芸薹属种间关系及其人工合成甘蓝型油菜早期世代蛋白质组学的研究
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摘要
芸薹属(Brassica)是十字花科(Cruciferae)植物中最为重要的一属,具有重要的经济价值。本研究采用细胞遗传学、分子生物学以及蛋白质组学等方法,对芸薹属中的A和C基本种及人工合成甘蓝型油菜形成过程中蛋白质组的变化规律进行研究,从而为异源四倍体物种的形成及其表观遗传学的研究提供重要的理论依据。主要研究结果如下:
1.基本种45S rDNA重复序列的有丝分裂与减数分裂的FISH定位分析
利用荧光原位杂交(FISH)技术,以标记的45S rDNA重复序列作探针,研究了芸薹属3个基本种Brassica rapa,B. oleracea与B. nigra的根尖体细胞中期染色体杂交信号的分布特点、花粉母细胞减数分裂粗线期染色体的空间分布、终变期染色体的配对构型等。研究结果表明B. rapa的10条(5对)染色体上表现明显而强烈的杂交信号,且分布在着丝粒和亚着丝粒区域;B. nigra的6条(3对)染色体上有杂交信号,主要分布在染色体短臂的近末端处,减数分裂后期I中,3个信号平均分配到细胞两极;B. oleracea中的4个45S rDNA杂交位点与B. nigra中类似,都位于染色体短臂的近末端处。其中B. rapa与B. nigra的45S rDNA的花粉母细胞的减数分裂FISH定位是首次报道。该结果旨在为研究A、B、C基因组间的亲缘关系和进化提供细胞学依据。
2.着丝粒重复序列FISH及CAPS分析芸薹属A、B和C基因组间的关系
以来源于B. rapa基因组(AA)的重复序列(151bp)为探针,分别同二倍体白菜型油菜、甘蓝和异源四倍体芥菜型油菜(AABB,2n=36)的中期染色体杂交,白菜型油菜和甘蓝的所有染色体上都有杂交信号,芥菜型油菜的染色体上显示出20个明显的信号,其余染色体上信号弱或无,可以区分出A与B基因组。对来源于油菜3个基本种与3个复合种FAE1基因进行CAPS分析表明,3个基本种表现出不同的酶切式样,用MboI和MspI酶切表现出多态性,基因组A和C非常相似,而基因组B与A、C关系较远,同时3个复合种也并不是2个基本种的简单相加,表明异源四倍体在进化过程中可能发生了重排和重组。
3.基本种与复合种间种子贮藏蛋白质亚基构成及聚类分析
根据种子贮藏蛋白形成的蛋白质谱带具有的稳定性、均匀性和可加性的特点,对组成芸薹属3个基本种和3个复合种的种子贮藏蛋白亚基的组成进行了SDS-PAGE比较分析,结果表明:不同种间的种子贮藏蛋白具有一定的差异,表现出丰富的多态性;6个种共有24条亚基带,并各自具有特有的蛋白谱带。利用贮藏蛋白亚基条带的信息,分析了种间的蛋白相似度,并进行了聚类分析,将供试材料分为两类。Ⅰ类为白菜型油菜、甘蓝与甘蓝型油菜。Ⅱ类为为黑芥、芥菜型油菜和埃塞俄比亚芥。
4.芸薹属A、C基因组间比较蛋白质组学的分析及PCR分子标记的开发
白菜和甘蓝亲缘关系非常接近。运用蛋白质组学方法比较了芸薹属二倍体种白菜型油菜(AA)和甘蓝(CC)幼苗期叶片蛋白质组学的变化,通过比较研究,以期探寻它们在蛋白组水平上基因表达特征。应用双向电泳对叶片总蛋白进行了分离,从2-D凝胶上各检测到95与111个蛋白点,应用PDQuest软件对凝胶图谱进行分析,二者间匹配到的蛋白质点数为29,占总数的28.2%,其中芸薹与甘蓝的的专化蛋白分别66和82个,分别占蛋白点总数的32.0 %与39.8 %。MALDI-TOF-MS质谱分析和数据库检索鉴定了其中的20个差异表达蛋白,但可靠差异蛋白的鉴定率仅为50%。该研究首次基于两个物种的特征(差异)蛋白,开发出10个用于区分A和C基因组的基于PCR的分子标记。
5.利用差异蛋白质组对人工合成甘蓝型油菜F1及早期世代蛋白质变化的研究
多倍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会出现广泛的基因组遗传和表观遗传变化,这些变化直接关系到物种的形成和稳定。人工合成的异源多倍体则为这方面的研究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基因组变化特点,从而为丰富多倍体物种进化理论提供重要的理论依据。本研究基于人工合成的异源四倍体甘蓝型油菜及其不同自交后代,比较研究杂种F1与双亲间、以及早期1~4代间的的叶片蛋白质组变化,探索种间杂交及其多倍体形成后引发的遗传和表观遗传变化的规律。具体结果如下:
(1)人工合成甘蓝型油菜F1及其亲本叶片比较蛋白质组学研究
