利用水稻代换系定位种子萌发速率和品质基因
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摘要
种子萌发的快慢是作物的一个重要农艺性状。高活性的种子是水稻直播的先决条件。一般条件下,籼稻的发芽速率比粳稻要快。利用这一差别可以区分这两个亚种。本研究利用一套以籼稻珍汕97B为背景、粳稻日本晴为供体的染色体片段代换(导入)系为材料,对水稻种子萌发速率进行数量性状位点(QTL)分析,并精细定位其中一个主效QTL qGR2。同时,利用该套日本晴染色体片段代换系对稻米的品质性状进行QTL定位和应用研究。主要结果如下：
1.在13℃、18℃、23℃和28℃条件下,珍汕97B与日本晴之间的种子萌动速率差异是稳定存在的。42份栽培稻品种的发芽试验表明,籼稻与粳稻两个亚种间存在显著的萌动速率差异。在23℃条件下,籼稻品种的平均萌动速率比粳稻品种快约5.8倍。
2.利用143份日本晴染色体片段代换(导入)系,分别在第2、5、6和10四个染色体上定位到4个与水稻萌动速率相关的QTL,其来源于日本晴的等位基因在一定程度上降低了种子的萌发速率。
3.利用其中1份代换系CSSL29衍生的F2群体,对第2染色体的QTL (qGR2)进行验证和精细定位。初步定为结果显示,qGR2在RM12532-RM12544区间,其解释的变异为24.3%。选取含有目标片段为杂合的1个单株,自交获得F3大群体(2720个单株),并从中筛选出23株qGR2区段交换单株。利用分子标记与表型相结合的方法,最终将qGR2精细定位到MC04和RM423之间,物理距离10.4kb,位于一个BAC克隆上。该区间预测含有3个候选基因,Loc_Os02g07410、 Loc_Os02g07420和Loc_Os02g07430。
4.对143份代换系的种子长宽比,直链淀粉含量,蛋白质含量和千粒重与萌发速率进行相关分析,结果表明,种子的萌发速率只与蛋白质含量呈显著正相关。
5.半定量(RT-PCR)表达分析显示,候选基因Loc_Os02g07430(OsMADS29)在珍汕97B和代换系CSSL29的萌动过程中表现出不同的表达模式。候选基因在两材料种子中的表达时间与各自种子胚根的突出时间相一致。
6.珍汕97B与日本晴在直链淀粉含量,蛋白质含量,碱消值,垩白度上存在较大差异。利用143份日本晴染色体片段代换系,通过IciMapping v3.0软件共检测到6个品质性状共36个QTL。这些QTL有的含有已经被克隆的品质基因如Wx、alk等。这些主效QTL可以显著改良珍汕97B的稻米品质。
7.143份代换系的品质性状与农艺性状的相关性分析表明,蛋白质含量,碱消值和垩白度与抽穗期相关,可能极易受环境影响。
8.构建了7个分别含有不同品质基因的代换(导入)系材料,通过其与明恢63测交,评价其品质性状的表现,结果发现,代换系品质性状的改变可以影响其杂交种的品质。试验结果为改良杂交种稻米品质提供了一定理论指导和实践基础。
Rapid and uniform seed germination is one of the important agronomic traits and critical for direct seeding in rice. The Asian cultivated rice (O. sativa L.) consists of two subspecies, indica (O. sativa L. ssp. indica) and japonica (O. sativa L. ssp. japonica). Generally, indica cultivars geminate faster than japonica. Here, we developed a set of chromosomal segment substitution lines (CSSL) by backcrossing and marker-assisted selection in which the japonica Nipponbare was the donor parent, and the recurrent parent was the indica 'Zhenshan97B'(ZS97B). Each line contains a substituted Nipponbare donor segment of a particular chromosomal region within the uniform genetic background of the ZS97B, and all the substitution segments together cover the entire Nipponbare genome. We surveyed genetic bases of germination rate using this set of143CSSLs, validated and finely mapped a major QTL (qGR2) for germination rate. The main results are as follows:
1. The differences in germination rate existed stably between ZS97B and Nipponbare at various genmination temperature conditions (13℃,18℃,23℃and28℃). Besides the two parents (ZS97B and Nipponbare), the other42cultivars also showed great variation in germination rate under23℃at2days after imbibition. On average, the germination rate of indica cultivars was5.8times faster than that in the japonica.
