盐和低温胁迫下水稻种子萌发的遗传研究
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摘要
水稻是世界上最重要的粮食作物,盐、低温和干旱等是水稻生产上常见的非生物胁迫因子,严重影响水稻的生长和生产,阐明水稻耐这些逆境胁迫的遗传机理,改良水稻的抗逆性一直是水稻遗传育种研究的热点问题之一。本论文利用两个水稻重组自交系群体,研究了在盐和低温两种逆境胁迫下水稻种子萌发的遗传机理。
以IR26 (Oryza sativa L. spp. indica)和韭菜青(japonica)、IR28 (indica)和大关稻(japonica)为亲本,通过“单粒传法”获得IR26/韭菜青和IR28/大关稻重组自交系(RILs)群体(F2：7),并构建相应的SSR分子连锁图谱进行比较,结果表明,IR26/韭菜青和IR28/大关稻RILs群体亲本DNA多态率分别为25.9%和24.6%,基因组中分别有57和74个SSR座位发生偏分离,偏分离率分别为42.2%和44.3%,均主要偏向于籼型亲本。分析群体内各株系每条染色体的基因型,发现IR26/韭菜青和IR28/大关稻RILs群体中均存在异常偏分离家系,偏分离率分别为47.2%和52.9%；亲本对各家系遗传贡献率呈正态分布,表明双亲对子代的遗传贡献基本上是平衡的,且群体中存在多个遗传结构相似的家系；构建的IR26/韭菜青、IR28/大关稻分子连锁图谱分别能覆盖水稻基因组2225.3 cM、1846.6 cM,平均图距分别为16.5 cM、11.1 cM,适合于在全基因组进行QTL检测。在IR26/韭菜青、IR28/大关稻基因组中分别检测到6、8个偏分离热点区(SDR),其中的3个偏分离热点区(SDR 2、SDR 4-2、SDR 12-1)为本研究首次报道。
利用IR26/韭菜青F2：9重组自交系(RILs)为作图群体构建水稻分子遗传连锁图谱,分别在正常条件下(水)和100 mmol/L的NaCl胁迫下处理水稻种子10 d,鉴定种子的萌发能力,包括吸胀速率、发芽率、发芽指数、根长、芽长和活力指数。采用主基因-多基因遗传模型分离分析法进行遗传分析和复合区间作图法进行QTL定位。结果表明,盐胁迫显著抑制了水稻种子萌发,发芽早期(0～5d)是水稻种子萌发盐敏感期,RILs家系间种子萌发存在显著差异。除吸胀速率外,其他种子萌发性状之间均呈极显著正相关。RILs种子萌发性状的次数分布呈连续变异,表明种子萌发性状是由多基因控制的数量遗传性状,且多数RILs偏向于盐敏感型。水稻不同的萌发性状受不同遗传模式控制,其中吸胀速率由2对主基因模型控制,发芽指数、活力指数由2对主基因+多基因模型控制,根长由2对主基因或2对主基因+多基因模型控制,发芽率、芽长由3对主基因+多基因模型控制,以主基因遗传为主,主基因遗传率为12.5%～99.0%。在正常条件下,共检测到12个QTLs：2个控制吸胀速率(qIR-8、qIR-10)、1个控制发芽率(qGR-7)、1个控制发芽指数(qGI-2)、4个控制根长(qRL-1、qRL-4、qRL-9、qRL-10)、2个控制芽长(qSL-7、qSL-11)、2个控制活力指数(qVI-6、qVI-7),单个QTL能解释12.5%～25.5%的表型变异。在盐胁迫条件下,共检测到4个QTLs：2个控制吸胀速率(qIR-4、qIR-9)、1个控制发芽率(qGR-2)、1个控制活力指数(qVI-8),单个QTL能解释9.1%-46.6%的表型变异,其中控制发芽率的qGR-2为一主效QTL贡献率为46.6%。QTLs的表达存在时效性,比较以往报道的水稻耐盐相关QTLs,未发现与qVI-8、qGI-8位置相近的QTL,可能为两个新的耐盐基因座。
利用IR28/大关稻F2：9重组自交系(RILs)为作图群体构建水稻分子遗传连锁图谱,分别在正常条件下(30℃)处理10 d和低温14℃下处理23 d鉴定种子的萌发能力,包括吸胀速率、发芽率、发芽指数、根长、芽长和活力指数。采用主基因-多基因混合遗传模型分离分析法进行遗传分析和复合区间作图法进行QTL定位。结果表明,水稻种子萌发能力受低温胁迫抑制,RILs家系间种子萌发能力存在显著差异。除吸胀速率外,其他性状之间均呈极显著正相关。RILs种子萌发性状的次数分布呈连续变异,表明种子萌发性状是由多基因控制的数量遗传性状,且多数RILs偏向于冷敏感型。水稻不同的萌发性状受不同遗传模式控制,其中吸胀速率、根长、芽长、活力指数由2对主基因+多基因模型控制,发芽率由2对或3对主基因模型控制,发芽指数由2对主基因控制,以主基因遗传为主,主基因遗传率为26.4%-95.3%。在正常条件下,共检测到11个QTLs：3个控制吸胀速率(qIR-6、qIR-9、qIR-11)、2个控制发芽指数(qGI-1、qGI-7)、2个控制根长(qRL-11、qRL-12)、2个控制芽长(qSL-8、qSL-9)、2个控制活力指数(qVI-2、qVI-9),单个QTL能解释15.1%-32.4%的表型变异。在低温胁迫条件下,共检测到7个QTLs：2个控制吸胀速率(qIR-6、qIR-9)、1个控制发芽率(qGR-4)、2个控制发芽指数(qGI-4-1、qGI-4-2)、2个控制根长(qRL-4-1、qRL-4-2),单个QTL能解释9.1%～37.0%的表型变异,其中控制吸胀速率的qIR-6为一主效QTL,贡献率为31.0%～34.5%,控制发芽指数的qGI-4-2为另一主效QTL,贡献率为37.0%。QTLs的表达存在时效性,比较以往报道的水稻耐冷相关QTLs,未发现与qRL-4-2位置相近的QTL,可能为一个新的耐冷基因座。