以芸薹属二倍体B . rapa (AA,2n = 20)和B . oleracea(CC,2n =18)和人工合成甘蓝型油菜为实验材料,由于双亲及后代遗传背景清晰,为研究异源多倍体早期基因组在进化过程中的具体变化提供了良好的实验材料。结合蛋白质组学方法来解析新合成的B. napus F1代与其双亲叶片蛋白质组表达差异,鉴定了一些有价值的蛋白点。首先是亲本间的差异蛋白质几乎都在B. napus中表达,但显著偏离双亲丰度表达均值,表现为非加性表达效应。此外经MALDI-TOF-MS鉴定了杂种中7个有显著性意义的蛋白,其中1个与光合作用相关,推定为景天庚酮糖-1,7-二磷酸酶;2种与能量代谢相关的ATP合酶β-亚基;1个与物质代谢相关ADP-葡萄糖焦磷酸化酶小亚基;1个与转录相关的RNA聚合酶β-链;另1个与抗病相关的丝氨酸/苏氨酸蛋白激酶与1个假定蛋白。这些蛋白与具有杂合子潜力的杂种优势相关,为了解杂种优势在蛋白质组水平上的基因表达基础积累了重要的资料,是前人在转录水平上研究的必要补充,从而为进一步阐明杂种优势的机制提供理论依据。此外实验还表明B. napus在多倍化后可能发生了基因重组,并且新蛋白的功能可能会影响F1杂种的表型性状。
(2)人工合成甘蓝型油菜早期世代蛋白质组的变化
我们对人工合成甘蓝型油菜1~4代叶片蛋白质进行了比较分析发现,在后代中发生了非孟德尔式的表观遗传变异,变异主要表现为基因沉默的方式。依据蛋白表达变化特点将F1~F4的差异蛋白质归为五类:1)F2专化类型;2)F3专化类型;3)F1中丢失的蛋白,而F2~F4中表达的类型;4)F1~F2丢失,而F3~F4中表达的类型;5)F1~F4中蛋白丰度逐渐上调的类型。表明丢失的蛋白可能并不是真正的丢失,而可能是发生了基因沉默,而且基因沉默随时可能被激活。在已鉴定的蛋白中,有与物质与能量代谢、信号转导、解毒酶类、蛋白质降解、反转座子相关以及功能未知的假定蛋白。统计后分析尽管基因组早1~4代中发生了随机表观遗传变异,但保证细胞正常基因功能的持家蛋白并没有随基因表达的变化而完全消失,也间接证明了早期多倍化事件中的基因组冲击未必带来蛋白质组上的冲击。相反会有一个新的快速的协调顺序进化在新合成的异源甘蓝型油菜中。
Brassica is the third largest oilseed crop in the world, providing approximately 13% of the world’s supply of vegetable oil. The relationship between three diploids and three allotetraploids was demonstrated in a classical cytogenetic study by U; this relationship is commonly referred to as the“U triangle”. On our research, cytological, molecular biological, and comparative proteome analyses were tentatively applied to study the relationship between them. This studies have provided important basis for Brassica evolution. Main results were described as follows:
1. Mitotic and meiotic FISH analysis of 45S rDNA in Brassica diploids
The position and number of 45S rDNA on mitotic and meiotic chromosomes of the three basic diploid species (Brassica rapa, B. oleracea and B. nigra) were detected by FISH analysis using 45S rDNA as probe. Ten out of 20 chromosomes can be easily identified in B. rapa, six out of 16 in B. nigra, and four out of 18 in B. oleracea. Among them, meiotic FISH analysis of 45S rDNA of B. rapa and B. nigra was reported for the first time. These investigations are useful for identifying the chromosomes of genome A, B and C and studying the evolution and phylogeny of the Brassica genomes.
