甜瓜属人工异源四倍体Cucumis×hytivus早期世代表型与基因表达变化研究
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摘要
多倍体化是高等植物进化过程的重要阶段,是植物进化的主要动力之一。研究表明,异源多倍体在形成的早期可发生广泛的基因组构成和基因表达水平的变化,与此同时,异源多倍体形成早期也常表现出不同于其二倍体祖先、且不能用孟德尔定律解释的新表型,这些变化直接关系到物种的形成和稳定。分子标记及比较基因组学的发展为认识种间杂交和多倍体化进程提供了重要依据。前人研究天然异源多倍体进化过程中发生的种种变化主要是通过比较其与二倍体祖先的“候选”后代而进行的。但现有的天然异源多倍体大多数形成于成千上万年以前,基因组经历了长期的“多倍体二倍化”过程,其二倍体祖先也不断进化或已灭绝,因此很难确定它们在早期进化中发生的表型和基因表达变化的具体过程和机制。
新合成的异源多倍体及一些“年轻”的异源多倍体,由于其亲缘关系明晰,为准确、深入研究多倍体基因组进化及相关机制提供了良好的模式系统。通过这种模式系统,可以精确比较亲本二倍体种与人工异源多倍体早期世代间的表型和基因表达变化特点,从而为丰富多倍体物种进化理论提供重要的例证。本研究基于实验室已合成的甜瓜属人工异源四倍体C.×hytivus(2n=4x=38),比较研究了其早期世代间的形态学和细胞学变化特征、基因表达变化的特点和黄瓜por基因在异源四倍早期世代的表达和序列变化特征,探讨了异源多倍化引发以上变化的相关机制。具体如下：
1.甜瓜属人工异源四倍体C.×hytivus早期世代表型变化研究
研究了甜瓜属人工异源四倍体C.×hytivus早期四个自交世代S1-S4的主要形态学性状、花粉母细胞减数分裂过程中的染色体行为、雄配子发育和花粉育性的变化特征。形态学研究表明,形态学性状在世代间表现出明显的不稳定性,其中以节间长、侧枝数、叶片厚度、雄花花梗长和子房纵径的变异系数较大。伴随自交代数的增加,该异源多倍体叶片逐渐变薄,子房逐渐变短,其它性状的变化表现为无明显规律性。
减数分裂行为研究结果表明,花粉母细胞减数分裂中期Ⅰ的染色体构型以二价体为主,伴随着自交代数的增加,每个花粉细胞中平均所含二价体的比例逐渐增加,单价体、多价体等非二价体比例减少,含19个二价体的细胞数增加。四分体时期主要以四分孢子形态存在,并随着自交世代的增高,四分孢子所占比例逐渐增加,多分孢子比例逐渐减少。花粉活力分析表明花粉育性伴随着自交代数的增加而逐渐提高。以上结果表明,该异源四倍体在早期进化过程中,花粉母细胞减数分裂过程中的染色体配对行为和雄配子发育正向稳定性方向进化。
2.甜瓜属人工异源四倍体C.×hytivus早期世代基因表达变化特点研究
以甜瓜属人工异源四倍体C.×hytivus早期世代S1和S2及其二倍体亲本为试材,利用cDNA-AFLP和reverse-Northern blot技术比较分析了C.×hytivus中基因表达变化的特点,包括频率、时间和类型。结果发现,亲本基因在异源四倍体中大多能表达,部分基因表现为差异表达。本研究共检测到36个基因的表达发生变化,占检测总基因数的3.37%,其中29个表现为沉默,7个表现为激活。上述变化可发生于S1代或S2代。
对15个差异表达的片段进行了回收和测序,BLAST分析表明这些基因主要是rRNA和蛋白质编码基因。进一步的reverse-Northern blot验证了上述结果。综合cDNA-AFLP和reverse-Northern blot的分析结果将C.×hytivus中基因表达变化分为四种类型：双亲基因共沉默、栽培种基因沉默、野生种基因沉默和和基因激活表达,其中单亲基因沉默为主要类型。以上结果表明该甜瓜属异源四倍体在形成早期发生着快速的基因沉默和激活。
利用cDNA-SSCP技术分析了二倍体亲本中部分同源的rpl2基因在甜瓜属人工异源四倍体C.×hytivus早期四个自交世代S1-S4中表达水平的差异。结果发现,两个部分同源的rpl2基因在异源四倍体C.×hytivus中表达水平存在差异,黄瓜rpl2基因表达水平高于野生种rpl2基因,且在世代间有一定的变化。以上结果表明异源多倍化诱发了异源多倍体中部分同源基因表达水平的变化。
3.黄瓜por基因在甜瓜属人工异源四倍体C.×hytivus早期世代的表达和序列变化特征
为探明不同植物por基因的分子系统发生关系,本研究利用BLAST程序分析了不同物种间por基因cDNA序列和POR蛋白质的同源性,并利用MEGA 4.0软件构建了por基因树,分析了不同por基因间亲缘关系。结果发现,不同物种在por基因cDNA序列和POR氨基酸序列具有较高的保守性,表明不同物种的POR具有相同的功能。研究还发现,同一物种内不同的por基因的cDNA序列间存在较大的差异,并存在着物种间por基因的同源性高于物种内同源性的现象。
以甜瓜属人工异源四倍体C.×hytivus早期4个自交世代S1-S4及其二倍体亲本为材料,利用RT-PCR和序列比较技术研究了异源多倍化对黄瓜por基因分子进化的影响。基因表达分析表明,黄瓜por基因在异源四倍体的S1代发生了快速的沉默,从S2代起又重新表达,但在S3代和S4代,表达产物大小发生了变化。进一步的序列分析表明,单碱基置换包括2个转换和1个颠换分别发生于S1代和S3代。在S3代的转录物中发生了内含子滞留现象。以上结果表明,异源多倍化诱发了黄瓜por基因的快速沉默和突变,基因突变包括碱基置换和内含子滞留也是新合成多倍体中重复基因的进化模式。
Polyploidization is a prominent process and has played an important role in the evolutionary history of higher plants. Recent studies indicated that extensive changes of genome composition and gene expression occurred in the early stage of genome formation of allopolyploid, also, novel, non-Mendelian phenotypes arised in synthesized allopolyploids. These changes have played a significant role in the stabilization of newly