水稻心白突变体flo2灌浆期籽粒中miRNA鉴定与表达分析
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摘要
miRNA作为重要的负调控因子在植物中广泛存在,调控植物生长发育、响应生物和非生物胁迫等各类生物学过程。水稻种子在灌浆期的生长是一个复杂的生理过程,其发育程度和物质积累状况决定稻米的产量与品质。目前对灌浆期水稻基因表达谱研究以及对一些参与物质积累,尤其淀粉合成相关的基因挖掘已有大量阐述。但目前关于miRNA在水稻灌浆期是如何表达并在参与怎样的调控作用还未见报道。本研究以一个淀粉积累发生变化的心白突变体flo2和对应野生型一个地方籼稻品种白丰B为实验系统,利用高通量测序和信息学分析小RNA库,鉴定出在灌浆期表达的水稻miRNA,并通过小RNA芯片,比较灌浆不同时期(乳熟,蜡熟,完熟),以及白丰B和flo2中各个miRNA的表达变化,找出在灌浆期优势表达和变化显著的miRNA,并通过对靶基因的预测和功能分析阐述miRNA在水稻灌浆过程中对颖果发育,尤其是对淀粉积累过程的影响。
从构建的两个水稻灌浆时期白丰B和flo2种子小RNA库中,通过高通量测序获得的小RNA序列总数分别为3240709和3266135个,小RNA种类为974934和1542192个,其中与9311基因组匹配的序列数为1363246和1990385,测序深度足够作进一步研究。对数据库中的分析结果表明20个保守家族和约33个非保守家族的miRNA可以在库中检测到。此外还鉴定出了11个新的miRNA和200多个在已知基因座上但不同位置的miRNA变体。
为了进一步研究文库中鉴定得到的miRNA在灌浆期是如何变化,在flo2和白丰B灌浆的三个时期(乳熟期、蜡熟期和完熟期)分别取样,通过小RNA芯片来分析miRNA的表达变化。芯片结果验证了142个已知miRNA及47个已知miRNA变体的表达；有45个miRNA表达水平较高(信号值大于500)。以花后10天miRNA的表达量为参照,表达量上升的保守miRNA家族有4个,非保守家族5个；表达量下降的保守家族5个,非保守家族4个。8个新miRNA也在芯片结果中验证。对应白丰B灌浆各时期miRNA的表达量,发现flo2在花后10天差异显著(p-value<0.01)的miRNA最多,说明两者miRNA表达差异主要发生在灌浆早期。
对这些miRNA做进一步的靶基因预测,验证和功能分析,结果显示这些靶基因参与多种生理过程。通过5'RACE验证部分靶基因,其中miR1862d和miR1874-5p的靶基因GBSS1b和BE1分别参与直链淀粉和支链淀粉的合成,并且两者在flo2和白丰B的不同时期积累水平也不一样。qPCR结果显示GBSS1b和BE1也呈现相对应的负调控趋势,这可能与flo2和白丰B中直链淀粉和支链淀粉的含量及构成存在差异相关,其中miR1862在加2乳熟期的表达量要显著高于白丰B,同时GBSS1b在flo2乳熟期的表达量要低于白丰B,该变化来自miRNA的调控并影响到加2的直链淀粉含量.Q-PCR结果显示大部分靶基因与miRNA表达呈负相关；另一些呈正相关的miRNA如miR164和miR167,可能因为靶基因对miRNA的表达存在反馈调控作用。对靶基因的功能分析发现多数靶基因参与种子的物质积累和成熟过程。
此外,我们还发现心白突变体加2的突变基因可能会影响到体内miRNA的表达水平。一些预测能够标靶该基因的miRNA在flo2中的表达显著下降,但这种调控机制目前还不清楚。
本研究通过对水稻颖果发育时期的miRNA进行分离、鉴定和表达谱分析,发现了一批在水稻灌浆期高表达并参与物质积累和种子成熟途径的miRNA,并首次发现miRNA可能直接调控一些淀粉合成途径中的关键酶,拓宽了对植物miRNA的认知,并为开展后续的功能研究提供了信息。
MicroRNA (miRNA) is a group of short (21-24nt), non-coding RNAs which is widely existed in various tissues, and can modulate biological processes such as growth, development and response to biotic or abiotic stress in plants. The periodjjfrom spikelet filling to maturation is a complex physiological process in rice seed, which is also extremely important for the yield and quality of the production. However, the probable connection of the procedure and the miRNA has not been researched so far. In this study, using two indica varieties of white-core flo2and its corresponding wild type Baifeng B, we isolated several new miRNAs in seeds of10-20days after flowering (DAF) and analyzed the expression profiles of both novel and known miRNAs in this period. The possible role of miRNA in seed development was also investigated through the function prediction and analyzing of the miRNA target genes.
