水稻广亲和基因S5-n和光敏核不育基因pms3功能分析及作用机理研究，以及水稻Hsp20基因家族分析
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摘要
水稻籼粳亚种间具有比品种间更强的杂种优势,但籼粳亚种间杂种的不育性限制了对其杂种优势的利用。在水稻中存在一类特殊的种质资源称为广亲和品种,它们分别与籼稻和粳稻杂交,其后代均表现正常可育。S5基因位于水稻第6染色体上,它是控制籼粳广亲和性状的一个主效基因。本研究的目的就是分离克隆水稻广亲和基因S5,并对该基因功能、作用机理及其参与水稻生殖隔离的调控机制做出研究。在以前的工作基础上,本研究成功分离克隆水稻广亲和基因S5,并通过RACE技术分别获得在籼稻、粳稻和广亲和品种中S5等位基因的全长cDNA。在核苷酸与蛋白水平上比较籼稻、粳稻和广亲和品种的基因结构发现籼稻和粳稻的编码区段只有两个碱基的差别,引起相应蛋白质两个氨基酸的替换。对应广亲和品种的S5等位基因(广亲和基因)蛋白N-端缺失导致功能丧失。BLASTp分析表明S5基因编码蛋白与天冬氨酸蛋白酶高度同源。来源于CERP(http://crep.ncpgr.cn/)芯片表达谱数据表明S5基因在全生育期都极低水平表达。通过RT-PCR分别检测S5基因在三个亲本幼穗发育不同时期组织中的表达量,结果表明该基因在叶片中极低水平表达而在幼穗中表达量相对较高。使用Real-time PCR对不同亲本和杂交组合F_1代S5表达量进行检测,结果表明不同亲本和杂种中S5的表达差异显著。使用Real-time PCR检测S5基因在55个不同基因型材料中的表达量,并对其中13个杂交组合F_1代胚囊育性做出统计。结果表明S5基因表达量与水稻品种不相关。其中杂交组合F_1代材料胚囊育性和小穗育性正相关,但是和S5基因表达量不相关。这些结果表明S5基因通过控制雌配子发育影响亚种间杂种的结实率,但这种调控机制和该基因表达量高低无关。
光敏感雄性核不育水稻农垦58S具有长日高温不育、短日低温可育的特点,是发展水稻“两系”法育种的重要种质资源。此前的研究中光敏感核不育基因pms3已被限定在一段28.4kb的范围内,且该范围内有且仅有一个SNP。本研究的目的就是进一步确定pms3的候选基因并对其功能和作用机制做出研究。通过生物信息学方法对目标区段进行分析,针对预测的候选基因Gene M设计引物,通过RT-PCR扩增出所对应cDNA并测序验证。进一步RT-PCR分析获得Gene M的四个转录本在58S和58N以及在长日照和短日照幼穗发育不同时期不同组织中的表达谱信息。对SNP附近序列随机设计引物扩增发现该位点上存在一个表达的EST,Gene EST。通过RACE技术获得Gene EST全长eDNA,结果表明Gene EST的5'端与Gene M中的一个转录本GENE M3的3'端部分序列重叠。通过Real-time PCR对Gene EST和GENE M3在58S和58N以及在长日照和短日照不同发育时期的幼穗中进行表达谱分析,结果表明Gene EST在幼穗6期高表达。原位杂交结果表明Gene EST和GENEM3均在幼穗中表达。这些结果为进一步确定候选基因并阐明其作用机制提供基础。
Hsp20基因是植物热激蛋白家族中最大的一类家族成员,它参与热激反应和多种抗逆反应,并对许多环境因子做出应答。迄今为止,对水稻Hsp20基因的研究非常有限,且尚未有对Hsp20整个基因家族做出系统研究的报道。本研究一一列举出水稻中39个OsHsp20基因,对它们的基因结构、表达、染色体定位以及进化关系作了系统的分析,并通过RT-PCR对部分OsHsp20基因受热激诱导的反应做出研究。与此同时,本研究在三个水稻品种的25个发育时期中对OsHsp20基因进行了系统的表达聚类分析。分析结果表明OsHsp20基因在营养生长时期和生殖生长时期差异表达,且在汕优63中下降差异表达基因增加。进一步研究表明整个OsHsp20家族在汕优63中都表现出杂种优势。这些结果表明OsHsp20基因不仅在不同发育时期差异表达,在不同品种间也表现出不同的表达趋势。
Hybrids between indica and japonica varieties demonstrate stronger hybrid vigor,but the partial sterility observed in the hybrids blocks the utility.A special group of rice germplasm,referred to as wide compatibility varieties,is able to produce highly fertile hybrids when crossed to both indica and japonica.S5 is a major locus for indica-japonica hybrid sterility and wide compatibility,and was previously located on chromosome 6.The objective of our study was to clone S5,which was referred to as a wide compatibility gene, and characterize the function and molecular mechanism of this gene.In this study,we cloned S5 and obtained the full length cDNA sequence of the different alleles by RACE in three cultivars.The S5 gene is comprised of three exons and two introns.The indica(S5-i) and japonica(S5-j) alleles differ by two nucleotides.The wide compatibility gene(S5-n) has a large deletion in the N-terminus of the predicted S5 protein,causing subcellular mislocalization of the protein,and thus is presumably nonfunctional.BLASTp analysis showed that S5 encodes an aspartic protease.We searched a dataset of whole-genome expression arrays spanning the entire life cycle and the result showed that expression of S5 was extremely low throughout the life cycle.We also analyzed the expression of S5 in the developing panicles during different stages in comparison with the leaves harvested at the corresponding stages.S5 expression was not detectable in leaves,whereas variable levels of expression were observed in the developing panicles in all three genotypes, Balilla,Nanjing 11,and 02428.Real-time PCR was used to compare the S5 expression levels in different parents and their hybrids in certain stage.The analysis revealed significant differences in S5 expression among the parents as well as among the hybrids. Real-time PCR was also performed using developing panicles at stage 6 to compare the S5 expression levels in 55 cultivars.The result showed that the S5 expression levels were not relevant to different varieties.We examined the embryo fertility in 13 hybrids,and the analysis revealed that the embryo fertility was positive relevant to spikelet fertility,but not relevant to the S5 expression levels.These results showed that S5 affected the indica-japonica grain production by conditioning embryo-sac fertility and the expression level of S5 was not essential in this progress.
