些序列在NCBI中进行BLAST比对分析，发现其中有17条ESTs与已知功能基因高度同源，3条ESTs在猪上有预测序列，15条ESTs序列与未知功能的cDNA片段高度同源。
二、应用SSH技术构建了莱芜猪与大白猪正反抑制性消减杂交文库。正反向文库扩增后分别得到1039和856个阳性克隆，PCR鉴定结果表明插入片段主要分布在0.1-2kb之间。使用反Northen斑点杂交技术对正反向文库进行筛选，以莱芜猪为Tester，大白猪为Driver的正向文库中获得154个阳性差异克隆，以大白猪为Tester，莱芜猪为Driver的反向文库中获得93个阳性克隆。进行测序、聚类拼接后，正向文库得到83条单一的ESTs序列，反向文库获得55条单一ESTs。在NCBI中进行BLAST比对分析后发现，正向文库中有33条ESTs与已知功能基因高度同源，15条ESTs在猪上有预测序列，25条ESTs序列与未知功能的cDNA片段高度同源，另有10条ESTs未找到明显的同源序列；反向文库中有21条ESTs与已知功能基因高度同源，8条ESTs在猪上有预测序列，18条ESTs序列与未知功能的cDNA片段高度同源，另有8条ESTs未找到明显的同源序列。
三、对与已知功能基因以及有预测序列的基因进行在线分类分析，发现这些基因参与了多种生物学过程；对其中的部分基因或ESTs进行了real-time PCR的验证，有13个基因或EST与文库筛选结果一致，其中上调基因11个，分别是：SERF2、ATP6、NDUFS4、SERPINF1、h142（EST）、ACSL1、ADFP、ACADM、HNRNPA2B1、PDK4、P311基因，下调基因2个，分别是：AMPD1和PGK1基因。
四、通过RT-PCR及RACE技术，我们得到了猪NDUFS4基因完整的cDNA序列。猪NDUFS4基因编码区核苷酸序列与人、小鼠、牛、大鼠的同源性分别为：92.99%、87.31%、93.56%、86.55%。猪NDUFS4基因氨基酸序列与牛的同源性最高为92.57%，与人、小鼠、大鼠的同源性分别为90.29%、88.57%、86.29%。对猪NDUFS4基因的在11种组织中的表达谱分析发现，该基因在检测组织中呈特异性表达，在背最长肌、脾脏、肾脏中高表达，肝脏、背膘、脑、脊髓中中度表达，心脏中低表达，肺、胃和大肠中几乎不表达。试验还对莱芜猪、大白猪背最长肌组织中NDUFS4基因mRNA的表达情况进行了real-time PCR的分析，结果表明莱芜猪中NDUFS4基因的mRNA表达量显著高于大白猪。
综上所述，本研究对莱芜猪IMF沉积的机理进行了探讨，构建了高、低IMF莱芜猪和莱芜猪、大白猪抑制性消减杂交文库，经过筛选获得了一些在猪背最长肌中表达，并与IMF沉积有关的差异基因。另外首次克隆了猪NDUFS4基因并对其组织表达进行了分析，证明了NDUFS4基因分别在高、低IMF含量莱芜猪和莱芜猪、大白猪中的mRNA表达水平存在差异。所得研究结果为进一步揭示猪背最长肌中IMF沉积与遗传机理奠定了重要的分子基础。
Intramuscular fat (IMF) content, correlated positively with meat tenderness, juiciness,and taste in pigs, has been revealed to be a major determinant factor affecting sensory meatquality. Conventional breeding is difficult to be carried out, because the IMF content isdifficult to measure in vivo and in piglet. At present, people conducted a large number ofstudies to explore the mechanism of IMF deposition in view of nutritional and genetic point.However, the nutritional control can only improve the IMF deposition, and the key geneaffecting IMF deposition has not yet been determined. Thus, this study was aimed atscreening the genes related to IMF deposition, to further reveal the molecular mechanism ofthe IMF deposition. Laiwu pig and Large White were used to construct high, low IMFLaiwu pig and Laiwu pig, Large White forward and reverse suppression subtractivehybridization (SSH) libraries to identify differentially expressed target genes, and some ofthese genes were varified by real-time PCR. In addition, studies of cloning and expressionwere done in pig NDUFS4gene. The main results are as follows:
1. High IMF Laiwu pig and low IMF Laiwu pig positive and negative cDNA librarieswere constructed by using SSH technology.631and486positive clones were obtainedfrom positive and reverse cDNA libraries, respectively. The PCR results showed that theinserted fragments are mainly distributed in the0.1-1.0kb. Forward library, in which highIMF Laiwu Black was Tester and low IMF Laiwu Black was Driver, was screened byreverse Northen blot.35ESTs was obtained from97positive differancial clones throughsequencing. By analysis of BLAST alignment in NCBI, the differential expression geneswere divided to17known functional genes,3hypothetical genes and15unknownsequences.