formed species'genome. The development of molecular markers and comparative genomics have provide important basis for understanding of allopolyploidization. Studies on such changes of nature allopolyploids were compared to their candidate diploid progenitors. While nature allopolyploids formed thousands upon thousands years ago, their genomes have evolved for a long time, and diploid progenitors also have evolved or not existed. So it is difficult to expore the concrete information during allopolyploid evolution.
Newly synthesized allopolyploids and'young'allopolyploids can be a very useful model system to study allopolyploidization for their clear genetic relationship, and the information at the early stage can be obtained exactly. With the newly formed allopolyploids, the changes of phenotype and gene expression can be studied accurately compared to their diploid parents, which might help enriching the evolutionary theory of allopolyploidization. In this work, the characterization of changes of morphological traits, cytology behavior and gene expression in early generations of C.×hytivus were studied, and expression and sequence variation of cucumber por gene in C.×hytivus were also investigated. Some mechanisms resolved in these changes were discussed. The detailed results are as follows:
1. Changes of phenotype in early generations of the synthesized allotetraploid C.×hytivus
The characterization of changes of morphological traits, meiotic chromosome behavior and pollen fertility in early generations (S1-S4) of the synthesized allotetraploid C.×hytivus were studied. The results from observation of morphological traits indicated that these traits showed instability, and some traits including internodes'length, lateral branches, leaf thickness, pedicle length of male flower and ovary length showed high coefficient of variation; From S1 generation to S4 generation, the leaf thickness got to thinner, the ovary tended to shorter and the appearance of first female flower became later, while other traits showed variation without regularity.
Investigations on meiotic chromosome behavior showed that most meiotic chromosome configurations at metaphaseⅠphase were bivalents. The frequency of bivalent at metaphaseⅠincreased, from S1 generation to S4 generation, while which of univalent and multivalent decreased. The number of cells with nineteen bivalents also increased obviously; at metaphaseⅡ, the allotetraploid mainly produced tetrads, and the frequency of tetrads increased from S1 generation to S4 generation. Accordingly, pollen fertility was recovered generally. Above results indicated instability of morphological traits and diploidization of meiotic chromosome behavior in the evolution of early generations of the allotetraploid C.×hytivus.