Rice is the most important crop in the world. However, the growth and production of rice are limitted frequently by some abiotic stresses, such as salinity, drought, and low temperature. Therefore, improving the abiotic stress tolerance in rice has become one main objective of rice research. Two recombine inbred lines (RILs) populations were used to investigate the genetic control of rice seed germination under salt and cold stress in this thesis.
In the last decade, the development of rice molecular linkage maps has provided powerful tool to carry out rice genomic researches, such as QTL mapping, map-based cloning, comparative genomics, genetic diversity research and marker-assisted selection breeding. Here, two F2:1 recombinant inbred lines (RILs) populations, IR26/Jiucaiqing and IR28/Daguandao, respectively, derived from a cross between IR26 (Oryza sativa L. spp. indica) and Jiucaiqing (japonica), and IR28 (indica) and Daguandao (japonica), were used to construct two SSR molecular linkage maps. The results showed that the DNA polymorphism between parents of IR26/Jiucaiqing and IR28/Daguandao were similar, with polymorphic rate 42.2% and 44.3%, respectively. There were 57 and 74 SSR loci showing genetic distortion, mainly partial to indica parents, among IR26/Jiucaiqing and IR28/Daguandao genome, respectively, with the segregation distortion rate 42.2% and 44.3%. The genotype of each line at each chromosome was analyzed; there were genetic distortion lines in two RILs with segregation distortion rate 47.2% and 52.9%, respectively. The distribution of paternal contribution was normal in progenies which illustrated that genetic contributions from the parents were equals, and some lines with similar genotypic components in two RILs. In addition, the two genetic maps of IR26/Jiucaiqing and IR28/Daguandao covered 2225.3 cM and 1846.6 cM of rice genome, respectively, with the average interval of 16.5 cM and 11.1 cM, which were suitable for QTL mapping. The two maps differed in mapped markers, sequenced order of markers, genetic distance and average distance on the maps. Finally, six and eight segregation distortion regions (SDRs) were detected on IR26/Jiucaiqing and IR28/Daguandao chromosomes, respectively, three new SDRs (SDR 2, SDR 4-2, SDR 12-1) were detected here, and several gametophytic genes (ga) and sterile gene (s) were located near some SDRs, indicating that segregation distortion could be partially caused by gametophytic genes and sterile genes.
