稻米品质突变体库的构建及粉质胚乳垩白突变体（flo6）的基因定位
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摘要
水稻是主要粮食作物之一,其基因组的全序列测定已经完成,但基因组中多数基因的功能仍是未知。所以,对基因功能的注释与研究己成为单子叶模式植物水稻遗传学与分子生物学研究的重点。本研究利用化学诱变剂甲基磺酸乙酯(EMS)处理己完成测序的粳稻品种日本晴构建包括垩白、蒸煮品质、营养品质性状在内的水稻品质性状突变体库。利用近红外光谱分析对一个包含2210份诱变处理材料的群体进行2次筛选,对获得的品质突变体进行化学分析验证,确定了该突变体的突变性状。同时对其中一份垩白突变体进行了基因定位。得到结果如下：
1.在外观品质和蒸煮品质方面获得27份突变体。其中垩白突变体5份(突变频率为2.26‰)、直链淀粉含量突变体5份(2.26%o)、胶稠度突变体4份(1.81‰)、碱消值突变体2份(0.90‰)、糊化温度突变体4份(1.81‰)、稻米米粉黏滞性突变体7份(3.17‰)。
2.在营养品质方面获得61份突变体。以相对含量低于或高于野生型10%作为筛选标准,对诱变群体的不同氨基酸含量和蛋白质含量进行了突变体筛选。结果共获得赖氨酸突变体1份(0.45‰)、亮氨酸突变体1份(0.45‰)、缬氨酸突变体11份(4.98‰)、谷氨酸突变体1份(0.45‰)、精氨酸突变体7份(3.17‰)、丙氨酸突变体6份(2.71‰)、丝氨酸突变体、甘氨酸突变体各1份(各0.45‰)、酪氨酸突变体3份(1.36%o)、脯氨酸突变体5份(2.26‰)、组氨酸突变体1份(0.45‰)、蛋氨酸突变体5份(2.26‰),半胱氨酸突变体7份(3.17‰)、蛋白质含量突变体11份(4.98‰)。异亮氨酸、苯丙氨酸、苏氨酸,天冬氨酸、苯丙氨酸和苏氨酸未筛选到相应的突变体。
3.利用一个粉质胚乳垩白突变体(flo6)构建了定位群体,flo6垩白突变体具有大垩白、胚乳中心部位淀粉粒结合松散等突变性状。同时还具有千粒重下降、籽粒变小、胶稠度变软、糊化温度降低和稻米粉的黏滞性系数降低等特性；但蛋白质含量有所提高,其中多种氨基酸含量也发生了明显变化。遗传分析表明此垩白突变为隐性单基因突变。
4.通过图位克隆策略将垩白突变基因定位在1号染色体长臂中段区域约500kb范围内。根据水稻基因组注释计划(RAP)数据库的相关注释信息,对候选区段内的推定基因进行分析,其中编号为LOC_Os01g44220的基因被初步确定为突变基因。该基因编码水稻AGPase的一个大亚基OsAGPL2,催化着AGPase淀粉合成途径中第一步反应的合成,是水稻淀粉合成的主要限制因素。测序结果表明该基因的第4个转录本LOC_Os01g44220.4的第10号外显子发生了一个碱基的突变(G→A),导致其转录蛋白序列也产生变异(E→K)。
5.由于DNA序列单碱基替换引起的蛋白质序列氨基酸替换没有导致AGPase大亚基OsAPL2功能的完全丧失,蛋白质三级结构的预测结果表明突变位点只引起了二级结构的微小改变,但突变位点紧邻AGPase与ADP-Glu互作区域,且由带负电荷的谷氨酸突变为带有正电荷的赖氨酸,影响了互作区域的电荷环境,进而影响了AGPase的催化能力。所以,基于以上关于突变位点对蛋白质序列的影响及AGPase作用模型分析,推测在胚乳发育早期大亚基OsAPL2参与构成的AGPase复合物在细胞质内含量较低,且由于突变造成的催化功能降低,质体内由OsAPS1和OsAPL1形成的AGPase复合物的酶活性较低(约为5%),大部分是由细胞质型AGPase提供催化活性,造成胚乳淀粉合成底物ADP-G的量不足,减少了淀粉的合成,形成早期发育部位淀粉粒结合松散的性状。后期大亚基OsAPL2含量迅速增加,弥补了由于突变而造成的AGPase催化能力的下降,使得ADP-G合成趋于正常,以至胚乳淀粉积累也恢复正常,最终形成了胚乳内部呈粉质而外部边缘正常的flo6垩白突变体的突变表型。
Rice (Oryza sativa L.) is not only a pivotal key cereal crop that provides the staple food for more than half of the world's population as a source of daily carbon intake, but also a plant that has attracted broad interest in basic and applied research. The published of draft genome sequences of two rice cultivars to proclaim that the study of both the indica and japonica subspecies has entered into post-genomic era. The completed sequence variety Oryza sativa cv. Nipponbare as experimental material can be found in this paper. Seeds of this variety were treated with ethyl methane sulphonate (EMS). A total of2210materials were first screened by NIR from which208mutants were obtained. A second screening yielded73mutants that were all identified by the chemical experiment. The following results were observed in present experiment.