2. Changes of gene expression in early generations of the synthesized allotetraploid C.×hytivus
Changes of gene expression played an important role in the evolution of plant allopolyploids. Characterization, including frequency, time and type of the changes of gene expression between the first two self-pollinated generations (S1 and S2) of the synthesized allotetraploid C.×hytivus and in its diploid parents was analyzed with cDNA-AFLP and reverse-Northern blot technique. Sequences similarity of genes involved in changed expression were also analyzed with BLAST package. The results from cDNA-AFLP analysis showed that 36 (3.37%) genes showed silencing (27) or activation (9) in allotetraploids. These changes initiated in S1 or S2 generation. The silenced/activated genes included rRNA and protein-coding genes. Further reverse-Northern blot analysis validated the above results. Thus four types of changes of gene expression were observed, including silencing of genes from both parents, maternal parent, paternal parent, and gene's novel expression. Above results indicated rapid gene silencing and activation in early generations of C.×hytivus, which contributed to the evolution of the allotetraploid.
Changes of expression level of homoeologous rpl2 gene from diploid parents were analyzed in early generations of allotetraploid C. x hytivus with cDNA-SSCP technique. The results indicated that homoeologous rpl2 genes showed different expression level in C. X hytivus. The expression level of gene from C. sativus was high than that from wide species C. hystrix, and it also showed instability in early generations. Above results indicated that allopolyploidy induced changes of expression level of homoeologous gene in allotetraploid C. x hytivus.
3. Expression and sequence variation of cucumber por gene in the newly synthesized allotetraploid C.×hytivus
The phylogeny of the plant por gene was investigated. Identities of cDNA sequence of Por gene and amino acid sequence of POR in some plant species were analyzed by BLAST, and gene tree was also constructed with MEGA software version 4.0. The results showed that cDNA and protein sequences were conservative in plant species, which indicating the common function of these genes. However, there also existed sequence difference of various por genes, and sometimes, identities of cDNA sequence of por genes from various species were higher than that from one species.
The molecular evolution of the cucumber por gene in early generations of the synthesized allotetraploid C. x hytivus was investigated. The results from gene expression analysis by RT-PCR showed that the cucumber por gene was silenced in the S1 generation, and re-activated in the S2 generation. In the S3 and S4 generations, the transcripts remained activated but sequence changes were observed. Further analysis indicated that base substitutions, including two transitions and one transversion, occurred in the S1 and S3 generation respectively, and in the S3 generation, an intron was found to be retained in the transcript. This indicates allopolyploidy induced rapid silencing and mutation of the cucumber por gene. Further, gene mutations such as base substitution and intron retention are also modes of evolution for duplicated genes in newly formed polyploid.
