普通野生稻遗传多样性及2个特有基因的功能初步研究
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摘要
水稻(Oryza sativa L.)是全世界最重要的粮食作物之一,世界上三分之一的人口以稻米为主要粮食。普通野生稻(Oryza rufipogon Griff.)被研究者广泛认为是栽培稻的祖先,保存着栽培稻不具有或已经消失了的许多优异基因,是水稻育种的天然基因库,所以研究普通野生稻的遗传多样性进,挖掘普通野生稻的优异基因并应用于水稻育种是当前水稻科学研究的重要方向。本研究以分布我国北纬18.73N至28.14N的12个普通野生稻为材料,以典型籼稻、粳稻为对照,对普通野生稻的叶绿体DNA(cpDNA)和第四染色体的分子遗传多态性进行研究,以期促进对普通野生稻分子遗传多态性的认识,为将普通野生稻资源更好的应用于水稻分育种提供更丰富的理论基础。另外,对17个三系不育系叶绿体DNA也进行了比较分析。主要研究结果如下：
1.普通野生稻与栽培稻叶绿体分子遗传多样性的研究
供试的12个普通野生稻和18个栽培稻在9个cpDNA多变区共计9080个碱基中,共检测到多态性碱基144个。其中普通野生稻间具多态性碱基117个表明分布在不同区域的普通野生稻间存在遗传分化。典型籼稻与典型粳稻之间有131个具亚种特征性差异碱基；爪哇稻在这些特征性位点的碱基序列与粳稻完全一致,说明爪哇稻的cpDNA与粳稻有更近的遗传关系。ORF29-TrnCGCA和ORF100两个扩增片段是快速区分籼粳两种类型cpDNA的分子标记,用这2个分子标记也可将12个普通野生稻cpDNA分成籼粳两种类型,但在9个cpDNA序列中,同一个普通野生稻在不同位点的籼粳属性不同,由此说明普通野生稻cpDNA具有一定籼粳分化趋势,但不能仅凭几对分子标记结果将普通野生稻像栽培稻一样分为型籼型或粳型。本研究支持籼型亚洲栽培稻和粳型亚洲栽培稻分别由具有一定籼粳分化趋势的普通野生稻演化而来的二元起源学说。
2.不同类型三系不育系材料cpDNA遗传多态性的比较
对17个不同细胞质来源的三系不育系材料cpDNA的遗传多态性进行比较表明,17个三系不育系可分为三种细胞质类型,即野败型、红莲型和BT型。生产中所称的印水型、冈型、K型不育系cpDNA的9个多变区序列与野败型完全一致,因此都应为野败型细胞质。野败型、红莲型细胞质虽然都来自于海南野生稻,但野败型叶绿体rps16内含子的第220-225位点具独有GTTGAG碱基序列,红莲型在rps16内含子的第595位具特有的碱基G,而其他材料都为T；所谓籼稻质源的BT型不育系cpDNA序列却仅在ccsA基因的540-543位点的碱基与籼稻相同,其余序列均与典型粳稻完全一致,因此本文结果认为BT型不育系的细胞质应为粳型,而粳稻cpDNA背景的ccsA基因的540-543位点的籼型特征性GCTT序列可作为BT型不育系cpDNA特征性分子标记。雄性不育系cpDNA的这些特征性碱基可作为相应不育细胞质类型的分子标记。推测这些特征性碱基是细胞质发生了遗传变异导致的,但这些突变序列与花粉不育有否关系有待于进-步研究。
3.普通野生稻与栽培稻第四染色体的分子遗传多样性分析
本研究选用471对SSR标记,对供试普通野生稻和栽培稻第四染色体的遗传多态性进行研究。供试普通野生稻在第四染色体上也呈现出丰富的遗传多态性,遗传距离分析显示普通野生稻内的遗传多样性远大于栽培稻内的遗传多样性,且普通野生稻中含有一些栽培稻中不具有的等位基因,说明从普通野生稻中发掘用于栽培稻品种改良的新基因具有巨大的潜力。通过比对典型籼稻、粳稻亚种间的遗传差异,在第四染色体上建立了141个籼粳亚种间的特征性分子标记。不同纬度来源的普通野生稻在141个籼粳特征性分子标记位点也出现了不同程度的籼粳分化趋势,聚类分析也显示一部分普通野生稻材料归为籼稻一支,另一部分归为粳稻一支。因此,本研究从水稻第四染色体的水平上再次为水稻二元起源学说提供了分子遗传学证据。与cpDNA不同,供试爪哇稻材料在第四染色体上出现了籼粳分化。因此,本文认为基于爪哇稻cpDNA与粳亚种一致性程度高,将爪哇稻归为粳亚种是适合的,但根据第四染色体以及前人关于ITS和IGS序列的遗传多态性分析的综合结果,将爪哇稻归为独立籼稻、粳稻亚种间的一个中间型亚种也有一定遗传基础。
4.普通野生稻第四染色体特有基因的筛选及其功能初步分析
本研究筛选得到2个位于第四染色体上的普通野生稻特有基因,并将这两个基因遗传转化到栽培稻中,对其中一个基因遗传转化植株的叶绿素和脯氨酸含量进行了测定,发现其叶绿素和脯氨酸含量均高于野生型对照。同时对此转基因植株进行了各种非生物逆境处理中,初步认为此基因可能与水稻耐高盐胁迫有关。
综上所述,通过对普通野生稻cpDNA和第四染色体的遗传多态性分析,发现普通野生稻具有丰富的遗传多态性,并且具有一定的籼粳分化趋势。这为亚洲栽培稻的二元起源学说提供了分子遗传证据。同时,本研究还筛选到普通野生稻特有的基因,并认为其中一个基因可能与水稻耐高盐胁迫有关,为加速对普通野生稻资源的认识并进一步挖掘应用普通野生稻种质资源提供了一定的理论参考。另外cpDNA序列差异为基础,将三系不育系材料分为野败型、红莲型和BT型,并首次提出区分3种细胞质的分子标记。
Cultivated rice (Oryza sativa L.) is a major source of nutrition for more than half the global population. Asian common wild rice(Oryza rufipogon Griff.) has long been believed to be the direct ancestor of Asian cultivated rice. It serves as a valuable gene pool for the improvement of cultivated rice because of its many extraordinary traits, therefore, a better understanding of the genetic diversity of Asian common wild rice will be beneficial for the efficient use of the Oryza gene pool and will certainly have significant impact on rice production. In the present study,12different common wild rice distributed from18.73N to28.14N in China were studied, and six indica cultivars, four japonica cultivars were used as controls. A more comprehensive comparison of nine highly variable cpDNA regions and471SSR markers on chromosome4were performed to elucidate the genetic diversity of common wild rice.The results will deepen our understanding of the genetic diversity of common wild rice and ultimately accelerate the efficient use of the extraordinary genes of common wild rice for the genetic improvement of cultivated rice. Meanwhile, the cpDNA genetic diversity of17different cytoplasm male sterile (CMS) lines was also studied in this research. The main results are as follows:
1. CpDNA genetic diversity analysis of common wild rice and cultivated rice The chloroplast DNA (cpDNA) polymorphism among18cultivated rice and12Asian common wild rice were analyzed by comparing the polymorphic sites in nine highly variable regions. A total of144polymorphic bases were detected. O. rufipogon from different distributions, with117polymorphic bases, showed rich genetic diversity. The131bases in13sites were identified with indica/japonica characteristics, as they showed differences between the indica and japonica subspecies at these sites. The javanica strains and japonica shared similar bases at these131polymorphic sites, suggesting that javanica has a close relationship with japonica. Using the amplified fragment length analysis of ORF100and ORF29-TrnCGCA can simply and