2. Four QTL (qGR2, qGR5, qGR6and qGR10) were identified for germination rate in the CSSL population, of which all the japonica alleles decreased the germination rate.
3. Using a F2population derived from a CSSL (CSSL29) that contains the target substitution region on chromosome2and ZS97B, qGR2was confirmed as a major QTL explained24.3%of phenotypic variance, and located in the interval of RM12532-RM12544. A large segregation population comprised2,720individuals was further generated by selfing a single F2individual heterozygous at the qGR2region. Twenty-three informative recombinants were identified with8markers in the region, and grouped into six genotype classes according to the positions of recombinant points and allelic composition. Multiple comparisons of the germination rate among the six genotypes and the control (ZS97B) narrowed qGR2down to a genomic region between RM12530and RM423, a segment about60-kb in length. The position of the QTL underlying germination rate was narrowed down even further to a10.4-kb length defined by markers MC04and RM423by analyzing more SNP markers in the interval. This small region is on a single bacterial artificial chromosome clone and contains three predicted genes, namely Loc_Os02g07410, Loc_Os02g07420, and Loc_Os02g07430(OsMADS29).
4. Germination rate was significantly and positively correlated with protein content, but not with seed shape, amylose content, and1,000-grain weight in the143CSSL.
5. Expression analysis by RT-PCR revealed different expression patterns of the gene OsMADS29in ZS97B and CSSL29during seed germination. These differences in the time of expression were highly consistent with that time taken for radicle protrusion in ZS97B and CSSL29.
6. There were significant differences in amylose content, protein content, gel consistency, and grain chalkiness between ZS97B and Nipponpare. We detected36QTLs for six grain quality traits. Several major QTLs co-located with the known quality genes such as Wx, alk, of which Nipponbare alleles could improve the grain quality of ZS97B.
7. Association analysis showed that the grain quality including protein content, gel consistency, grain chalkiness are associated with heading date in the143CSSLs, indicating that these grain quality traits in rice is highly influenced by environment.
8. We have constructed seven CSSLs each containing at least one favorable gene from Nippobare for grain quality. The testcrossing hybrids between the CSSL and Minghui63, an elite restorer line, showed a remarkable improvement in grain quality, suggesting a potential way to improve the grain quality of ZS97B and its hybrids.
1.在13℃、18℃、23℃和28℃条件下,珍汕97B与日本晴之间的种子萌动速率差异是稳定存在的。42份栽培稻品种的发芽试验表明,籼稻与粳稻两个亚种间存在显著的萌动速率差异。在23℃条件下,籼稻品种的平均萌动速率比粳稻品种快约5.8倍。
2.利用143份日本晴染色体片段代换(导入)系,分别在第2、5、6和10四个染色体上定位到4个与水稻萌动速率相关的QTL,其来源于日本晴的等位基因在一定程度上降低了种子的萌发速率。
3.利用其中1份代换系CSSL29衍生的F2群体,对第2染色体的QTL (qGR2)进行验证和精细定位。初步定为结果显示,qGR2在RM12532-RM12544区间,其解释的变异为24.3%。选取含有目标片段为杂合的1个单株,自交获得F3大群体(2720个单株),并从中筛选出23株qGR2区段交换单株。利用分子标记与表型相结合的方法,最终将qGR2精细定位到MC04和RM423之间,物理距离10.4kb,位于一个BAC克隆上。该区间预测含有3个候选基因,Loc_Os02g07410、 Loc_Os02g07420和Loc_Os02g07430。
4.对143份代换系的种子长宽比,直链淀粉含量,蛋白质含量和千粒重与萌发速率进行相关分析,结果表明,种子的萌发速率只与蛋白质含量呈显著正相关。
5.半定量(RT-PCR)表达分析显示,候选基因Loc_Os02g07430(OsMADS29)在珍汕97B和代换系CSSL29的萌动过程中表现出不同的表达模式。候选基因在两材料种子中的表达时间与各自种子胚根的突出时间相一致。
6.珍汕97B与日本晴在直链淀粉含量,蛋白质含量,碱消值,垩白度上存在较大差异。利用143份日本晴染色体片段代换系,通过IciMapping v3.0软件共检测到6个品质性状共36个QTL。这些QTL有的含有已经被克隆的品质基因如Wx、alk等。这些主效QTL可以显著改良珍汕97B的稻米品质。
7.143份代换系的品质性状与农艺性状的相关性分析表明,蛋白质含量,碱消值和垩白度与抽穗期相关,可能极易受环境影响。
8.构建了7个分别含有不同品质基因的代换(导入)系材料,通过其与明恢63测交,评价其品质性状的表现,结果发现,代换系品质性状的改变可以影响其杂交种的品质。试验结果为改良杂交种稻米品质提供了一定理论指导和实践基础。