新合成的异源多倍体及一些“年轻”的异源多倍体,由于其亲缘关系明晰,为准确、深入研究多倍体基因组进化及相关机制提供了良好的模式系统。通过这种模式系统,可以精确比较亲本二倍体种与人工异源多倍体早期世代间的表型和基因表达变化特点,从而为丰富多倍体物种进化理论提供重要的例证。本研究基于实验室已合成的甜瓜属人工异源四倍体C.×hytivus(2n=4x=38),比较研究了其早期世代间的形态学和细胞学变化特征、基因表达变化的特点和黄瓜por基因在异源四倍早期世代的表达和序列变化特征,探讨了异源多倍化引发以上变化的相关机制。具体如下：
1.甜瓜属人工异源四倍体C.×hytivus早期世代表型变化研究
研究了甜瓜属人工异源四倍体C.×hytivus早期四个自交世代S1-S4的主要形态学性状、花粉母细胞减数分裂过程中的染色体行为、雄配子发育和花粉育性的变化特征。形态学研究表明,形态学性状在世代间表现出明显的不稳定性,其中以节间长、侧枝数、叶片厚度、雄花花梗长和子房纵径的变异系数较大。伴随自交代数的增加,该异源多倍体叶片逐渐变薄,子房逐渐变短,其它性状的变化表现为无明显规律性。
减数分裂行为研究结果表明,花粉母细胞减数分裂中期Ⅰ的染色体构型以二价体为主,伴随着自交代数的增加,每个花粉细胞中平均所含二价体的比例逐渐增加,单价体、多价体等非二价体比例减少,含19个二价体的细胞数增加。四分体时期主要以四分孢子形态存在,并随着自交世代的增高,四分孢子所占比例逐渐增加,多分孢子比例逐渐减少。花粉活力分析表明花粉育性伴随着自交代数的增加而逐渐提高。以上结果表明,该异源四倍体在早期进化过程中,花粉母细胞减数分裂过程中的染色体配对行为和雄配子发育正向稳定性方向进化。
2.甜瓜属人工异源四倍体C.×hytivus早期世代基因表达变化特点研究
以甜瓜属人工异源四倍体C.×hytivus早期世代S1和S2及其二倍体亲本为试材,利用cDNA-AFLP和reverse-Northern blot技术比较分析了C.×hytivus中基因表达变化的特点,包括频率、时间和类型。结果发现,亲本基因在异源四倍体中大多能表达,部分基因表现为差异表达。本研究共检测到36个基因的表达发生变化,占检测总基因数的3.37%,其中29个表现为沉默,7个表现为激活。上述变化可发生于S1代或S2代。
对15个差异表达的片段进行了回收和测序,BLAST分析表明这些基因主要是rRNA和蛋白质编码基因。进一步的reverse-Northern blot验证了上述结果。综合cDNA-AFLP和reverse-Northern blot的分析结果将C.×hytivus中基因表达变化分为四种类型：双亲基因共沉默、栽培种基因沉默、野生种基因沉默和和基因激活表达,其中单亲基因沉默为主要类型。以上结果表明该甜瓜属异源四倍体在形成早期发生着快速的基因沉默和激活。
利用cDNA-SSCP技术分析了二倍体亲本中部分同源的rpl2基因在甜瓜属人工异源四倍体C.×hytivus早期四个自交世代S1-S4中表达水平的差异。结果发现,两个部分同源的rpl2基因在异源四倍体C.×hytivus中表达水平存在差异,黄瓜rpl2基因表达水平高于野生种rpl2基因,且在世代间有一定的变化。以上结果表明异源多倍化诱发了异源多倍体中部分同源基因表达水平的变化。
3.黄瓜por基因在甜瓜属人工异源四倍体C.×hytivus早期世代的表达和序列变化特征
为探明不同植物por基因的分子系统发生关系,本研究利用BLAST程序分析了不同物种间por基因cDNA序列和POR蛋白质的同源性,并利用MEGA 4.0软件构建了por基因树,分析了不同por基因间亲缘关系。结果发现,不同物种在por基因cDNA序列和POR氨基酸序列具有较高的保守性,表明不同物种的POR具有相同的功能。研究还发现,同一物种内不同的por基因的cDNA序列间存在较大的差异,并存在着物种间por基因的同源性高于物种内同源性的现象。
以甜瓜属人工异源四倍体C.×hytivus早期4个自交世代S1-S4及其二倍体亲本为材料,利用RT-PCR和序列比较技术研究了异源多倍化对黄瓜por基因分子进化的影响。基因表达分析表明,黄瓜por基因在异源四倍体的S1代发生了快速的沉默,从S2代起又重新表达,但在S3代和S4代,表达产物大小发生了变化。进一步的序列分析表明,单碱基置换包括2个转换和1个颠换分别发生于S1代和S3代。在S3代的转录物中发生了内含子滞留现象。以上结果表明,异源多倍化诱发了黄瓜por基因的快速沉默和突变,基因突变包括碱基置换和内含子滞留也是新合成多倍体中重复基因的进化模式。
Polyploidization is a prominent process and has played an important role in the evolutionary history of higher plants. Recent studies indicated that extensive changes of genome composition and gene expression occurred in the early stage of genome formation of allopolyploid, also, novel, non-Mendelian phenotypes arised in synthesized allopolyploids. These changes have played a significant role in the stabilization of newly formed species'genome. The development of molecular markers and comparative genomics have provide important basis for understanding of allopolyploidization. Studies on such changes of nature allopolyploids were compared to their candidate diploid progenitors. While nature allopolyploids formed thousands upon thousands years ago, their genomes have evolved for a long time, and diploid progenitors also have evolved or not existed. So it is difficult to expore the concrete information during allopolyploid evolution.