2. Relationships among genome A, B and C revealed by centromere repetitive sequence FISH and CAPS analysis
Physical locatization of repetitive DNA sequence from genome A (151bp) was carried out on the chromosome of the selected Brassica species by FISH (fluorescence in situ hybridization). The signals distributed on all the chromosomes of A (Brassica.rapa, 2n=20) or C genome (B. oleracea, 2n=18). For B. Juncea (AABB,2n=36), the signals were found on all the chromosome of genome A and the strength of signal varied among different chromosomes, while the chromosomes of genome B showed weak or no signals. Application of this method to 151bp centromere satellite repeats distinguished the 10 chromosome of AA from B. juncea (AABB). FAE1 gene is a related-limiting gene for erucic acid synthesis in Brassica. The genes from six Brassica species of U-triangule were cloned by PCR. These PCR products were digested with different restriction endonucleases. MboI and MspI were found to produce informative CAPS patterns of FAE1 gene. Three diploids display different patterns, the pattern of genome A was very similar to that of genome C, while the pattern of genome B was the most diverged out of the patterns of the A and C genomes. Three amphidiploids generally exhibited additive patterns of the progenitors, but not strictly in all cases, indicating that rearrangements and recombinations did occur in the formation and evolution of amphidiploids. Genetic relationships among Brassica species could be demonstrated through CAPS analysis of FAE1 gene and FISH method when repetitive DNA sequence (not ribosomal RNA genes) was used as a probe.
3. The analysis of constitute of protein subunits and clustering
Seed storage proteins extracted from six species of Brassica were analysed with SDS-PAGE technique. The constituents of seed storage proteins contained 24 subunits, and polymorphisms and specific protein bands among different species were observed. Prominent bands were characterized at all the diploid species. The result of cluster analysis indicates that 6 species are classified into two types. First type includes B. rapa, B. oleracea and B. napus. The second type includes B. nigra, B. juncea and B. carinata.
4. Characterization of seedling proteomes and development of markers to distinguish the Brassica A and C genomes
The diploid species Brassica rapa (genome AA) and B. oleracea (genome CC) were compared by full-scale proteome analyses of developing seedling. A total of 95 and 111 protein spots were detected in Brassica rapa and B. oleracea, correspondingly. Among these were 29 mutual spots, accounting for 28.2 % of the total spots, indicating the existence of a basal or ubiquitous proteome. while 66 spots were specific to the A genome and 82 to the C genome (32.0 % and 39.8 %, respectively). Nine A genome specific spots and eleven C genome specific spots were excised for subsequent MALDI-TOF-MS analyses. Six of the excised nine spots from the A genome and four of the eleven C genome spots could be reliably identified by MALDI-TOF-MS and protein database searching, the identification rate was 50%. Based on the sequences of deduced contrasting AA and CC protein spots, a number of PCR-based markers to distinguish B. rapa (genome AA) and B. oleracea (genome CC) species were developed as well. Ten primer pairs were contrived and tested for their efficiency in detecting polymorphisms between the A and C genomes.
