水稻粒型主效基因qSS7的定位与鉴定
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摘要
水稻是世界上最重要的粮食作物之一。随着世界人口的迅速增长,粮食短缺成为困扰世界各国的重大问题。同时,随着人们物质生活水平的提高,稻米品质越来越受到消费者的重视。水稻粒型包括粒长、粒宽和长宽比,是水稻粒重的决定因子,也是外观品质的重要指标。因此改良水稻粒型是提高产量和改善稻米品质的有效途径。发掘和深入研究水稻粒型基因对分子标记辅助选择进行水稻育种具有重要的理论和实践意义。本研究利用以珍汕97B为受体、热带粳稻Cypress为供体的染色体片段代换系,定位和鉴定水稻粒型主效QTL,研究其遗传效应,精细定位QTL,结合测序、表达量分析和生物信息学的方法确定候选基因,揭示该QTL的作用模式；考察该QTL对籽粒灌浆速率、产量和品质等相关性状的影响。主要结果如下：
1.通过对水稻染色体片段代换系的筛选,鉴定出一份粒型与受体亲本珍汕97B有显著差异的代换系08Q043。08Q043较珍汕97B粒长增加约1.5mm,粒宽减小约0.7mm,长宽比增加约1.5,千粒重下降约3g。图示基因型显示08Q043共有8个Cypress导入片段,分别位于第1、4、5、6、7和12染色体,基因组其它背景与珍汕97B一致。
2.通过08Q043与珍汕97B构建的F2分离群体及F2：3群体,采用BSA法将控制粒型的QTL定位于第7染色体长臂上RM21930-RM21936区间内,08Q043等位基因同时增加粒长和长宽比,减小粒宽,不影响粒重,故命名为qSS7。
3.在F2：3群体中挑选了一个目标片段为杂合且只在第4染色体长臂上有一个纯合导入片段的单株衍生了一个含有1025个单株的分离群体,共筛选到18个重组交换单株。通过对这18个单株的后代家系考察,将qSS7精细定位到23kb的区间。分析重组交换单株的后代表型发现,该区间可能有两个紧密连锁的基因对粒型产生影响。
4.对双亲候选区间测序及基因预测发现该区间共有4个预测基因,其中两个基因双亲间没有序列差异,另两个基因(LOC_Os07g41200和LOC_Os07g41210)存在一定序列差异。双亲LOC_Os07g41200的启动子区和编码区分别有26个和14个SNP和InDel,其中编码区2个SNP导致编码氨基酸的改变；LOC_Os07g41210在启动子区和编码区分别有30个和9个SNP和InDel,其中编码区3个SNP导致编码氨基酸的改变,1个SNP导致珍汕97B编码蛋白的提前终止。
5.两个侯选基因在08Q043和珍汕97B的穗发育阶段存在表达差异。随着幼穗发育,LOC_Os07g41200的表达量随之降低,08Q043的表达量都比珍汕97B高。LOC_Os07g41210两亲本呈U字形表达,幼穗发育前期该基因的表达量较高,随着幼穗发育,该基因的表达量逐渐下降,到幼穗发育后期,该基因又呈上升表达,在幼穗发育成熟前的所有时期08Q043的表达量均比珍汕97B低。
6.利用两个InDel标记和LOC_Os07g41210编码区的序列将核心种质的qSS7分为10种单倍型。其中珍汕97B单倍型(H1)主要分布于籼稻,08Q043单倍型(H2)主要分布于热带粳稻,日本晴单倍型(H3)主要分布于温带粳稻。籼稻H4粒长显著长于H1和H5；温带粳稻H2粒长显著大于H3和H5,粒宽显著大于H1、H3和H5。
7.构建了目标位点qSS7的近等基因系,观察发现08Q043近等基因系外稃内表皮细胞长度比珍汕97B长13.7%,宽度窄11.8%,与粒型的差异基本吻合,表明qSS7主要通过影响颖壳细胞大小控制粒型。
8.利用近等基因系考察了颖壳发育动态和灌浆速率。穗长大于8cm时,08Q043等位基因近等基因系颖壳比珍汕97B等位基因近等基因系细长,与表达量分析和颖壳细胞观察的结果吻合。在水稻灌浆过程中,两个近等基因系间灌浆速率没有显著差异。
9.近等基因系的产量和品质相关性状的考察结果显示,qSS7除了影响粒型外,还影响抽穗期、穗长、着粒密度、垩白率和垩白度,不影响其他农艺性状。
Rice is one of the most important crops. With the population growing, food shortage becomes the main problem in most countries. With the improvement of people's living standard, rice quality has been paid more attention by consumers. Seed shape, consisting of seed length, seed width and length to width ratio, is the determinant of grain weight and one of important appearance quality traits. It's considered an effective method to improve grain yield and quality by improving seed shape. Characterization and identification of novel genes for seed shape can help facilitate the improvement of grain yield and quality by marker-assisted selection in rice breeding program. In this study, using a chromosome segment substitution line derived from a cross between a tropical japonica variety Cypress and an indica variety ZS97B, a major quantitative trait locus qSS7controlling seed shape was identified. Candidate genes for qSS7were characterized by sequencing, expression and bioinformatics analysis. The grain filling rate, grain yield and quality were also surveyed in the near-isogenic line (NIL) developed for qSS7. The main results are as follows:
1. One line with long seeds, named as08Q043, was selected from the chromosome segment substitution lines in which they have the similar genetic background of ZS97B.08Q043has significantly longer and slender seeds than that of ZS97B. Graphic genotype of08Q043showed at least8Cypress chromosomal segments introduced, which located on the chromosomes1,4,5,6,7,12, respectively.