Photoperiod-sensitive genie male sterility(PSGMS) rice Nongken 58S,which under long-day condition is sterile while under short-day condition is fertile,is a very important germplasm to develop the "two-line" hybrid in rice breeding program.Previous studies have delimited pms3 to a 28.4kb DNA fragment containing only one SNP.The objective of our study was to determine the pms3 candidate and characterize the function and molecular mechanism of it.Sequence analysis of this fragment in database predicted the presence of Gene M.RT-PCR was performed to confirm the cDNAs by sequencing. Further analysis by RT-PCR showed that the four transcripts of Gene M expressed differently in different conditions in 58S and 58N.Primers were designed randomly near the SNP locus and an expression EST was found crossing the SNP,which was named as Gene SNP.We obtained the full length cDNA sequence of the Gene SNP by RACE. Interestingly,the 5' fragment of Gene SNP was overlapped with the 3' end of GENE M3, one of the transcripts in Gene M.Real-time PCR was performed to exam the expression level of Gene SNP and GENE M3 in panicles in different developmental stages,and the result showed that Gene SNP was highly expressed in stage 6 in panicle.In situ hybridization showed that Gene SNP and GENE M3 were expressed in young panicles. These results may be helpful for identifying the candidate genes of pms3 and provide a basal approach for the mechanism of pms3.
The Hsp20 genes represent the most abundant small heat shock proteins in plants. Hsp20 gene family has been shown to be involved in preventing heat shock and promoting resistance to environmental stressors,but very little is known about this gene family in rice.Here,we report the identification and characterization of 39 OsHsp20 genes in rice,describing the gene structure,gene expression,genome localization,and phylogenetic relationship of each member.We have used RT-PCR to perform a characterization of the normal and heat shock-induced expression of selective OsHsp20 genes.A dataset of whole-genome expression arrays spanning the entire life cycle involving 25 stages in 3 rice cultivars has revealed that 36 OsHsp20 genes were expressed in at least one of the experimental stages studied.Among these,transcripts for OsHsp20 were accumulated differentially during vegetative and reproductive developmental stages and preferentially down-regulated in Shanyou 63.Meanwhile,OsHsp20 genes were identified as showing prominent heterosis in family-level.Our results suggest that the expression patterns of the OsHsp20 genes are diversified not only in development but also in variety level.