2. Laiwu pig and Large White positive and negative cDNA libraries were constructedby using SSH technology.1039and856positive clones were obtained from positive andreverse cDNA library, respectively. The PCR results showed that the inserted fragments aremainly distributed in the0.1-2.0kb. Forward library, in which Laiwu pig was Tester andLarge White was Driver, and reverse library, in which Large White was Tester and Laiwupig was Driver, were screened by reverse Northen blot.83and55ESTs were obtained from154and93positive differantial clone through sequencing, respectively. By analysis ofBLAST alignment in NCBI, these differential expression genes in positive library were divided to33known functional genes,15hypothetical genes,25unknown sequences and10ESTs which have no apparent homologe with sequences in NCBI; while in reverselibrary that were divided to21known functional genes,8hypothetical genes,18unknownsequences and8ESTs which have no apparent homologe with sequences in NCBI.
3. Online classification analysis was done on the known functional genes andhypothetical genes, and found that these genes were involved in a variety of biologicalprocesses. By real-time PCR, we analysis the mRNA expression of fourteen differentiallyexpressed genes, the results showed that thirteen of the genes are consistent with screeningof library, including eleven up-regulated genes, which are SERF2, ATP6, NDUFS4,SERPINF1, h142, ACSL1, ADFP, ACADM, HNRNPA2B1, PDK4, P311, and twodown-regulated genes, which are AMPD1and PGK1.
4. Porcine NDUFS4cDNA was cloned by using RT-PCR and5′RACE. PorcineNDUFS4cDNA shares93.56%,92.99%,87.31%and86.55%identity in nucleotidesequence, and92.57%,90.29%,88.57%and86.29%homology in amino acid sequencewith those of cattle, human, mouse and rat, respectively. Tissue expression profile analysiswas carried out using tissue cDNAs of the Laiwu pig as the templates to perform real-timePCR and the results revealed that the pig NDUFS4gene was highly expressed in LD,spleen and kidney, moderately expressed in liver, backfat, brain and spinal cord, weaklyexpressed in heart, and hardly expressed in lung, stomach and large intestine. Real-timePCR demonstrated that the difference of expression was significant between the two breeds(P<0.05), which was higher in Laiwu pig than in Large White.
To sum up, we discussed IMF deposition mechanism of Laiwu Black pigs, constructedhigh, low IMF Laiwu Black and Laiwu Black, Large White forward and reverse SSHlibraries, and obtained some differentially expressed target genes, which may affect IMFdeposition. In addition, we firstly cloned the NDUFS4gene of pigs, and analyzed itsexpression profiles in tissues. Real-time PCR analysis indicated that the level of NDUFS4mRNA expression was higher in high IMF Laiwu Black group than in low IMF LaiwuBlack group, and in Laiwu Black than in Large White. The results laid an importantmolecular basis for further study of the pig muscle fat deposition and the geneticmechanism.