We constructed two small RNA libraries of developing spikelet (flo2&Baifeng B), and3240709and3266135miRNAs were collected respectively through high throughput sequencing. By comparing to the9311genome,1363246(74.4%) and1990385(72.6%) matching miRNAs were chosed for further analysis.20conserved families and33nonconserved families could be detected in our libraries, and280more candidate miRNA were also identified.
Through microarray strategy, we compared miRNA profiles among3filling stages (the milky, soft dough and hard dough stage). The chip analysis confirmed the expression of142known miRNAs,8novel miRNAs and47annotated miRNA variants. There were45miRNAs with a high signal value. By comparing to signals in10DAF, the results showed that4conserved miRNAs and5nonconserved miRNAs were up-regulated,5conserved miRNAs and4nonconserved miRNAs were down-regulated with available variants (p-value<0.05).8novel miRNAs were also confirmed by chip detection. By comparing to wild type, a number of miRNAs showed reduced or increased signal values in flo2especially in10DAF, which suggest the difference between flo2and Baifeng B mainly exist in the early filling phase.
MiRNAs with high and variant expression levels during the spikelet development were selected for the prediction of target genes, the results of which implied the possible involvements of miRNA in various biological processes. Transcription factors of NAC and GAMYB families, regulated by miR164and miR159respectively by prediction, has been reported to participate in the endosperm development and substance accumulation; GBSS1b and BE1, regulated by miR1862d and miR1874-5p respectively by prediction, directly involves in the biosynthesis of starch in seeds. The expression level of miR1862in flo2was higher at milky-ripe stage than Baifeng B and the level of GBSS1was much lower in flo2at milky-ripe stage, which suggested the possible role of miRNA in the regulation of starch biosynthesis in rice seeds. Q-PCR verified the negative correlation between the expression profiles of miRNAs and their target genes. Some miRNAs like miR164and miR167had a positive correlation with their target genes, which suggested a feed-back circuit of miRNA and their targets.
By sequencing, the phenotype of flo2in our research was mainly caused by8bp deletion in exon10of FLO2, a gene well reported previously. Target miRNA prediction showed the3'UTR region of FLO2could be affected by miR444and other miRNAs, which expressed in a lower level in flo2than in Baifeng B. The function of FLO2has been less known and its possible regulation mechanism by miRNA needs to be further investigated.
Through the identification and expression profiles analysis, we found a group of miRNAs involved in the substance accumulation in rice caryopsis development stages and we found miRNA can have effect on starch sythensis pathway for the first time. Our study grained a deeper understanding of plant miRNAs and offered more imformation on the research of miRNAs in rice filling phase.
从构建的两个水稻灌浆时期白丰B和flo2种子小RNA库中,通过高通量测序获得的小RNA序列总数分别为3240709和3266135个,小RNA种类为974934和1542192个,其中与9311基因组匹配的序列数为1363246和1990385,测序深度足够作进一步研究。对数据库中的分析结果表明20个保守家族和约33个非保守家族的miRNA可以在库中检测到。此外还鉴定出了11个新的miRNA和200多个在已知基因座上但不同位置的miRNA变体。
为了进一步研究文库中鉴定得到的miRNA在灌浆期是如何变化,在flo2和白丰B灌浆的三个时期(乳熟期、蜡熟期和完熟期)分别取样,通过小RNA芯片来分析miRNA的表达变化。芯片结果验证了142个已知miRNA及47个已知miRNA变体的表达；有45个miRNA表达水平较高(信号值大于500)。以花后10天miRNA的表达量为参照,表达量上升的保守miRNA家族有4个,非保守家族5个；表达量下降的保守家族5个,非保守家族4个。8个新miRNA也在芯片结果中验证。对应白丰B灌浆各时期miRNA的表达量,发现flo2在花后10天差异显著(p-value<0.01)的miRNA最多,说明两者miRNA表达差异主要发生在灌浆早期。
对这些miRNA做进一步的靶基因预测,验证和功能分析,结果显示这些靶基因参与多种生理过程。通过5'RACE验证部分靶基因,其中miR1862d和miR1874-5p的靶基因GBSS1b和BE1分别参与直链淀粉和支链淀粉的合成,并且两者在flo2和白丰B的不同时期积累水平也不一样。qPCR结果显示GBSS1b和BE1也呈现相对应的负调控趋势,这可能与flo2和白丰B中直链淀粉和支链淀粉的含量及构成存在差异相关,其中miR1862在加2乳熟期的表达量要显著高于白丰B,同时GBSS1b在flo2乳熟期的表达量要低于白丰B,该变化来自miRNA的调控并影响到加2的直链淀粉含量.Q-PCR结果显示大部分靶基因与miRNA表达呈负相关；另一些呈正相关的miRNA如miR164和miR167,可能因为靶基因对miRNA的表达存在反馈调控作用。对靶基因的功能分析发现多数靶基因参与种子的物质积累和成熟过程。
此外,我们还发现心白突变体加2的突变基因可能会影响到体内miRNA的表达水平。一些预测能够标靶该基因的miRNA在flo2中的表达显著下降,但这种调控机制目前还不清楚。