光敏感雄性核不育水稻农垦58S具有长日高温不育、短日低温可育的特点,是发展水稻“两系”法育种的重要种质资源。此前的研究中光敏感核不育基因pms3已被限定在一段28.4kb的范围内,且该范围内有且仅有一个SNP。本研究的目的就是进一步确定pms3的候选基因并对其功能和作用机制做出研究。通过生物信息学方法对目标区段进行分析,针对预测的候选基因Gene M设计引物,通过RT-PCR扩增出所对应cDNA并测序验证。进一步RT-PCR分析获得Gene M的四个转录本在58S和58N以及在长日照和短日照幼穗发育不同时期不同组织中的表达谱信息。对SNP附近序列随机设计引物扩增发现该位点上存在一个表达的EST,Gene EST。通过RACE技术获得Gene EST全长eDNA,结果表明Gene EST的5'端与Gene M中的一个转录本GENE M3的3'端部分序列重叠。通过Real-time PCR对Gene EST和GENE M3在58S和58N以及在长日照和短日照不同发育时期的幼穗中进行表达谱分析,结果表明Gene EST在幼穗6期高表达。原位杂交结果表明Gene EST和GENEM3均在幼穗中表达。这些结果为进一步确定候选基因并阐明其作用机制提供基础。
Hsp20基因是植物热激蛋白家族中最大的一类家族成员,它参与热激反应和多种抗逆反应,并对许多环境因子做出应答。迄今为止,对水稻Hsp20基因的研究非常有限,且尚未有对Hsp20整个基因家族做出系统研究的报道。本研究一一列举出水稻中39个OsHsp20基因,对它们的基因结构、表达、染色体定位以及进化关系作了系统的分析,并通过RT-PCR对部分OsHsp20基因受热激诱导的反应做出研究。与此同时,本研究在三个水稻品种的25个发育时期中对OsHsp20基因进行了系统的表达聚类分析。分析结果表明OsHsp20基因在营养生长时期和生殖生长时期差异表达,且在汕优63中下降差异表达基因增加。进一步研究表明整个OsHsp20家族在汕优63中都表现出杂种优势。这些结果表明OsHsp20基因不仅在不同发育时期差异表达,在不同品种间也表现出不同的表达趋势。
Hybrids between indica and japonica varieties demonstrate stronger hybrid vigor,but the partial sterility observed in the hybrids blocks the utility.A special group of rice germplasm,referred to as wide compatibility varieties,is able to produce highly fertile hybrids when crossed to both indica and japonica.S5 is a major locus for indica-japonica hybrid sterility and wide compatibility,and was previously located on chromosome 6.The objective of our study was to clone S5,which was referred to as a wide compatibility gene, and characterize the function and molecular mechanism of this gene.In this study,we cloned S5 and obtained the full length cDNA sequence of the different alleles by RACE in three cultivars.The S5 gene is comprised of three exons and two introns.The indica(S5-i) and japonica(S5-j) alleles differ by two nucleotides.The wide compatibility gene(S5-n) has a large deletion in the N-terminus of the predicted S5 protein,causing subcellular mislocalization of the protein,and thus is presumably nonfunctional.BLASTp analysis showed that S5 encodes an aspartic protease.We searched a dataset of whole-genome expression arrays spanning the entire life cycle and the result showed that expression of S5 was extremely low throughout the life cycle.We also analyzed the expression of S5 in the developing panicles during different stages in comparison with the leaves harvested at the corresponding stages.S5 expression was not detectable in leaves,whereas variable levels of expression were observed in the developing panicles in all three genotypes, Balilla,Nanjing 11,and 02428.Real-time PCR was used to compare the S5 expression levels in different parents and their hybrids in certain stage.The analysis revealed significant differences in S5 expression among the parents as well as among the hybrids. Real-time PCR was also performed using developing panicles at stage 6 to compare the S5 expression levels in 55 cultivars.The result showed that the S5 expression levels were not relevant to different varieties.We examined the embryo fertility in 13 hybrids,and the analysis revealed that the embryo fertility was positive relevant to spikelet fertility,but not relevant to the S5 expression levels.These results showed that S5 affected the indica-japonica grain production by conditioning embryo-sac fertility and the expression level of S5 was not essential in this progress.
Photoperiod-sensitive genie male sterility(PSGMS) rice Nongken 58S,which under long-day condition is sterile while under short-day condition is fertile,is a very important germplasm to develop the "two-line" hybrid in rice breeding program.Previous studies have delimited pms3 to a 28.4kb DNA fragment containing only one SNP.The objective of our study was to determine the pms3 candidate and characterize the function and molecular mechanism of it.Sequence analysis of this fragment in database predicted the presence of Gene M.RT-PCR was performed to confirm the cDNAs by sequencing. Further analysis by RT-PCR showed that the four transcripts of Gene M expressed differently in different conditions in 58S and 58N.Primers were designed randomly near the SNP locus and an expression EST was found crossing the SNP,which was named as Gene SNP.We obtained the full length cDNA sequence of the Gene SNP by RACE. Interestingly,the 5' fragment of Gene SNP was overlapped with the 3' end of GENE M3, one of the transcripts in Gene M.Real-time PCR was performed to exam the expression level of Gene SNP and GENE M3 in panicles in different developmental stages,and the result showed that Gene SNP was highly expressed in stage 6 in panicle.In situ hybridization showed that Gene SNP and GENE M3 were expressed in young panicles. These results may be helpful for identifying the candidate genes of pms3 and provide a basal approach for the mechanism of pms3.
The Hsp20 genes represent the most abundant small heat shock proteins in plants. Hsp20 gene family has been shown to be involved in preventing heat shock and promoting resistance to environmental stressors,but very little is known about this gene family in rice.Here,we report the identification and characterization of 39 OsHsp20 genes in rice,describing the gene structure,gene expression,genome localization,and phylogenetic relationship of each member.We have used RT-PCR to perform a characterization of the normal and heat shock-induced expression of selective OsHsp20 genes.A dataset of whole-genome expression arrays spanning the entire life cycle involving 25 stages in 3 rice cultivars has revealed that 36 OsHsp20 genes were expressed in at least one of the experimental stages studied.Among these,transcripts for OsHsp20 were accumulated differentially during vegetative and reproductive developmental stages and preferentially down-regulated in Shanyou 63.Meanwhile,OsHsp20 genes were identified as showing prominent heterosis in family-level.Our results suggest that the expression patterns of the OsHsp20 genes are diversified not only in development but also in variety level.
引文
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