5. Comparative proteomics in the early generations of newly synthesized Brassica napus allotetraploid
Polyploidy is a prominent process in higher plants and is often described as a genomic shock that may induce stress and defense responses. Recent studies indicate that extensive genetic and epigenetic changes often occur at the early stage of allopolyploid's genome formation, these changes have played a significant role in stabilization of newly formed genome of species. Synthetic Brassica napus provides a model system to study early events in the evolution of ploidy genomes, because the exact progenitors (B. rapa and B. oleracea) for a synthetic polyploid are known. Large-scale analysis of proteome from leaf organ can be studied accurately compared to their homozygous diploid progenitors B. rapa and B. oleracea, and gene expression changes of F1~F4 generations, which might help enriching the mechanisms of genetic and epigenetic changes. The detailed results are as follows:
1) Comparative proteomics between newly synthesized B. napus and its progenitors
Leaf proteins of B. napus and its pprogenitors (B. rapa and B. oleracea) were separated with 2-DE. It was remarkable that the abundance of all these differentially expressed proteins in the hybrid was different from that of corresponding proteins expressed in its progenitors, some of them deviated relatively mid-parent predictions, exhibiting somewhat non-additive expression repatterning. Seven of the differentially expressed proteins were identified by MALDI-TOF-MS and database searching. Biological functional analysis showed these identified proteins were related with substance and energy metabolism: ATP synthase beta subunit was manifested involving in energy metabolism; ADP-glucose pyrophosphorylase small subunit may be an enzyme in substance metabolism; sedoheptulose-bisphosphatase precursor was involving in photosynthesis; DNA-directed RNA polymerase beta-2 chain was related to transcriptional regulation; Serine/Threonine protein kinase, possible related to disease resistance; and a hypothetical unknown protein. The function of these proteins was showed to be related with heterosis, and our explanation of heterosis mechanism was carried out at the protein level. In addition, our analysis of leaf proteome indicated that genome restructuring by recombination occurred in B. napus synthetics the first generation. This process created novel plant phenotypes and should be addressed in terms of evolutionary consequences.
2) Comparative proteomics in early generations of newly synthesized B. napus allotetraploid
We analyzed genetic and epigenetic changes in resynthesized Brassica napus from the first to forth generations using comparative proteomics. The differentially expressed proteins were sorted into five categories after statistical analyses of the 4 generations: 1) polypeptide specific in F2; 2) polypeptide only occurred in F3; 3) polypeptide loss in F1 and reoccurred in F2~F4; 4) polypeptide loss in F1~F2 and reoccurred in F3~F4; 5) gradually up-regulated polypeptide from F1 to F4. The results indicated that gene silencing was not permanent phenomenon and could be reactivated at any moment. Biological function showed these identified proteins related with substance and energy metabolism, Signal