1. A number of27mutants with appearance and cooking quality traits have been obtained:5chalky mutants were screened and the mutation frequency of chalkiness was2.26%o, followed by5amylose content (AC) mutants (2.26%o), both4gelatinization temperature (GT) and gel consistency (GC) mutants (1.81‰),2alkali spreading value (ASV) mutants (0.9%o), and7rapid visco analyzer (RVA) profile mutants (3.17%o).
2. A number of61mutants of nutrition quality have been obtained:11protein content (PC) mutants were detected at a mutation frequency of4.98%o. Relative contents of17kinds of amino acid mutations, including7kinds of essential amino acid and10kinds of nonessential were identified. When the screening standard was set at10%, mutants of lysine and leucine (0.45‰), and valine (4.98‰) were screened, but no mutant was obtained for isoleucine, phenylalanine or threonine in essential amino acids. For nonessential amino acids, mutants of glutamic (0.45‰), arginine (3.17‰), alanine (2.71‰), serine (0.45‰), glycine (0.45‰), tyrosine (1.36‰), proline (2.26‰), and histidine (0.45‰) were obtained, but no mutant was obtained for aspartic, phenylalanine or threonine. With the screening standard for methionine and cysteine set at100%, the mutation frequencies of these two amino acids were2.26‰and4.98‰, respectively. Mutants of this preliminary library for rice quality mutants would play important role in the study of gene function and breeding for rice quality.
3. A floury endosperm (flo6) mutant with chalky phenotype was used to constructed gene mapping population. The scanning electron microscopic results showed that the starch granules of flo6mutant were comprised round and loosely packed, some starch granules compounded by the film coating. Cooking and nutrition quality analysis indicated that the value of GC, GT or RVA profile of flo6mutant was lower than that of WT; and the thermodynamic parameters Tp and△T1/2between WT and flo6mutant were different. PC of flo6mutant was higher than that of WT. According to the relative contents of17amino acids analyzed,9of them were different between WT and flo6mutant. Genetic analysis revealed that flo6mutation was controlled by a single recessive nuclear gene.
4. The flo6locus was located on a500kb region by primary mapping. Map-based cloning and sequencing showed that there was a single nucleotide mutation (G→A) in LOC_Os01g44220.4.exon10, which resulted in the sequence of transcript protein of locus LOC_Os01g44220had been changed (E→K). This gene was annotated encodes glucose-1-phosphate adenylyltransferase large subunit in database, and it was named OsAPL2. The protein of this gene catalyzed the first step of starch synthesis in rice endosperm, and this reaction was considered to be the main limiting factors of rice starch synthesis. The tertiary structure had been changed because of the site mutation.
5. The result of comparison of protein sequences showed that the amino acid residue mutant site was closed to the residues interacting with ADP-Glu of AGPase, and the original residue was Glu with negative charge mutated into Lys with positive charge, so the charge environment about the interact residues was changed by this mutation. Thus, the site mutation of protein sequence did not lead to the complete lost of gene function for OsAPL2, it just decreased its capability to catalyze or polymerize with others subunits. Based on the model of AGPase works, the content of AGPase complex which was composed by OsAPL2with other subunits was lower in the early stage of endosperm development, and the capability of the complex was also decreased because of the site mutant. Meanwhile, the enzymatic activity of AGPase complex which was composed by OsAPS1and OsAPL1was lower (only5%), the catalyzed activity was mostly supplied by the cytoplasm AGPase. As a result, at the early stage of endosperm development, the lack of ADP-G whcih was the substrate of starch synthesis, reduced the speed of starch synthesis, which was why the starch granules were loosen in the central section of grains of flo6mutant. At the later stage, the content of OsAPL2increased rapidly in a short time, so it was a compensation for the decrease of catalyzed capabilities that was induced by the site mutation. Under these conditions, the synthesis of ADP-G and starch returned to normal. Finally, the mutation phenotype at the interior of the endosperm was floury-white while the outer portion was normal has formed.