一、应用SSH技术构建了高IMF莱芜猪与低IMF莱芜猪正反消减杂交文库。正反向文库扩增后分别得到631和486个阳性克隆，PCR鉴定结果表明插入片段主要分布在0.1-1.0kb之间。使用反Northen斑点杂交技术对以高IMF莱芜猪为Tester，低IMF莱芜猪为Driver的正向文库进行筛选，得到97个阳性差异克隆，进行测序、聚类拼接后得到35条单一ESTs序列。将这些序列在NCBI中进行BLAST比对分析，发现其中有17条ESTs与已知功能基因高度同源，3条ESTs在猪上有预测序列，15条ESTs序列与未知功能的cDNA片段高度同源。
二、应用SSH技术构建了莱芜猪与大白猪正反抑制性消减杂交文库。正反向文库扩增后分别得到1039和856个阳性克隆，PCR鉴定结果表明插入片段主要分布在0.1-2kb之间。使用反Northen斑点杂交技术对正反向文库进行筛选，以莱芜猪为Tester，大白猪为Driver的正向文库中获得154个阳性差异克隆，以大白猪为Tester，莱芜猪为Driver的反向文库中获得93个阳性克隆。进行测序、聚类拼接后，正向文库得到83条单一的ESTs序列，反向文库获得55条单一ESTs。在NCBI中进行BLAST比对分析后发现，正向文库中有33条ESTs与已知功能基因高度同源，15条ESTs在猪上有预测序列，25条ESTs序列与未知功能的cDNA片段高度同源，另有10条ESTs未找到明显的同源序列；反向文库中有21条ESTs与已知功能基因高度同源，8条ESTs在猪上有预测序列，18条ESTs序列与未知功能的cDNA片段高度同源，另有8条ESTs未找到明显的同源序列。
三、对与已知功能基因以及有预测序列的基因进行在线分类分析，发现这些基因参与了多种生物学过程；对其中的部分基因或ESTs进行了real-time PCR的验证，有13个基因或EST与文库筛选结果一致，其中上调基因11个，分别是：SERF2、ATP6、NDUFS4、SERPINF1、h142（EST）、ACSL1、ADFP、ACADM、HNRNPA2B1、PDK4、P311基因，下调基因2个，分别是：AMPD1和PGK1基因。
四、通过RT-PCR及RACE技术，我们得到了猪NDUFS4基因完整的cDNA序列。猪NDUFS4基因编码区核苷酸序列与人、小鼠、牛、大鼠的同源性分别为：92.99%、87.31%、93.56%、86.55%。猪NDUFS4基因氨基酸序列与牛的同源性最高为92.57%，与人、小鼠、大鼠的同源性分别为90.29%、88.57%、86.29%。对猪NDUFS4基因的在11种组织中的表达谱分析发现，该基因在检测组织中呈特异性表达，在背最长肌、脾脏、肾脏中高表达，肝脏、背膘、脑、脊髓中中度表达，心脏中低表达，肺、胃和大肠中几乎不表达。试验还对莱芜猪、大白猪背最长肌组织中NDUFS4基因mRNA的表达情况进行了real-time PCR的分析，结果表明莱芜猪中NDUFS4基因的mRNA表达量显著高于大白猪。
综上所述，本研究对莱芜猪IMF沉积的机理进行了探讨，构建了高、低IMF莱芜猪和莱芜猪、大白猪抑制性消减杂交文库，经过筛选获得了一些在猪背最长肌中表达，并与IMF沉积有关的差异基因。另外首次克隆了猪NDUFS4基因并对其组织表达进行了分析，证明了NDUFS4基因分别在高、低IMF含量莱芜猪和莱芜猪、大白猪中的mRNA表达水平存在差异。所得研究结果为进一步揭示猪背最长肌中IMF沉积与遗传机理奠定了重要的分子基础。
Intramuscular fat (IMF) content, correlated positively with meat tenderness, juiciness,and taste in pigs, has been revealed to be a major determinant factor affecting sensory meatquality. Conventional breeding is difficult to be carried out, because the IMF content isdifficult to measure in vivo and in piglet. At present, people conducted a large number ofstudies to explore the mechanism of IMF deposition in view of nutritional and genetic point.However, the nutritional control can only improve the IMF deposition, and the key geneaffecting IMF deposition has not yet been determined. Thus, this study was aimed atscreening the genes related to IMF deposition, to further reveal the molecular mechanism ofthe IMF deposition. Laiwu pig and Large White were used to construct high, low IMFLaiwu pig and Laiwu pig, Large White forward and reverse suppression subtractivehybridization (SSH) libraries to identify differentially expressed target genes, and some ofthese genes were varified by real-time PCR. In addition, studies of cloning and expressionwere done in pig NDUFS4gene. The main results are as follows:
1. High IMF Laiwu pig and low IMF Laiwu pig positive and negative cDNA librarieswere constructed by using SSH technology.631and486positive clones were obtainedfrom positive and reverse cDNA libraries, respectively. The PCR results showed that theinserted fragments are mainly distributed in the0.1-1.0kb. Forward library, in which highIMF Laiwu Black was Tester and low IMF Laiwu Black was Driver, was screened byreverse Northen blot.35ESTs was obtained from97positive differancial clones throughsequencing. By analysis of BLAST alignment in NCBI, the differential expression geneswere divided to17known functional genes,3hypothetical genes and15unknownsequences.