transduction, detoxification enzymes, protein degradation, retrotransposon protein and other unknown proteins. Although leaf proteins were extensively modified in synthetic B. napus, however, the distribution of the“housekeeping”proteins into metabolic pathways, functional categories and signal transduction were not disturbed. Moreover, there is no evidence for chaos or a large disorder following the merging of two genomes. Instead, a novel order established quickly and may evolve in further generations of synthetic B. napus.
1.基本种45S rDNA重复序列的有丝分裂与减数分裂的FISH定位分析
利用荧光原位杂交(FISH)技术,以标记的45S rDNA重复序列作探针,研究了芸薹属3个基本种Brassica rapa,B. oleracea与B. nigra的根尖体细胞中期染色体杂交信号的分布特点、花粉母细胞减数分裂粗线期染色体的空间分布、终变期染色体的配对构型等。研究结果表明B. rapa的10条(5对)染色体上表现明显而强烈的杂交信号,且分布在着丝粒和亚着丝粒区域;B. nigra的6条(3对)染色体上有杂交信号,主要分布在染色体短臂的近末端处,减数分裂后期I中,3个信号平均分配到细胞两极;B. oleracea中的4个45S rDNA杂交位点与B. nigra中类似,都位于染色体短臂的近末端处。其中B. rapa与B. nigra的45S rDNA的花粉母细胞的减数分裂FISH定位是首次报道。该结果旨在为研究A、B、C基因组间的亲缘关系和进化提供细胞学依据。
2.着丝粒重复序列FISH及CAPS分析芸薹属A、B和C基因组间的关系
以来源于B. rapa基因组(AA)的重复序列(151bp)为探针,分别同二倍体白菜型油菜、甘蓝和异源四倍体芥菜型油菜(AABB,2n=36)的中期染色体杂交,白菜型油菜和甘蓝的所有染色体上都有杂交信号,芥菜型油菜的染色体上显示出20个明显的信号,其余染色体上信号弱或无,可以区分出A与B基因组。对来源于油菜3个基本种与3个复合种FAE1基因进行CAPS分析表明,3个基本种表现出不同的酶切式样,用MboI和MspI酶切表现出多态性,基因组A和C非常相似,而基因组B与A、C关系较远,同时3个复合种也并不是2个基本种的简单相加,表明异源四倍体在进化过程中可能发生了重排和重组。
3.基本种与复合种间种子贮藏蛋白质亚基构成及聚类分析
根据种子贮藏蛋白形成的蛋白质谱带具有的稳定性、均匀性和可加性的特点,对组成芸薹属3个基本种和3个复合种的种子贮藏蛋白亚基的组成进行了SDS-PAGE比较分析,结果表明:不同种间的种子贮藏蛋白具有一定的差异,表现出丰富的多态性;6个种共有24条亚基带,并各自具有特有的蛋白谱带。利用贮藏蛋白亚基条带的信息,分析了种间的蛋白相似度,并进行了聚类分析,将供试材料分为两类。Ⅰ类为白菜型油菜、甘蓝与甘蓝型油菜。Ⅱ类为为黑芥、芥菜型油菜和埃塞俄比亚芥。
4.芸薹属A、C基因组间比较蛋白质组学的分析及PCR分子标记的开发
白菜和甘蓝亲缘关系非常接近。运用蛋白质组学方法比较了芸薹属二倍体种白菜型油菜(AA)和甘蓝(CC)幼苗期叶片蛋白质组学的变化,通过比较研究,以期探寻它们在蛋白组水平上基因表达特征。应用双向电泳对叶片总蛋白进行了分离,从2-D凝胶上各检测到95与111个蛋白点,应用PDQuest软件对凝胶图谱进行分析,二者间匹配到的蛋白质点数为29,占总数的28.2%,其中芸薹与甘蓝的的专化蛋白分别66和82个,分别占蛋白点总数的32.0 %与39.8 %。MALDI-TOF-MS质谱分析和数据库检索鉴定了其中的20个差异表达蛋白,但可靠差异蛋白的鉴定率仅为50%。该研究首次基于两个物种的特征(差异)蛋白,开发出10个用于区分A和C基因组的基于PCR的分子标记。
5.利用差异蛋白质组对人工合成甘蓝型油菜F1及早期世代蛋白质变化的研究
多倍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会出现广泛的基因组遗传和表观遗传变化,这些变化直接关系到物种的形成和稳定。人工合成的异源多倍体则为这方面的研究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基因组变化特点,从而为丰富多倍体物种进化理论提供重要的理论依据。本研究基于人工合成的异源四倍体甘蓝型油菜及其不同自交后代,比较研究杂种F1与双亲间、以及早期1~4代间的的叶片蛋白质组变化,探索种间杂交及其多倍体形成后引发的遗传和表观遗传变化的规律。具体结果如下:
(1)人工合成甘蓝型油菜F1及其亲本叶片比较蛋白质组学研究
以芸薹属二倍体B . rapa (AA,2n = 20)和B . oleracea(CC,2n =18)和人工合成甘蓝型油菜为实验材料,由于双亲及后代遗传背景清晰,为研究异源多倍体早期基因组在进化过程中的具体变化提供了良好的实验材料。结合蛋白质组学方法来解析新合成的B. napus F1代与其双亲叶片蛋白质组表达差异,鉴定了一些有价值的蛋白点。首先是亲本间的差异蛋白质几乎都在B. napus中表达,但显著偏离双亲丰度表达均值,表现为非加性表达效应。此外经MALDI-TOF-MS鉴定了杂种中7个有显著性意义的蛋白,其中1个与光合作用相关,推定为景天庚酮糖-1,7-二磷酸酶;2种与能量代谢相关的ATP合酶β-亚基;1个与物质代谢相关ADP-葡萄糖焦磷酸化酶小亚基;1个与转录相关的RNA聚合酶β-链;另1个与抗病相关的丝氨酸/苏氨酸蛋白激酶与1个假定蛋白。这些蛋白与具有杂合子潜力的杂种优势相关,为了解杂种优势在蛋白质组水平上的基因表达基础积累了重要的资料,是前人在转录水平上研究的必要补充,从而为进一步阐明杂种优势的机制提供理论依据。此外实验还表明B. napus在多倍化后可能发生了基因重组,并且新蛋白的功能可能会影响F1杂种的表型性状。
(2)人工合成甘蓝型油菜早期世代蛋白质组的变化
我们对人工合成甘蓝型油菜1~4代叶片蛋白质进行了比较分析发现,在后代中发生了非孟德尔式的表观遗传变异,变异主要表现为基因沉默的方式。依据蛋白表达变化特点将F1~F4的差异蛋白质归为五类:1)F2专化类型;2)F3专化类型;3)F1中丢失的蛋白,而F2~F4中表达的类型;4)F1~F2丢失,而F3~F4中表达的类型;5)F1~F4中蛋白丰度逐渐上调的类型。表明丢失的蛋白可能并不是真正的丢失,而可能是发生了基因沉默,而且基因沉默随时可能被激活。在已鉴定的蛋白中,有与物质与能量代谢、信号转导、解毒酶类、蛋白质降解、反转座子相关以及功能未知的假定蛋白。统计后分析尽管基因组早1~4代中发生了随机表观遗传变异,但保证细胞正常基因功能的持家蛋白并没有随基因表达的变化而完全消失,也间接证明了早期多倍化事件中的基因组冲击未必带来蛋白质组上的冲击。相反会有一个新的快速的协调顺序进化在新合成的异源甘蓝型油菜中。