One F2:9 recombinant inbred lines (RILs) population, derived from a cross between IR26 (Oryza sativa L. spp. indica) and Jiucaiqing (japonica), was used to determine the germination ability including imbibition rate, germination rate, germination index, root length, shoot length and vigor index under control (water) and salt stress (100 mM NaCl) for 10 d. A major gene plus polygene mix inheritance model and the composite interval mapping (CIM) were applied to conduct genetic analysis for germination ability. The results showed that the performances of rice seed germination were mostly limited by salt stress and the early germination stage (0-5 d) might be the salt sensitive stage in rice. There were significant differences in all germination traits under salt stress among RILs. Correlation coefficients among the germination traits, except the imbibition rate, under salt stress were all positively significant. The frequency distributions of germination traits in RILs population showed continuous segregation, suggesting these were quantitative traits controlled by several genes, and more RILs were skewed to salt sensitive type. Each trait was controlled by the specific genetic model:imbibition rate controlled by two major genes, germination index and vigor index controlled by two major genes plus polygene, germination rate and shoot length regulated by three major genes plus polygene, and root length controlled by two major genes or two major genes plus polygene, and mainly dominated by major genes with high heritability values, accounted for 12.5%-99.0% of the total phenotypic variation. In the control group, twelve QTLs were identified:two for imbibition rate (qIR-8 qIR-10), one for germination rate (qGR-7), one for germination index (qGI-2), four for root length (qRL-1 qRL-4 qRL-9 qRL-10), two for shoot length (qSL-7 qSL-11) and two for vigor index (qVI-6 qⅥ-7), respectively, accounting for 12.5%-25.5% of the total phenotypic variance individually. In the saline group, four QTLs were identified: two for imbibition rate (qIR-4 qIR-9), one for germination rate (qGR-2) and one for vigor index (qⅥ-8), respectively, explaining 9.1%-46.6% of the total phenotypic variance individually. One major QTL qGR-2 was explaning 46.6% of the total phenotypic variance. The expression of QTLs was developmentally regulated and growth stage-specific. Most of the QTLs observed here were located in regions similar to the QTLs for rice salt tolerance reported previously, but qⅥ-8 and qGI-8 are reported here for the first time.
One F2:9 recombinant inbred lines (RILs) population, derived from a cross between IR28(Oryza sativa L. spp. indica) and Daguandao (japonica), was used to determine the germination ability including imbibition rate, germination rate, germination index, root length, shoot length and vigor index under control (30℃) for 10 d and cold stress (14℃) for 23 d. A major gene plus polygene mix inheritance model and the composite interval mapping (CIM) were applied to conduct genetic analysis for germination ability. The results showed that the performances of rice seed germination were mostly limited by cold stress and there were significant differences in all germination traits under cold stress among RILs. Correlation coefficients among the germination traits, except the imbibition rate, under cold stress were all positively significant. The frequency distributions of germination traits in RILs population showed continuous segregation, suggesting these were quantitative traits controlled by several genes, and more RILs were skewed to cold sensitive type. Each trait was controlled by the specific genetic model:imbibition rate, root length, shoot length and vigor index controlled by two major genes plus polygene, germination rate controlled by two or three major genes and germination index regulated by two major genes, and mainly dominated by major genes with high heritability values, accounted for 26.4%～95.3% of the total phenotypic variation. In the control group, eleven QTLs were identified:three for imbibition rate(qIR-6 qIR-9 qIR-11), two for germination index (qGI-1 qGI-7), two for root length (qRL-11 qRL-12), two for shoot length (qSL-8 qSL-9) and two for vigor index (qVI-2 qVI-9), respectively, accounting for 15.1%～32.4% of the total phenotypic variance individually. In the cold group, seven QTLs were identified: two for imbibition rate (qIR-6 qIR-9), one for germination rate (qGR-4), two for germination index (qGI-4-1 qGI-4-2) and two for root length (qRL-4-1 qRL-4-2), respectively, explaining 9.1%～37.0% of the total phenotypic variance individually. One major QTL qIR-6 explained for 31.0%～34.5% of the total phenotypic variance, and another major QTL qGI-4-2 accounted for 37.0% of the total phenotypic variance. The expression of QTLs was developmentally regulated and growth stage-specific. Most of the QTLs observed here were located in regions similar to the QTLs for rice cold tolerance reported previously, but qRL-4-2 is reported here for the first time.