2. The major quantitative trait locus (QTL) for seed shape in the F2and F23populations derived from08Q043and ZS97B was initially mapped to the interval of RM21930-RM21936on the long arm of chromosome7by BSA method The Cypress allele increased seed length and the ratio of seed length to width, and decreased seed width, but did not significantly change seed weight. The QTL was thus designed as qSS7.
3. A large segregating population that was developed by selfing an introgression line heterozygous at qSS7locus was used for fine mapping. The genotype analysis of1025 plants in the population using several markers surrounding the QTL region identified18recombinant individuals. qSS7was then finely mapped to a23kb region by progeny test. Further analysis of the most important recombinant plants and thier derived segregation populations suggested at least two genes in this region affecting seed shape.
4. By sequencing the small region, numerous polymorphic variations were identified between ZS97B and08Q043. There were four predicted genes predicted in the small region of23kb in length. Among them, two genes have no differences in the sequences between the two parents, and the other two genes (LOC_Os07g41200and LOC_Os07g41210) have several sequence differences. There are26and14SNPs or InDels between the two parents in the promoter and encoding region of LOC_Os07g41200, respectively, of which two SNPs might change amino acids. There are30and9SNPs or InDels between the two parents in the promoter and encoding region of LOC_Os07g41210, respectively, of which three SNPs changed amino acids, specifically one SNP resulting in a premature termination of the gene in ZS97B. These two predicted genes were thus considered as the most likely candidates for qSS7.
5. The expression levels of the candidate genes were analyzed at various stages of panicle development. LOC_Os07g41200in08Q043expressed at higher levels than in ZS97B through almost the entire panicle development stage (panicles ranging3-23cm in length), except the early stage (panicles2cm in length). In contrast, the expression levels of LOC_Os07g41210in ZS97B were higher at most of the panicle development stages except the late one (panicles reaching23cm in length) than those in08Q043.
6. Ten haplotypes were revealed by two InDel markers and coding sequence of LOC_Os07gg41210. ZS97B haplotype (HI) exists mainly in indica,08Q043haplotype (H2) exists mainly in tropical japonica, and Nipponbare haplotype (H3) exists mainly in temporal japonica. Seed length of H4is longer than that of H1and H5; seed width of H2is wider than that of H3and H5, and ratio of length to width of H2is larger than that of H3and H5.
7. To characterize the qSS7effect in details, a pair of NIL (NTL-08Q043and NIL-ZS97B) with different alleles at the qSS7were developed. The length and width of the inner epidermal cells of the outer glume (lemma) was measured by SEM, showing that the cell length was13.7%longer and the cell width was11.8%narrower in NIL-08Q043than in ZS97B. These differences are consistent with that of seed shape, showing that qSS7controls seed shape possibly by affecting cell shape of spikelets.