Newly synthesized allopolyploids and'young'allopolyploids can be a very useful model system to study allopolyploidization for their clear genetic relationship, and the information at the early stage can be obtained exactly. With the newly formed allopolyploids, the changes of phenotype and gene expression can be studied accurately compared to their diploid parents, which might help enriching the evolutionary theory of allopolyploidization. In this work, the characterization of changes of morphological traits, cytology behavior and gene expression in early generations of C.×hytivus were studied, and expression and sequence variation of cucumber por gene in C.×hytivus were also investigated. Some mechanisms resolved in these changes were discussed. The detailed results are as follows:
1. Changes of phenotype in early generations of the synthesized allotetraploid C.×hytivus
The characterization of changes of morphological traits, meiotic chromosome behavior and pollen fertility in early generations (S1-S4) of the synthesized allotetraploid C.×hytivus were studied. The results from observation of morphological traits indicated that these traits showed instability, and some traits including internodes'length, lateral branches, leaf thickness, pedicle length of male flower and ovary length showed high coefficient of variation; From S1 generation to S4 generation, the leaf thickness got to thinner, the ovary tended to shorter and the appearance of first female flower became later, while other traits showed variation without regularity.
Investigations on meiotic chromosome behavior showed that most meiotic chromosome configurations at metaphaseⅠphase were bivalents. The frequency of bivalent at metaphaseⅠincreased, from S1 generation to S4 generation, while which of univalent and multivalent decreased. The number of cells with nineteen bivalents also increased obviously; at metaphaseⅡ, the allotetraploid mainly produced tetrads, and the frequency of tetrads increased from S1 generation to S4 generation. Accordingly, pollen fertility was recovered generally. Above results indicated instability of morphological traits and diploidization of meiotic chromosome behavior in the evolution of early generations of the allotetraploid C.×hytivus.
2. Changes of gene expression in early generations of the synthesized allotetraploid C.×hytivus
Changes of gene expression played an important role in the evolution of plant allopolyploids. Characterization, including frequency, time and type of the changes of gene expression between the first two self-pollinated generations (S1 and S2) of the synthesized allotetraploid C.×hytivus and in its diploid parents was analyzed with cDNA-AFLP and reverse-Northern blot technique. Sequences similarity of genes involved in changed expression were also analyzed with BLAST package. The results from cDNA-AFLP analysis showed that 36 (3.37%) genes showed silencing (27) or activation (9) in allotetraploids. These changes initiated in S1 or S2 generation. The silenced/activated genes included rRNA and protein-coding genes. Further reverse-Northern blot analysis validated the above results. Thus four types of changes of gene expression were observed, including silencing of genes from both parents, maternal parent, paternal parent, and gene's novel expression. Above results indicated rapid gene silencing and activation in early generations of C.×hytivus, which contributed to the evolution of the allotetraploid.
Changes of expression level of homoeologous rpl2 gene from diploid parents were analyzed in early generations of allotetraploid C. x hytivus with cDNA-SSCP technique. The results indicated that homoeologous rpl2 genes showed different expression level in C. X hytivus. The expression level of gene from C. sativus was high than that from wide species C. hystrix, and it also showed instability in early generations. Above results indicated that allopolyploidy induced changes of expression level of homoeologous gene in allotetraploid C. x hytivus.
3. Expression and sequence variation of cucumber por gene in the newly synthesized allotetraploid C.×hytivus
The phylogeny of the plant por gene was investigated. Identities of cDNA sequence of Por gene and amino acid sequence of POR in some plant species were analyzed by BLAST, and gene tree was also constructed with MEGA software version 4.0. The results showed that cDNA and protein sequences were conservative in plant species, which indicating the common function of these genes. However, there also existed sequence difference of various por genes, and sometimes, identities of cDNA sequence of por genes from various species were higher than that from one species.
The molecular evolution of the cucumber por gene in early generations of the synthesized allotetraploid C. x hytivus was investigated. The results from gene expression analysis by RT-PCR showed that the cucumber por gene was silenced in the S1 generation, and re-activated in the S2 generation. In the S3 and S4 generations, the transcripts remained activated but sequence changes were observed. Further analysis indicated that base substitutions, including two transitions and one transversion, occurred in the S1 and S3 generation respectively, and in the S3 generation, an intron was found to be retained in the transcript. This indicates allopolyploidy induced rapid silencing and mutation of the cucumber por gene. Further, gene mutations such as base substitution and intron retention are also modes of evolution for duplicated genes in newly formed polyploid.
引文
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