以IR26 (Oryza sativa L. spp. indica)和韭菜青(japonica)、IR28 (indica)和大关稻(japonica)为亲本,通过“单粒传法”获得IR26/韭菜青和IR28/大关稻重组自交系(RILs)群体(F2：7),并构建相应的SSR分子连锁图谱进行比较,结果表明,IR26/韭菜青和IR28/大关稻RILs群体亲本DNA多态率分别为25.9%和24.6%,基因组中分别有57和74个SSR座位发生偏分离,偏分离率分别为42.2%和44.3%,均主要偏向于籼型亲本。分析群体内各株系每条染色体的基因型,发现IR26/韭菜青和IR28/大关稻RILs群体中均存在异常偏分离家系,偏分离率分别为47.2%和52.9%；亲本对各家系遗传贡献率呈正态分布,表明双亲对子代的遗传贡献基本上是平衡的,且群体中存在多个遗传结构相似的家系；构建的IR26/韭菜青、IR28/大关稻分子连锁图谱分别能覆盖水稻基因组2225.3 cM、1846.6 cM,平均图距分别为16.5 cM、11.1 cM,适合于在全基因组进行QTL检测。在IR26/韭菜青、IR28/大关稻基因组中分别检测到6、8个偏分离热点区(SDR),其中的3个偏分离热点区(SDR 2、SDR 4-2、SDR 12-1)为本研究首次报道。
利用IR26/韭菜青F2：9重组自交系(RILs)为作图群体构建水稻分子遗传连锁图谱,分别在正常条件下(水)和100 mmol/L的NaCl胁迫下处理水稻种子10 d,鉴定种子的萌发能力,包括吸胀速率、发芽率、发芽指数、根长、芽长和活力指数。采用主基因-多基因遗传模型分离分析法进行遗传分析和复合区间作图法进行QTL定位。结果表明,盐胁迫显著抑制了水稻种子萌发,发芽早期(0～5d)是水稻种子萌发盐敏感期,RILs家系间种子萌发存在显著差异。除吸胀速率外,其他种子萌发性状之间均呈极显著正相关。RILs种子萌发性状的次数分布呈连续变异,表明种子萌发性状是由多基因控制的数量遗传性状,且多数RILs偏向于盐敏感型。水稻不同的萌发性状受不同遗传模式控制,其中吸胀速率由2对主基因模型控制,发芽指数、活力指数由2对主基因+多基因模型控制,根长由2对主基因或2对主基因+多基因模型控制,发芽率、芽长由3对主基因+多基因模型控制,以主基因遗传为主,主基因遗传率为12.5%～99.0%。在正常条件下,共检测到12个QTLs：2个控制吸胀速率(qIR-8、qIR-10)、1个控制发芽率(qGR-7)、1个控制发芽指数(qGI-2)、4个控制根长(qRL-1、qRL-4、qRL-9、qRL-10)、2个控制芽长(qSL-7、qSL-11)、2个控制活力指数(qVI-6、qVI-7),单个QTL能解释12.5%～25.5%的表型变异。在盐胁迫条件下,共检测到4个QTLs：2个控制吸胀速率(qIR-4、qIR-9)、1个控制发芽率(qGR-2)、1个控制活力指数(qVI-8),单个QTL能解释9.1%-46.6%的表型变异,其中控制发芽率的qGR-2为一主效QTL贡献率为46.6%。QTLs的表达存在时效性,比较以往报道的水稻耐盐相关QTLs,未发现与qVI-8、qGI-8位置相近的QTL,可能为两个新的耐盐基因座。
利用IR28/大关稻F2：9重组自交系(RILs)为作图群体构建水稻分子遗传连锁图谱,分别在正常条件下(30℃)处理10 d和低温14℃下处理23 d鉴定种子的萌发能力,包括吸胀速率、发芽率、发芽指数、根长、芽长和活力指数。采用主基因-多基因混合遗传模型分离分析法进行遗传分析和复合区间作图法进行QTL定位。结果表明,水稻种子萌发能力受低温胁迫抑制,RILs家系间种子萌发能力存在显著差异。除吸胀速率外,其他性状之间均呈极显著正相关。RILs种子萌发性状的次数分布呈连续变异,表明种子萌发性状是由多基因控制的数量遗传性状,且多数RILs偏向于冷敏感型。水稻不同的萌发性状受不同遗传模式控制,其中吸胀速率、根长、芽长、活力指数由2对主基因+多基因模型控制,发芽率由2对或3对主基因模型控制,发芽指数由2对主基因控制,以主基因遗传为主,主基因遗传率为26.4%-95.3%。在正常条件下,共检测到11个QTLs：3个控制吸胀速率(qIR-6、qIR-9、qIR-11)、2个控制发芽指数(qGI-1、qGI-7)、2个控制根长(qRL-11、qRL-12)、2个控制芽长(qSL-8、qSL-9)、2个控制活力指数(qVI-2、qVI-9),单个QTL能解释15.1%-32.4%的表型变异。在低温胁迫条件下,共检测到7个QTLs：2个控制吸胀速率(qIR-6、qIR-9)、1个控制发芽率(qGR-4)、2个控制发芽指数(qGI-4-1、qGI-4-2)、2个控制根长(qRL-4-1、qRL-4-2),单个QTL能解释9.1%～37.0%的表型变异,其中控制吸胀速率的qIR-6为一主效QTL,贡献率为31.0%～34.5%,控制发芽指数的qGI-4-2为另一主效QTL,贡献率为37.0%。QTLs的表达存在时效性,比较以往报道的水稻耐冷相关QTLs,未发现与qRL-4-2位置相近的QTL,可能为一个新的耐冷基因座。