2. Laiwu pig and Large White positive and negative cDNA libraries were constructedby using SSH technology.1039and856positive clones were obtained from positive andreverse cDNA library, respectively. The PCR results showed that the inserted fragments aremainly distributed in the0.1-2.0kb. Forward library, in which Laiwu pig was Tester andLarge White was Driver, and reverse library, in which Large White was Tester and Laiwupig was Driver, were screened by reverse Northen blot.83and55ESTs were obtained from154and93positive differantial clone through sequencing, respectively. By analysis ofBLAST alignment in NCBI, these differential expression genes in positive library were divided to33known functional genes,15hypothetical genes,25unknown sequences and10ESTs which have no apparent homologe with sequences in NCBI; while in reverselibrary that were divided to21known functional genes,8hypothetical genes,18unknownsequences and8ESTs which have no apparent homologe with sequences in NCBI.
3. Online classification analysis was done on the known functional genes andhypothetical genes, and found that these genes were involved in a variety of biologicalprocesses. By real-time PCR, we analysis the mRNA expression of fourteen differentiallyexpressed genes, the results showed that thirteen of the genes are consistent with screeningof library, including eleven up-regulated genes, which are SERF2, ATP6, NDUFS4,SERPINF1, h142, ACSL1, ADFP, ACADM, HNRNPA2B1, PDK4, P311, and twodown-regulated genes, which are AMPD1and PGK1.
4. Porcine NDUFS4cDNA was cloned by using RT-PCR and5′RACE. PorcineNDUFS4cDNA shares93.56%,92.99%,87.31%and86.55%identity in nucleotidesequence, and92.57%,90.29%,88.57%and86.29%homology in amino acid sequencewith those of cattle, human, mouse and rat, respectively. Tissue expression profile analysiswas carried out using tissue cDNAs of the Laiwu pig as the templates to perform real-timePCR and the results revealed that the pig NDUFS4gene was highly expressed in LD,spleen and kidney, moderately expressed in liver, backfat, brain and spinal cord, weaklyexpressed in heart, and hardly expressed in lung, stomach and large intestine. Real-timePCR demonstrated that the difference of expression was significant between the two breeds(P<0.05), which was higher in Laiwu pig than in Large White.
To sum up, we discussed IMF deposition mechanism of Laiwu Black pigs, constructedhigh, low IMF Laiwu Black and Laiwu Black, Large White forward and reverse SSHlibraries, and obtained some differentially expressed target genes, which may affect IMFdeposition. In addition, we firstly cloned the NDUFS4gene of pigs, and analyzed itsexpression profiles in tissues. Real-time PCR analysis indicated that the level of NDUFS4mRNA expression was higher in high IMF Laiwu Black group than in low IMF LaiwuBlack group, and in Laiwu Black than in Large White. The results laid an importantmolecular basis for further study of the pig muscle fat deposition and the geneticmechanism.
引文
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