1.在外观品质和蒸煮品质方面获得27份突变体。其中垩白突变体5份(突变频率为2.26‰)、直链淀粉含量突变体5份(2.26%o)、胶稠度突变体4份(1.81‰)、碱消值突变体2份(0.90‰)、糊化温度突变体4份(1.81‰)、稻米米粉黏滞性突变体7份(3.17‰)。
2.在营养品质方面获得61份突变体。以相对含量低于或高于野生型10%作为筛选标准,对诱变群体的不同氨基酸含量和蛋白质含量进行了突变体筛选。结果共获得赖氨酸突变体1份(0.45‰)、亮氨酸突变体1份(0.45‰)、缬氨酸突变体11份(4.98‰)、谷氨酸突变体1份(0.45‰)、精氨酸突变体7份(3.17‰)、丙氨酸突变体6份(2.71‰)、丝氨酸突变体、甘氨酸突变体各1份(各0.45‰)、酪氨酸突变体3份(1.36%o)、脯氨酸突变体5份(2.26‰)、组氨酸突变体1份(0.45‰)、蛋氨酸突变体5份(2.26‰),半胱氨酸突变体7份(3.17‰)、蛋白质含量突变体11份(4.98‰)。异亮氨酸、苯丙氨酸、苏氨酸,天冬氨酸、苯丙氨酸和苏氨酸未筛选到相应的突变体。
3.利用一个粉质胚乳垩白突变体(flo6)构建了定位群体,flo6垩白突变体具有大垩白、胚乳中心部位淀粉粒结合松散等突变性状。同时还具有千粒重下降、籽粒变小、胶稠度变软、糊化温度降低和稻米粉的黏滞性系数降低等特性；但蛋白质含量有所提高,其中多种氨基酸含量也发生了明显变化。遗传分析表明此垩白突变为隐性单基因突变。
4.通过图位克隆策略将垩白突变基因定位在1号染色体长臂中段区域约500kb范围内。根据水稻基因组注释计划(RAP)数据库的相关注释信息,对候选区段内的推定基因进行分析,其中编号为LOC_Os01g44220的基因被初步确定为突变基因。该基因编码水稻AGPase的一个大亚基OsAGPL2,催化着AGPase淀粉合成途径中第一步反应的合成,是水稻淀粉合成的主要限制因素。测序结果表明该基因的第4个转录本LOC_Os01g44220.4的第10号外显子发生了一个碱基的突变(G→A),导致其转录蛋白序列也产生变异(E→K)。
5.由于DNA序列单碱基替换引起的蛋白质序列氨基酸替换没有导致AGPase大亚基OsAPL2功能的完全丧失,蛋白质三级结构的预测结果表明突变位点只引起了二级结构的微小改变,但突变位点紧邻AGPase与ADP-Glu互作区域,且由带负电荷的谷氨酸突变为带有正电荷的赖氨酸,影响了互作区域的电荷环境,进而影响了AGPase的催化能力。所以,基于以上关于突变位点对蛋白质序列的影响及AGPase作用模型分析,推测在胚乳发育早期大亚基OsAPL2参与构成的AGPase复合物在细胞质内含量较低,且由于突变造成的催化功能降低,质体内由OsAPS1和OsAPL1形成的AGPase复合物的酶活性较低(约为5%),大部分是由细胞质型AGPase提供催化活性,造成胚乳淀粉合成底物ADP-G的量不足,减少了淀粉的合成,形成早期发育部位淀粉粒结合松散的性状。后期大亚基OsAPL2含量迅速增加,弥补了由于突变而造成的AGPase催化能力的下降,使得ADP-G合成趋于正常,以至胚乳淀粉积累也恢复正常,最终形成了胚乳内部呈粉质而外部边缘正常的flo6垩白突变体的突变表型。
Rice (Oryza sativa L.) is not only a pivotal key cereal crop that provides the staple food for more than half of the world's population as a source of daily carbon intake, but also a plant that has attracted broad interest in basic and applied research. The published of draft genome sequences of two rice cultivars to proclaim that the study of both the indica and japonica subspecies has entered into post-genomic era. The completed sequence variety Oryza sativa cv. Nipponbare as experimental material can be found in this paper. Seeds of this variety were treated with ethyl methane sulphonate (EMS). A total of2210materials were first screened by NIR from which208mutants were obtained. A second screening yielded73mutants that were all identified by the chemical experiment. The following results were observed in present experiment.
