水稻糙米垩白粒率的QTL分析与垩白突变体的初步研究
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摘要
垩白是指稻米胚乳中白色不透明的部分。垩白粒率(Percentage of grains with chalkiness, PGWC)是稻米最重要的外观品质指标之一。垩白的形成是由于籽粒胚乳中淀粉的不正确积累而导致的一种复杂的表型,垩白不仅降低稻米外观品质,而且降低碾米品质以及蒸煮食味品质。研究表明,稻米垩白性状属于复杂的数量性状,受多基因控制,日前对于垩白形成的分子机制尚不清楚,这在很大程度上阻碍了稻米品质的遗传改良。本研究利用以IR24为受体、Asominori为供体构建染色体片段置换系群体,进行水稻糙米粒长、粒宽与垩白粒率QTL检测及稳定性分析；利用高垩白粒率的染色体片段置换系CSSL64和Asominori的次级F2和F3群体,分析垩白粒率QTL并对稳定表达的qPGWC-9进行定位；此外对2个高垩白突变体进行遗传分析和侧翼序列分析。为水稻垩白粒率的改良提供理论依据,为垩白粒率QTL图位克隆奠定基础,为研究垩白的形成提供材料。主要结论如下：
1.利用IR24为遗传背景插入Asominori的全基因组CSSLs (Chromosome segment substitution lines)群体为材料,分析控制水稻糙米粒长、粒宽和垩白粒率QTL和稳定性。相关分析表明,群体糙米粒宽和垩白粒率在2007年3个环境下均呈显著正相关。3个环境下共检测到粒宽QTL7个,其中3个在金湖和南京2个环境下重复检测到。共检测到粒长QTL2个,均在两个环境下重复检测到。垩白粒率QTL4个,2个在3个环境下重复检测到,其余2个QTL只在1个环境下重复检测到。qGW-1b、qGL-3、qGL-5、 qPGWC-5、qPGWC-7对应的置换系与背景亲本IR24在3个环境中相应性状的表现型之间都存在显著差异(P<0.05)。比较分析发现1个主效QTL同时控制粒宽和垩白粒率,粒宽和垩白粒率的增效等位基因来自同一亲本IR24,2个主效QTLs同时控制粒长和粒宽,没有检测到同时控制垩白粒率和粒长的QTL。一些与垩白粒率不相关的粒宽和粒长主效QTL,如qGW-1a、qGW-1b、qGW-3、qGW-5b、qGW-7、qGL-3和qGL-5,均可为育种所利用。
2.利用高垩白粒率的染色体片段置换系家系CSSL64与受体亲本Asominori构建的次级F2和F3群体为材料,分析了CSSL64高垩白粒率形成的遗传机理。利用CSS64×Asominori F2群体在连续3年检测到7个控制PGWC的主效QTLs,分布于水稻5条染色体上。qPGWC-9在3个环境中重复出现。为进一步定位qPGWC-9,利用分子标记,在2006年的CSS64×Asominori F2群体中选择在目的qPGWC-9位点杂合,而在其它QTLs位点为纯合的单株,自交形成F3,最终将qPGWC-9定位在了第9染色体的RM23958-RM1328之间。
3.利用两个胚乳垩白突变体(T2915和T4420),对其突变体的遗传组成进行研究。结果显示T4420突变体在垩白率、粒型、株高上与野生型日本晴相比较具有显著差异。通过对T4420×日本晴F2群体表型分离和潮霉素抗性分析表明,T4420是显性单基因突变,突变的原因是外源T-DNA的插入引起的。T4420来源于日本晴增强子捕获突变体库,PCR-WALKING侧翼序列分析发现外源片段插入第二染色体基因的非编码区。对插入位点上下游基因,进行Real-time RT-PCR分析,在10天的幼苗中,这一对基因的表达与日本晴相比差异较小。T2915突变体只在垩白率和株高上与日本晴具有差异显著,而百粒重与野生型日本晴没有差异显著。通过对T2915×日本晴F2群体表型分离和潮霉素抗性分析表明,T2915的突变是隐性单基因突变,外源T-DNA的插入引起突变。突变体T2915来源于日本晴的激活标签突变体库,PCR-WALKING侧翼序列分析发现外源片段插入位于第一染色体基因的非编码区。对插入位点上游基因,进行Real-time RT-PCR分析,在10天的幼苗中,这一基因的表达比日本晴显著增高,达36倍之多,这一结果说明T-DNA的插入,导致插入位点上游的基因增强表达,从而产生突变表型。这2个突变体表型和遗传上的差异,为稻米品质的研究提供了材料。
Chalky endosperm in rice refers to white opaque part. The formation of chalky endosperm starch is due to an abnormal accumulation starch in rice. Percentage of grains with chalkiness (PGWC) is important to the appearance quality of milled rice. PGWC is a physical characteristic which negatively affects not only the appearence and milling quality but also affects the cooking texture and palatability. Chalkiness grain is a complicated quantitative trait and its molecular mechanisms of formation are still poorly understood. This largely retarded the genetic improvement of rice quality In this study, a chromosome segment substhitute lines (CSSL) population derived from the cross of Asominori (Japonica) and IR24(Indica) were used to detect stable QTL analysis for grain length(GL), width(GW) and PGWC of brown rice. CSSL carried overlapping chromosome segments of Asominori in a genetic background of IR24. One chromosome segmental substitution line (CSSL64) with7segments derived from IR24was significantly higher PGWC than its parent Asominori. A secondary F2and F3populations derived from CSSL64crossed with Asominori were used to detect QTLs and to further explore the genetics of CSSL64with high PGWC. Two mutants with chalky endosperm were identified from a T-DNA insertion population derived from a Japonica rice variety (Nipponbare). The results would be useful for the simultaneous improvement of PGWC and map-based cloning of target QTL. The main conclusions are as follows:
1. A chromosome segment substitution line (CSSL)population, derived from the cross of Asominori and IR24with IR24as the recurrent parent, was phenotyped for GW, GL and PGWC of brown rice in three sites. The population was used to detect the correlations and stable QTLs on GW, GL and PGWC. Correlation analysis showed that there was a significantly positive correlation between GW and PGWC among the CSSL population in3sites. A total of7,2,4QTLs for GW, GL, PGWC were detected at3sites in2007, respectively. Moreover, phenotypic values were different significantly (P<0.05) between IR24and the target CSSLs harboring qGW-1b, qGL-3, qGL-5, qPGWC-5, qPGWC-7QTL alleles. One main-effect QTL simultaneously controlling GW and PGWC were detected and their alleles increasing GW and PGWC were from the same parent, IR24. Two main-effect QTLs simultaneously controlling GW and GL were detected. There is no QTL simultaneously controlling GL and PGWC. Some main-effect QTLs, controlling grain shape but not PGWC, such as qGW-1a、qGW-1b、qGW-3、qGW-5b、qGW-7, qGL-5,和qGL-3are useful for breeding.
2. To further explore the genetics of CSSL64with high PGWC, we constructed an F2secondary population derived from Asominori×CSSL64. qPGWC-9was identified repeatedly in continuous three years (2005-2007), and qPGWC-9with an average PVE of19.4%was identified in the F2secondary population in all three years (2005-2007), and was finally located in the interval of RM23958-RM1328on chromosome9by using the Asominori×CSSL64F3population. These results should be useful for fine-mapping and map-based cloning of the qPGWC-9allele and for marker-assisted transfer of the allele in rice breeding programs.
3. In this study, genetic characterization of two mutants with chalky endosperm in rice was conducted by the mutant and its related genetic populations with Nipponbare. The results showed that there was a significant difference between T4420mutant and Nipponbare (wild-type) in PGWC, GL, GW, HGW and plant height. Genetic analysis of the mutant showed that two kinds of phenotype, such as high and lower PGWC in the segregating population derived from the cross of T4420with Nipponbare. They were fit for the ratio of3(high PGWC):1(lower type), indicating the high PGWC gene is a dominant mutation. The high PGWC gene was further mapped on rice chromosome2using PCR-WALKING. Test for HPT resistance showed the high PGWC plants were resistant while the lower PGWC plants were susceptive, and the ratio of resistance and sensitive plants was3:1, indicating that the mutation was co-segregating with HPT resistance. These data showed that the rice high PGWC mutant phenotype is controlled by a dominant gene mutation, which is caused by T-DNA insertion. T4420from Nipponbare enhancer trap mutant library, the analysis of flanking sequence showed that exogenous gene inserted into the non-coding regions of chromosome2. According to the Real-time RT-PCR analysis of upstream and downstream genes of the insertion site with10days seedlings, there was little difference in gene expression. There is no significant difference in grain weight between T2915mutation and the wild-type with chalky endosperm. The genetic analysis showed that a single recessive locus was responsible for chalky phenotype, which is located on the long arm of chromosome1. Exogenous T-DNA insertion caused the mutation. The Real-time RT-PCR analysis showed that the expression of the gene which locates on the upstream of the insertion site was significantly higher than in Nipponbare, up to about36times. The results indicate that T-DNA insertion enhanced expression of the gene, resulted in mutant phenotypes.