8. The dynamics of seed development and grain filling rate were surveyed using the NILs. The seed shape was significantly different between the two NILs after panicle8cm in length. This result consisted with the expression levels during the panicle development stage. However, no difference in grain filling rate between two the NILs was observed at entire grain-filling stage.
9. Yield and quality-related traits in the NILs were investigated as well. There were differences in heading date, panicle length, spikelet density, grain chalk percentage and grain chalk degree between the two NILs (NIL-08Q043and NIL-ZS97B), but no difference in grain yield and grain quality.
1.通过对水稻染色体片段代换系的筛选,鉴定出一份粒型与受体亲本珍汕97B有显著差异的代换系08Q043。08Q043较珍汕97B粒长增加约1.5mm,粒宽减小约0.7mm,长宽比增加约1.5,千粒重下降约3g。图示基因型显示08Q043共有8个Cypress导入片段,分别位于第1、4、5、6、7和12染色体,基因组其它背景与珍汕97B一致。
2.通过08Q043与珍汕97B构建的F2分离群体及F2：3群体,采用BSA法将控制粒型的QTL定位于第7染色体长臂上RM21930-RM21936区间内,08Q043等位基因同时增加粒长和长宽比,减小粒宽,不影响粒重,故命名为qSS7。
3.在F2：3群体中挑选了一个目标片段为杂合且只在第4染色体长臂上有一个纯合导入片段的单株衍生了一个含有1025个单株的分离群体,共筛选到18个重组交换单株。通过对这18个单株的后代家系考察,将qSS7精细定位到23kb的区间。分析重组交换单株的后代表型发现,该区间可能有两个紧密连锁的基因对粒型产生影响。
4.对双亲候选区间测序及基因预测发现该区间共有4个预测基因,其中两个基因双亲间没有序列差异,另两个基因(LOC_Os07g41200和LOC_Os07g41210)存在一定序列差异。双亲LOC_Os07g41200的启动子区和编码区分别有26个和14个SNP和InDel,其中编码区2个SNP导致编码氨基酸的改变；LOC_Os07g41210在启动子区和编码区分别有30个和9个SNP和InDel,其中编码区3个SNP导致编码氨基酸的改变,1个SNP导致珍汕97B编码蛋白的提前终止。
5.两个侯选基因在08Q043和珍汕97B的穗发育阶段存在表达差异。随着幼穗发育,LOC_Os07g41200的表达量随之降低,08Q043的表达量都比珍汕97B高。LOC_Os07g41210两亲本呈U字形表达,幼穗发育前期该基因的表达量较高,随着幼穗发育,该基因的表达量逐渐下降,到幼穗发育后期,该基因又呈上升表达,在幼穗发育成熟前的所有时期08Q043的表达量均比珍汕97B低。
6.利用两个InDel标记和LOC_Os07g41210编码区的序列将核心种质的qSS7分为10种单倍型。其中珍汕97B单倍型(H1)主要分布于籼稻,08Q043单倍型(H2)主要分布于热带粳稻,日本晴单倍型(H3)主要分布于温带粳稻。籼稻H4粒长显著长于H1和H5；温带粳稻H2粒长显著大于H3和H5,粒宽显著大于H1、H3和H5。
7.构建了目标位点qSS7的近等基因系,观察发现08Q043近等基因系外稃内表皮细胞长度比珍汕97B长13.7%,宽度窄11.8%,与粒型的差异基本吻合,表明qSS7主要通过影响颖壳细胞大小控制粒型。
8.利用近等基因系考察了颖壳发育动态和灌浆速率。穗长大于8cm时,08Q043等位基因近等基因系颖壳比珍汕97B等位基因近等基因系细长,与表达量分析和颖壳细胞观察的结果吻合。在水稻灌浆过程中,两个近等基因系间灌浆速率没有显著差异。
9.近等基因系的产量和品质相关性状的考察结果显示,qSS7除了影响粒型外,还影响抽穗期、穗长、着粒密度、垩白率和垩白度,不影响其他农艺性状。
Rice is one of the most important crops. With the population growing, food shortage becomes the main problem in most countries. With the improvement of people's living standard, rice quality has been paid more attention by consumers. Seed shape, consisting of seed length, seed width and length to width ratio, is the determinant of grain weight and one of important appearance quality traits. It's considered an effective method to improve grain yield and quality by improving seed shape. Characterization and identification of novel genes for seed shape can help facilitate the improvement of grain yield and quality by marker-assisted selection in rice breeding program. In this study, using a chromosome segment substitution line derived from a cross between a tropical japonica variety Cypress and an indica variety ZS97B, a major quantitative trait locus qSS7controlling seed shape was identified. Candidate genes for qSS7were characterized by sequencing, expression and bioinformatics analysis. The grain filling rate, grain yield and quality were also surveyed in the near-isogenic line (NIL) developed for qSS7. The main results are as follows:
1. One line with long seeds, named as08Q043, was selected from the chromosome segment substitution lines in which they have the similar genetic background of ZS97B.08Q043has significantly longer and slender seeds than that of ZS97B. Graphic genotype of08Q043showed at least8Cypress chromosomal segments introduced, which located on the chromosomes1,4,5,6,7,12, respectively.