Brassica is the third largest oilseed crop in the world, providing approximately 13% of the world’s supply of vegetable oil. The relationship between three diploids and three allotetraploids was demonstrated in a classical cytogenetic study by U; this relationship is commonly referred to as the“U triangle”. On our research, cytological, molecular biological, and comparative proteome analyses were tentatively applied to study the relationship between them. This studies have provided important basis for Brassica evolution. Main results were described as follows:
1. Mitotic and meiotic FISH analysis of 45S rDNA in Brassica diploids
The position and number of 45S rDNA on mitotic and meiotic chromosomes of the three basic diploid species (Brassica rapa, B. oleracea and B. nigra) were detected by FISH analysis using 45S rDNA as probe. Ten out of 20 chromosomes can be easily identified in B. rapa, six out of 16 in B. nigra, and four out of 18 in B. oleracea. Among them, meiotic FISH analysis of 45S rDNA of B. rapa and B. nigra was reported for the first time. These investigations are useful for identifying the chromosomes of genome A, B and C and studying the evolution and phylogeny of the Brassica genomes.
2. Relationships among genome A, B and C revealed by centromere repetitive sequence FISH and CAPS analysis
Physical locatization of repetitive DNA sequence from genome A (151bp) was carried out on the chromosome of the selected Brassica species by FISH (fluorescence in situ hybridization). The signals distributed on all the chromosomes of A (Brassica.rapa, 2n=20) or C genome (B. oleracea, 2n=18). For B. Juncea (AABB,2n=36), the signals were found on all the chromosome of genome A and the strength of signal varied among different chromosomes, while the chromosomes of genome B showed weak or no signals. Application of this method to 151bp centromere satellite repeats distinguished the 10 chromosome of AA from B. juncea (AABB). FAE1 gene is a related-limiting gene for erucic acid synthesis in Brassica. The genes from six Brassica species of U-triangule were cloned by PCR. These PCR products were digested with different restriction endonucleases. MboI and MspI were found to produce informative CAPS patterns of FAE1 gene. Three diploids display different patterns, the pattern of genome A was very similar to that of genome C, while the pattern of genome B was the most diverged out of the patterns of the A and C genomes. Three amphidiploids generally exhibited additive patterns of the progenitors, but not strictly in all cases, indicating that rearrangements and recombinations did occur in the formation and evolution of amphidiploids. Genetic relationships among Brassica species could be demonstrated through CAPS analysis of FAE1 gene and FISH method when repetitive DNA sequence (not ribosomal RNA genes) was used as a probe.
3. The analysis of constitute of protein subunits and clustering
Seed storage proteins extracted from six species of Brassica were analysed with SDS-PAGE technique. The constituents of seed storage proteins contained 24 subunits, and polymorphisms and specific protein bands among different species were observed. Prominent bands were characterized at all the diploid species. The result of cluster analysis indicates that 6 species are classified into two types. First type includes B. rapa, B. oleracea and B. napus. The second type includes B. nigra, B. juncea and B. carinata.