1.利用IR24为遗传背景插入Asominori的全基因组CSSLs (Chromosome segment substitution lines)群体为材料,分析控制水稻糙米粒长、粒宽和垩白粒率QTL和稳定性。相关分析表明,群体糙米粒宽和垩白粒率在2007年3个环境下均呈显著正相关。3个环境下共检测到粒宽QTL7个,其中3个在金湖和南京2个环境下重复检测到。共检测到粒长QTL2个,均在两个环境下重复检测到。垩白粒率QTL4个,2个在3个环境下重复检测到,其余2个QTL只在1个环境下重复检测到。qGW-1b、qGL-3、qGL-5、 qPGWC-5、qPGWC-7对应的置换系与背景亲本IR24在3个环境中相应性状的表现型之间都存在显著差异(P<0.05)。比较分析发现1个主效QTL同时控制粒宽和垩白粒率,粒宽和垩白粒率的增效等位基因来自同一亲本IR24,2个主效QTLs同时控制粒长和粒宽,没有检测到同时控制垩白粒率和粒长的QTL。一些与垩白粒率不相关的粒宽和粒长主效QTL,如qGW-1a、qGW-1b、qGW-3、qGW-5b、qGW-7、qGL-3和qGL-5,均可为育种所利用。
2.利用高垩白粒率的染色体片段置换系家系CSSL64与受体亲本Asominori构建的次级F2和F3群体为材料,分析了CSSL64高垩白粒率形成的遗传机理。利用CSS64×Asominori F2群体在连续3年检测到7个控制PGWC的主效QTLs,分布于水稻5条染色体上。qPGWC-9在3个环境中重复出现。为进一步定位qPGWC-9,利用分子标记,在2006年的CSS64×Asominori F2群体中选择在目的qPGWC-9位点杂合,而在其它QTLs位点为纯合的单株,自交形成F3,最终将qPGWC-9定位在了第9染色体的RM23958-RM1328之间。
3.利用两个胚乳垩白突变体(T2915和T4420),对其突变体的遗传组成进行研究。结果显示T4420突变体在垩白率、粒型、株高上与野生型日本晴相比较具有显著差异。通过对T4420×日本晴F2群体表型分离和潮霉素抗性分析表明,T4420是显性单基因突变,突变的原因是外源T-DNA的插入引起的。T4420来源于日本晴增强子捕获突变体库,PCR-WALKING侧翼序列分析发现外源片段插入第二染色体基因的非编码区。对插入位点上下游基因,进行Real-time RT-PCR分析,在10天的幼苗中,这一对基因的表达与日本晴相比差异较小。T2915突变体只在垩白率和株高上与日本晴具有差异显著,而百粒重与野生型日本晴没有差异显著。通过对T2915×日本晴F2群体表型分离和潮霉素抗性分析表明,T2915的突变是隐性单基因突变,外源T-DNA的插入引起突变。突变体T2915来源于日本晴的激活标签突变体库,PCR-WALKING侧翼序列分析发现外源片段插入位于第一染色体基因的非编码区。对插入位点上游基因,进行Real-time RT-PCR分析,在10天的幼苗中,这一基因的表达比日本晴显著增高,达36倍之多,这一结果说明T-DNA的插入,导致插入位点上游的基因增强表达,从而产生突变表型。这2个突变体表型和遗传上的差异,为稻米品质的研究提供了材料。
Chalky endosperm in rice refers to white opaque part. The formation of chalky endosperm starch is due to an abnormal accumulation starch in rice. Percentage of grains with chalkiness (PGWC) is important to the appearance quality of milled rice. PGWC is a physical characteristic which negatively affects not only the appearence and milling quality but also affects the cooking texture and palatability. Chalkiness grain is a complicated quantitative trait and its molecular mechanisms of formation are still poorly understood. This largely retarded the genetic improvement of rice quality In this study, a chromosome segment substhitute lines (CSSL) population derived from the cross of Asominori (Japonica) and IR24(Indica) were used to detect stable QTL analysis for grain length(GL), width(GW) and PGWC of brown rice. CSSL carried overlapping chromosome segments of Asominori in a genetic background of IR24. One chromosome segmental substitution line (CSSL64) with7segments derived from IR24was significantly higher PGWC than its parent Asominori. A secondary F2and F3populations derived from CSSL64crossed with Asominori were used to detect QTLs and to further explore the genetics of CSSL64with high PGWC. Two mutants with chalky endosperm were identified from a T-DNA insertion population derived from a Japonica rice variety (Nipponbare). The results would be useful for the simultaneous improvement of PGWC and map-based cloning of target QTL. The main conclusions are as follows:
1. A chromosome segment substitution line (CSSL)population, derived from the cross of Asominori and IR24with IR24as the recurrent parent, was phenotyped for GW, GL and PGWC of brown rice in three sites. The population was used to detect the correlations and stable QTLs on GW, GL and PGWC. Correlation analysis showed that there was a significantly positive correlation between GW and PGWC among the CSSL population in3sites. A total of7,2,4QTLs for GW, GL, PGWC were detected at3sites in2007, respectively. Moreover, phenotypic values were different significantly (P<0.05) between IR24and the target CSSLs harboring qGW-1b, qGL-3, qGL-5, qPGWC-5, qPGWC-7QTL alleles. One main-effect QTL simultaneously controlling GW and PGWC were detected and their alleles increasing GW and PGWC were from the same parent, IR24. Two main-effect QTLs simultaneously controlling GW and GL were detected. There is no QTL simultaneously controlling GL and PGWC. Some main-effect QTLs, controlling grain shape but not PGWC, such as qGW-1a、qGW-1b、qGW-3、qGW-5b、qGW-7, qGL-5,和qGL-3are useful for breeding.
2. To further explore the genetics of CSSL64with high PGWC, we constructed an F2secondary population derived from Asominori×CSSL64. qPGWC-9was identified repeatedly in continuous three years (2005-2007), and qPGWC-9with an average PVE of19.4%was identified in the F2secondary population in all three years (2005-2007), and was finally located in the interval of RM23958-RM1328on chromosome9by using the Asominori×CSSL64F3population. These results should be useful for fine-mapping and map-based cloning of the qPGWC-9allele and for marker-assisted transfer of the allele in rice breeding programs.
3. In this study, genetic characterization of two mutants with chalky endosperm in rice was conducted by the mutant and its related genetic populations with Nipponbare. The results showed that there was a significant difference between T4420mutant and Nipponbare (wild-type) in PGWC, GL, GW, HGW and plant height. Genetic analysis of the mutant showed that two kinds of phenotype, such as high and lower PGWC in the segregating population derived from the cross of T4420with Nipponbare. They were fit for the ratio of3(high PGWC):1(lower type), indicating the high PGWC gene is a dominant mutation. The high PGWC gene was further mapped on rice chromosome2using PCR-WALKING. Test for HPT resistance showed the high PGWC plants were resistant while the lower PGWC plants were susceptive, and the ratio of resistance and sensitive plants was3:1, indicating that the mutation was co-segregating with HPT resistance. These data showed that the rice high PGWC mutant phenotype is controlled by a dominant gene mutation, which is caused by T-DNA insertion. T4420from Nipponbare enhancer trap mutant library, the analysis of flanking sequence showed that exogenous gene inserted into the non-coding regions of chromosome2. According to the Real-time RT-PCR analysis of upstream and downstream genes of the insertion site with10days seedlings, there was little difference in gene expression. There is no significant difference in grain weight between T2915mutation and the wild-type with chalky endosperm. The genetic analysis showed that a single recessive locus was responsible for chalky phenotype, which is located on the long arm of chromosome1. Exogenous T-DNA insertion caused the mutation. The Real-time RT-PCR analysis showed that the expression of the gene which locates on the upstream of the insertion site was significantly higher than in Nipponbare, up to about36times. The results indicate that T-DNA insertion enhanced expression of the gene, resulted in mutant phenotypes.
引文
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