Rice is the most important crop in the world. However, the growth and production of rice are limitted frequently by some abiotic stresses, such as salinity, drought, and low temperature. Therefore, improving the abiotic stress tolerance in rice has become one main objective of rice research. Two recombine inbred lines (RILs) populations were used to investigate the genetic control of rice seed germination under salt and cold stress in this thesis.
In the last decade, the development of rice molecular linkage maps has provided powerful tool to carry out rice genomic researches, such as QTL mapping, map-based cloning, comparative genomics, genetic diversity research and marker-assisted selection breeding. Here, two F2:1 recombinant inbred lines (RILs) populations, IR26/Jiucaiqing and IR28/Daguandao, respectively, derived from a cross between IR26 (Oryza sativa L. spp. indica) and Jiucaiqing (japonica), and IR28 (indica) and Daguandao (japonica), were used to construct two SSR molecular linkage maps. The results showed that the DNA polymorphism between parents of IR26/Jiucaiqing and IR28/Daguandao were similar, with polymorphic rate 42.2% and 44.3%, respectively. There were 57 and 74 SSR loci showing genetic distortion, mainly partial to indica parents, among IR26/Jiucaiqing and IR28/Daguandao genome, respectively, with the segregation distortion rate 42.2% and 44.3%. The genotype of each line at each chromosome was analyzed; there were genetic distortion lines in two RILs with segregation distortion rate 47.2% and 52.9%, respectively. The distribution of paternal contribution was normal in progenies which illustrated that genetic contributions from the parents were equals, and some lines with similar genotypic components in two RILs. In addition, the two genetic maps of IR26/Jiucaiqing and IR28/Daguandao covered 2225.3 cM and 1846.6 cM of rice genome, respectively, with the average interval of 16.5 cM and 11.1 cM, which were suitable for QTL mapping. The two maps differed in mapped markers, sequenced order of markers, genetic distance and average distance on the maps. Finally, six and eight segregation distortion regions (SDRs) were detected on IR26/Jiucaiqing and IR28/Daguandao chromosomes, respectively, three new SDRs (SDR 2, SDR 4-2, SDR 12-1) were detected here, and several gametophytic genes (ga) and sterile gene (s) were located near some SDRs, indicating that segregation distortion could be partially caused by gametophytic genes and sterile genes.