1. A number of27mutants with appearance and cooking quality traits have been obtained:5chalky mutants were screened and the mutation frequency of chalkiness was2.26%o, followed by5amylose content (AC) mutants (2.26%o), both4gelatinization temperature (GT) and gel consistency (GC) mutants (1.81‰),2alkali spreading value (ASV) mutants (0.9%o), and7rapid visco analyzer (RVA) profile mutants (3.17%o).
2. A number of61mutants of nutrition quality have been obtained:11protein content (PC) mutants were detected at a mutation frequency of4.98%o. Relative contents of17kinds of amino acid mutations, including7kinds of essential amino acid and10kinds of nonessential were identified. When the screening standard was set at10%, mutants of lysine and leucine (0.45‰), and valine (4.98‰) were screened, but no mutant was obtained for isoleucine, phenylalanine or threonine in essential amino acids. For nonessential amino acids, mutants of glutamic (0.45‰), arginine (3.17‰), alanine (2.71‰), serine (0.45‰), glycine (0.45‰), tyrosine (1.36‰), proline (2.26‰), and histidine (0.45‰) were obtained, but no mutant was obtained for aspartic, phenylalanine or threonine. With the screening standard for methionine and cysteine set at100%, the mutation frequencies of these two amino acids were2.26‰and4.98‰, respectively. Mutants of this preliminary library for rice quality mutants would play important role in the study of gene function and breeding for rice quality.
3. A floury endosperm (flo6) mutant with chalky phenotype was used to constructed gene mapping population. The scanning electron microscopic results showed that the starch granules of flo6mutant were comprised round and loosely packed, some starch granules compounded by the film coating. Cooking and nutrition quality analysis indicated that the value of GC, GT or RVA profile of flo6mutant was lower than that of WT; and the thermodynamic parameters Tp and△T1/2between WT and flo6mutant were different. PC of flo6mutant was higher than that of WT. According to the relative contents of17amino acids analyzed,9of them were different between WT and flo6mutant. Genetic analysis revealed that flo6mutation was controlled by a single recessive nuclear gene.
4. The flo6locus was located on a500kb region by primary mapping. Map-based cloning and sequencing showed that there was a single nucleotide mutation (G→A) in LOC_Os01g44220.4.exon10, which resulted in the sequence of transcript protein of locus LOC_Os01g44220had been changed (E→K). This gene was annotated encodes glucose-1-phosphate adenylyltransferase large subunit in database, and it was named OsAPL2. The protein of this gene catalyzed the first step of starch synthesis in rice endosperm, and this reaction was considered to be the main limiting factors of rice starch synthesis. The tertiary structure had been changed because of the site mutation.
5. The result of comparison of protein sequences showed that the amino acid residue mutant site was closed to the residues interacting with ADP-Glu of AGPase, and the original residue was Glu with negative charge mutated into Lys with positive charge, so the charge environment about the interact residues was changed by this mutation. Thus, the site mutation of protein sequence did not lead to the complete lost of gene function for OsAPL2, it just decreased its capability to catalyze or polymerize with others subunits. Based on the model of AGPase works, the content of AGPase complex which was composed by OsAPL2with other subunits was lower in the early stage of endosperm development, and the capability of the complex was also decreased because of the site mutant. Meanwhile, the enzymatic activity of AGPase complex which was composed by OsAPS1and OsAPL1was lower (only5%), the catalyzed activity was mostly supplied by the cytoplasm AGPase. As a result, at the early stage of endosperm development, the lack of ADP-G whcih was the substrate of starch synthesis, reduced the speed of starch synthesis, which was why the starch granules were loosen in the central section of grains of flo6mutant. At the later stage, the content of OsAPL2increased rapidly in a short time, so it was a compensation for the decrease of catalyzed capabilities that was induced by the site mutation. Under these conditions, the synthesis of ADP-G and starch returned to normal. Finally, the mutation phenotype at the interior of the endosperm was floury-white while the outer portion was normal has formed.
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