4. Characterization of seedling proteomes and development of markers to distinguish the Brassica A and C genomes
The diploid species Brassica rapa (genome AA) and B. oleracea (genome CC) were compared by full-scale proteome analyses of developing seedling. A total of 95 and 111 protein spots were detected in Brassica rapa and B. oleracea, correspondingly. Among these were 29 mutual spots, accounting for 28.2 % of the total spots, indicating the existence of a basal or ubiquitous proteome. while 66 spots were specific to the A genome and 82 to the C genome (32.0 % and 39.8 %, respectively). Nine A genome specific spots and eleven C genome specific spots were excised for subsequent MALDI-TOF-MS analyses. Six of the excised nine spots from the A genome and four of the eleven C genome spots could be reliably identified by MALDI-TOF-MS and protein database searching, the identification rate was 50%. Based on the sequences of deduced contrasting AA and CC protein spots, a number of PCR-based markers to distinguish B. rapa (genome AA) and B. oleracea (genome CC) species were developed as well. Ten primer pairs were contrived and tested for their efficiency in detecting polymorphisms between the A and C genomes.
5. Comparative proteomics in the early generations of newly synthesized Brassica napus allotetraploid
Polyploidy is a prominent process in higher plants and is often described as a genomic shock that may induce stress and defense responses. Recent studies indicate that extensive genetic and epigenetic changes often occur at the early stage of allopolyploid's genome formation, these changes have played a significant role in stabilization of newly formed genome of species. Synthetic Brassica napus provides a model system to study early events in the evolution of ploidy genomes, because the exact progenitors (B. rapa and B. oleracea) for a synthetic polyploid are known. Large-scale analysis of proteome from leaf organ can be studied accurately compared to their homozygous diploid progenitors B. rapa and B. oleracea, and gene expression changes of F1~F4 generations, which might help enriching the mechanisms of genetic and epigenetic changes. The detailed results are as follows:
1) Comparative proteomics between newly synthesized B. napus and its progenitors
Leaf proteins of B. napus and its pprogenitors (B. rapa and B. oleracea) were separated with 2-DE. It was remarkable that the abundance of all these differentially expressed proteins in the hybrid was different from that of corresponding proteins expressed in its progenitors, some of them deviated relatively mid-parent predictions, exhibiting somewhat non-additive expression repatterning. Seven of the differentially expressed proteins were identified by MALDI-TOF-MS and database searching. Biological functional analysis showed these identified proteins were related with substance and energy metabolism: ATP synthase beta subunit was manifested involving in energy metabolism; ADP-glucose pyrophosphorylase small subunit may be an enzyme in substance metabolism; sedoheptulose-bisphosphatase precursor was involving in photosynthesis; DNA-directed RNA polymerase beta-2 chain was related to transcriptional regulation; Serine/Threonine protein kinase, possible related to disease resistance; and a hypothetical unknown protein. The function of these proteins was showed to be related with heterosis, and our explanation of heterosis mechanism was carried out at the protein level. In addition, our analysis of leaf proteome indicated that genome restructuring by recombination occurred in B. napus synthetics the first generation. This process created novel plant phenotypes and should be addressed in terms of evolutionary consequences.
2) Comparative proteomics in early generations of newly synthesized B. napus allotetraploid
We analyzed genetic and epigenetic changes in resynthesized Brassica napus from the first to forth generations using comparative proteomics. The differentially expressed proteins were sorted into five categories after statistical analyses of the 4 generations: 1) polypeptide specific in F2; 2) polypeptide only occurred in F3; 3) polypeptide loss in F1 and reoccurred in F2~F4; 4) polypeptide loss in F1~F2 and reoccurred in F3~F4; 5) gradually up-regulated polypeptide from F1 to F4. The results indicated that gene silencing was not permanent phenomenon and could be reactivated at any moment. Biological function showed these identified proteins related with substance and energy metabolism, Signal transduction, detoxification enzymes, protein degradation, retrotransposon protein and other unknown proteins. Although leaf proteins were extensively modified in synthetic B. napus, however, the distribution of the“housekeeping”proteins into metabolic pathways, functional categories and signal transduction were not disturbed. Moreover, there is no evidence for chaos or a large disorder following the merging of two genomes. Instead, a novel order established quickly and may evolve in further generations of synthetic B. napus.
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