One F2:9 recombinant inbred lines (RILs) population, derived from a cross between IR26 (Oryza sativa L. spp. indica) and Jiucaiqing (japonica), was used to determine the germination ability including imbibition rate, germination rate, germination index, root length, shoot length and vigor index under control (water) and salt stress (100 mM NaCl) for 10 d. A major gene plus polygene mix inheritance model and the composite interval mapping (CIM) were applied to conduct genetic analysis for germination ability. The results showed that the performances of rice seed germination were mostly limited by salt stress and the early germination stage (0-5 d) might be the salt sensitive stage in rice. There were significant differences in all germination traits under salt stress among RILs. Correlation coefficients among the germination traits, except the imbibition rate, under salt stress were all positively significant. The frequency distributions of germination traits in RILs population showed continuous segregation, suggesting these were quantitative traits controlled by several genes, and more RILs were skewed to salt sensitive type. Each trait was controlled by the specific genetic model:imbibition rate controlled by two major genes, germination index and vigor index controlled by two major genes plus polygene, germination rate and shoot length regulated by three major genes plus polygene, and root length controlled by two major genes or two major genes plus polygene, and mainly dominated by major genes with high heritability values, accounted for 12.5%-99.0% of the total phenotypic variation. In the control group, twelve QTLs were identified:two for imbibition rate (qIR-8 qIR-10), one for germination rate (qGR-7), one for germination index (qGI-2), four for root length (qRL-1 qRL-4 qRL-9 qRL-10), two for shoot length (qSL-7 qSL-11) and two for vigor index (qVI-6 qⅥ-7), respectively, accounting for 12.5%-25.5% of the total phenotypic variance individually. In the saline group, four QTLs were identified: two for imbibition rate (qIR-4 qIR-9), one for germination rate (qGR-2) and one for vigor index (qⅥ-8), respectively, explaining 9.1%-46.6% of the total phenotypic variance individually. One major QTL qGR-2 was explaning 46.6% of the total phenotypic variance. The expression of QTLs was developmentally regulated and growth stage-specific. Most of the QTLs observed here were located in regions similar to the QTLs for rice salt tolerance reported previously, but qⅥ-8 and qGI-8 are reported here for the first time.
One F2:9 recombinant inbred lines (RILs) population, derived from a cross between IR28(Oryza sativa L. spp. indica) and Daguandao (japonica), was used to determine the germination ability including imbibition rate, germination rate, germination index, root length, shoot length and vigor index under control (30℃) for 10 d and cold stress (14℃) for 23 d. A major gene plus polygene mix inheritance model and the composite interval mapping (CIM) were applied to conduct genetic analysis for germination ability. The results showed that the performances of rice seed germination were mostly limited by cold stress and there were significant differences in all germination traits under cold stress among RILs. Correlation coefficients among the germination traits, except the imbibition rate, under cold stress were all positively significant. The frequency distributions of germination traits in RILs population showed continuous segregation, suggesting these were quantitative traits controlled by several genes, and more RILs were skewed to cold sensitive type. Each trait was controlled by the specific genetic model:imbibition rate, root length, shoot length and vigor index controlled by two major genes plus polygene, germination rate controlled by two or three major genes and germination index regulated by two major genes, and mainly dominated by major genes with high heritability values, accounted for 26.4%～95.3% of the total phenotypic variation. In the control group, eleven QTLs were identified:three for imbibition rate(qIR-6 qIR-9 qIR-11), two for germination index (qGI-1 qGI-7), two for root length (qRL-11 qRL-12), two for shoot length (qSL-8 qSL-9) and two for vigor index (qVI-2 qVI-9), respectively, accounting for 15.1%～32.4% of the total phenotypic variance individually. In the cold group, seven QTLs were identified: two for imbibition rate (qIR-6 qIR-9), one for germination rate (qGR-4), two for germination index (qGI-4-1 qGI-4-2) and two for root length (qRL-4-1 qRL-4-2), respectively, explaining 9.1%～37.0% of the total phenotypic variance individually. One major QTL qIR-6 explained for 31.0%～34.5% of the total phenotypic variance, and another major QTL qGI-4-2 accounted for 37.0% of the total phenotypic variance. The expression of QTLs was developmentally regulated and growth stage-specific. Most of the QTLs observed here were located in regions similar to the QTLs for rice cold tolerance reported previously, but qRL-4-2 is reported here for the first time.
引文
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