2. The major quantitative trait locus (QTL) for seed shape in the F2and F23populations derived from08Q043and ZS97B was initially mapped to the interval of RM21930-RM21936on the long arm of chromosome7by BSA method The Cypress allele increased seed length and the ratio of seed length to width, and decreased seed width, but did not significantly change seed weight. The QTL was thus designed as qSS7.
3. A large segregating population that was developed by selfing an introgression line heterozygous at qSS7locus was used for fine mapping. The genotype analysis of1025 plants in the population using several markers surrounding the QTL region identified18recombinant individuals. qSS7was then finely mapped to a23kb region by progeny test. Further analysis of the most important recombinant plants and thier derived segregation populations suggested at least two genes in this region affecting seed shape.
4. By sequencing the small region, numerous polymorphic variations were identified between ZS97B and08Q043. There were four predicted genes predicted in the small region of23kb in length. Among them, two genes have no differences in the sequences between the two parents, and the other two genes (LOC_Os07g41200and LOC_Os07g41210) have several sequence differences. There are26and14SNPs or InDels between the two parents in the promoter and encoding region of LOC_Os07g41200, respectively, of which two SNPs might change amino acids. There are30and9SNPs or InDels between the two parents in the promoter and encoding region of LOC_Os07g41210, respectively, of which three SNPs changed amino acids, specifically one SNP resulting in a premature termination of the gene in ZS97B. These two predicted genes were thus considered as the most likely candidates for qSS7.
5. The expression levels of the candidate genes were analyzed at various stages of panicle development. LOC_Os07g41200in08Q043expressed at higher levels than in ZS97B through almost the entire panicle development stage (panicles ranging3-23cm in length), except the early stage (panicles2cm in length). In contrast, the expression levels of LOC_Os07g41210in ZS97B were higher at most of the panicle development stages except the late one (panicles reaching23cm in length) than those in08Q043.
6. Ten haplotypes were revealed by two InDel markers and coding sequence of LOC_Os07gg41210. ZS97B haplotype (HI) exists mainly in indica,08Q043haplotype (H2) exists mainly in tropical japonica, and Nipponbare haplotype (H3) exists mainly in temporal japonica. Seed length of H4is longer than that of H1and H5; seed width of H2is wider than that of H3and H5, and ratio of length to width of H2is larger than that of H3and H5.
7. To characterize the qSS7effect in details, a pair of NIL (NTL-08Q043and NIL-ZS97B) with different alleles at the qSS7were developed. The length and width of the inner epidermal cells of the outer glume (lemma) was measured by SEM, showing that the cell length was13.7%longer and the cell width was11.8%narrower in NIL-08Q043than in ZS97B. These differences are consistent with that of seed shape, showing that qSS7controls seed shape possibly by affecting cell shape of spikelets.
8. The dynamics of seed development and grain filling rate were surveyed using the NILs. The seed shape was significantly different between the two NILs after panicle8cm in length. This result consisted with the expression levels during the panicle development stage. However, no difference in grain filling rate between two the NILs was observed at entire grain-filling stage.
9. Yield and quality-related traits in the NILs were investigated as well. There were differences in heading date, panicle length, spikelet density, grain chalk percentage and grain chalk degree between the two NILs (NIL-08Q043and NIL-ZS97B), but no difference in grain yield and grain quality.
引文
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