Rapid and uniform seed germination is one of the important agronomic traits and critical for direct seeding in rice. The Asian cultivated rice (O. sativa L.) consists of two subspecies, indica (O. sativa L. ssp. indica) and japonica (O. sativa L. ssp. japonica). Generally, indica cultivars geminate faster than japonica. Here, we developed a set of chromosomal segment substitution lines (CSSL) by backcrossing and marker-assisted selection in which the japonica Nipponbare was the donor parent, and the recurrent parent was the indica 'Zhenshan97B'(ZS97B). Each line contains a substituted Nipponbare donor segment of a particular chromosomal region within the uniform genetic background of the ZS97B, and all the substitution segments together cover the entire Nipponbare genome. We surveyed genetic bases of germination rate using this set of143CSSLs, validated and finely mapped a major QTL (qGR2) for germination rate. The main results are as follows:
1. The differences in germination rate existed stably between ZS97B and Nipponbare at various genmination temperature conditions (13℃,18℃,23℃and28℃). Besides the two parents (ZS97B and Nipponbare), the other42cultivars also showed great variation in germination rate under23℃at2days after imbibition. On average, the germination rate of indica cultivars was5.8times faster than that in the japonica.
2. Four QTL (qGR2, qGR5, qGR6and qGR10) were identified for germination rate in the CSSL population, of which all the japonica alleles decreased the germination rate.
3. Using a F2population derived from a CSSL (CSSL29) that contains the target substitution region on chromosome2and ZS97B, qGR2was confirmed as a major QTL explained24.3%of phenotypic variance, and located in the interval of RM12532-RM12544. A large segregation population comprised2,720individuals was further generated by selfing a single F2individual heterozygous at the qGR2region. Twenty-three informative recombinants were identified with8markers in the region, and grouped into six genotype classes according to the positions of recombinant points and allelic composition. Multiple comparisons of the germination rate among the six genotypes and the control (ZS97B) narrowed qGR2down to a genomic region between RM12530and RM423, a segment about60-kb in length. The position of the QTL underlying germination rate was narrowed down even further to a10.4-kb length defined by markers MC04and RM423by analyzing more SNP markers in the interval. This small region is on a single bacterial artificial chromosome clone and contains three predicted genes, namely Loc_Os02g07410, Loc_Os02g07420, and Loc_Os02g07430(OsMADS29).
4. Germination rate was significantly and positively correlated with protein content, but not with seed shape, amylose content, and1,000-grain weight in the143CSSL.
5. Expression analysis by RT-PCR revealed different expression patterns of the gene OsMADS29in ZS97B and CSSL29during seed germination. These differences in the time of expression were highly consistent with that time taken for radicle protrusion in ZS97B and CSSL29.
6. There were significant differences in amylose content, protein content, gel consistency, and grain chalkiness between ZS97B and Nipponpare. We detected36QTLs for six grain quality traits. Several major QTLs co-located with the known quality genes such as Wx, alk, of which Nipponbare alleles could improve the grain quality of ZS97B.
7. Association analysis showed that the grain quality including protein content, gel consistency, grain chalkiness are associated with heading date in the143CSSLs, indicating that these grain quality traits in rice is highly influenced by environment.
8. We have constructed seven CSSLs each containing at least one favorable gene from Nippobare for grain quality. The testcrossing hybrids between the CSSL and Minghui63, an elite restorer line, showed a remarkable improvement in grain quality, suggesting a potential way to improve the grain quality of ZS97B and its hybrids.
引文
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