本研究通过对水稻颖果发育时期的miRNA进行分离、鉴定和表达谱分析,发现了一批在水稻灌浆期高表达并参与物质积累和种子成熟途径的miRNA,并首次发现miRNA可能直接调控一些淀粉合成途径中的关键酶,拓宽了对植物miRNA的认知,并为开展后续的功能研究提供了信息。
MicroRNA (miRNA) is a group of short (21-24nt), non-coding RNAs which is widely existed in various tissues, and can modulate biological processes such as growth, development and response to biotic or abiotic stress in plants. The periodjjfrom spikelet filling to maturation is a complex physiological process in rice seed, which is also extremely important for the yield and quality of the production. However, the probable connection of the procedure and the miRNA has not been researched so far. In this study, using two indica varieties of white-core flo2and its corresponding wild type Baifeng B, we isolated several new miRNAs in seeds of10-20days after flowering (DAF) and analyzed the expression profiles of both novel and known miRNAs in this period. The possible role of miRNA in seed development was also investigated through the function prediction and analyzing of the miRNA target genes.
We constructed two small RNA libraries of developing spikelet (flo2&Baifeng B), and3240709and3266135miRNAs were collected respectively through high throughput sequencing. By comparing to the9311genome,1363246(74.4%) and1990385(72.6%) matching miRNAs were chosed for further analysis.20conserved families and33nonconserved families could be detected in our libraries, and280more candidate miRNA were also identified.
Through microarray strategy, we compared miRNA profiles among3filling stages (the milky, soft dough and hard dough stage). The chip analysis confirmed the expression of142known miRNAs,8novel miRNAs and47annotated miRNA variants. There were45miRNAs with a high signal value. By comparing to signals in10DAF, the results showed that4conserved miRNAs and5nonconserved miRNAs were up-regulated,5conserved miRNAs and4nonconserved miRNAs were down-regulated with available variants (p-value<0.05).8novel miRNAs were also confirmed by chip detection. By comparing to wild type, a number of miRNAs showed reduced or increased signal values in flo2especially in10DAF, which suggest the difference between flo2and Baifeng B mainly exist in the early filling phase.
MiRNAs with high and variant expression levels during the spikelet development were selected for the prediction of target genes, the results of which implied the possible involvements of miRNA in various biological processes. Transcription factors of NAC and GAMYB families, regulated by miR164and miR159respectively by prediction, has been reported to participate in the endosperm development and substance accumulation; GBSS1b and BE1, regulated by miR1862d and miR1874-5p respectively by prediction, directly involves in the biosynthesis of starch in seeds. The expression level of miR1862in flo2was higher at milky-ripe stage than Baifeng B and the level of GBSS1was much lower in flo2at milky-ripe stage, which suggested the possible role of miRNA in the regulation of starch biosynthesis in rice seeds. Q-PCR verified the negative correlation between the expression profiles of miRNAs and their target genes. Some miRNAs like miR164and miR167had a positive correlation with their target genes, which suggested a feed-back circuit of miRNA and their targets.
By sequencing, the phenotype of flo2in our research was mainly caused by8bp deletion in exon10of FLO2, a gene well reported previously. Target miRNA prediction showed the3'UTR region of FLO2could be affected by miR444and other miRNAs, which expressed in a lower level in flo2than in Baifeng B. The function of FLO2has been less known and its possible regulation mechanism by miRNA needs to be further investigated.
Through the identification and expression profiles analysis, we found a group of miRNAs involved in the substance accumulation in rice caryopsis development stages and we found miRNA can have effect on starch sythensis pathway for the first time. Our study grained a deeper understanding of plant miRNAs and offered more imformation on the research of miRNAs in rice filling phase.
引文
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