rapidly identify the indica/japonica types of O. sativa cytoplasm. Based on the results of the length analyses of the ORF100and the ORF29-TrnCGCA fragments, the O. rufipogon strains can also be classified into indica/japonica subgroups, which indicate that differences in indica and japonica also exist in the cpDNA genome of the O. rufipogon strains. However, these differences showed certain primitiveness and incompleteness, as an O. rufipogon line may show different indica/japonica attributes at different sites. Consequently, the O. rufipogon cannot be simply classified into the indica/japonica types according one or several molecular markers. Our data support the hypothesis that Asian cultivated rice, indica and japonica, separately evolved from different Asian common wild rice strains, which have different indica-japonica differentiation trends.
2. CpDNA genetic diversity analysis of cytoplasm male sterile (CMS) lines The cpDNA genetic diversity of different types of CMS lines was elucidated by comparing the polymorphic sites in nine highly variable regions, taking cultivated rice and common wild rice as controls. According to the cpDNA polymorphism, the17CMS lines were divided into three cytoplasmic types:CMS-WA (wild-abortive), CMS-HL (Honglian) and CMS-BT (Boro II). So-called CMS-Yinshui, CMS-GA and CMS-K types had the same sequences with CMS-WA lines, so they were redefined as CMS-WA cytoplasmic type. Each CMS type had specific bases:CMS-WA lines uniquely had a "GTTGAG" sequence at position220-225of rps16intron, CMS-HL lines contained a specific "G" base at position595of rps16intron, and CMS-BT lines were distinguishable by their indica specific sequences "GCTT" in the ccsA gene under a japonica cpDNA background. All of these specific sequences can be used as DNA fingerprinting for them. On the other hand, it was proved that some genetic variations occurred in cpDNA of CMS lines. However, further study is needed to reveal the correlationship between these variations and pollen sterility.
3. Genetic diversity analysis on chromosome4of common wild rice and cultivated rice471pairs of SSR markers were used in this study to explore the genetic diversity on chromosome4in common wild rice and cultivated rice. O. rufipogon from different distributions showed rich genetic diversity which is much higher than that of cultivated rice. And there also exists some allelic genes that cannot be found in cultivated rice, which indicated that common wild rice contains many extraordinary genes used for genetic improvement of cultivated rice.141indica-japonica characteristic SSR markers were identified, and O. rufipogon strains showed different indica-japonica differentiation at these sites. So it proved again that there exists an indica-japonica differentiation trend in genome of the O. rufipogon strains. The constructed dendrogram of these materials also showed this result. Thus, these results provided evidence for dual origin of cultivated rice on the level of molecular genetics. However, javanica rices in this study showed different indica-jaopnica differentiations, which was inconsistent with the results showed by using cpDNA sequences. So it is reasonable to classified javanica in to japonica subspecies based on the cpDNA sequences characteristic of them, while it also seems have a lag to stand on to regard javanica as an independent subspecies of cultivated rice according to the complex analysis results of IGS and ITS sequences (studied by the other researcher of our lab) and chromosome4.
4. Identification of specific genes in common wild rice and the functional analysis of these genes Two common wild rice specific genes located on chromosome4were identified, cloned and transferred into cultivated rice in this study. And the chlorophyll content and proline of one transgenic line were higer than wild type, which suggested this common wild rice specific gene might be related to the stress tolerance of plant. According to the primary results of abiotic stress treatment of this transgenic line, it was suuggetted that this gene might play a role in high salt tolerance of plant. Generally, common wild rice showed rich genentic diversity in both cpDNA and chromosome4. And there also exist indica-japonica differentiation trend in common wild rice which supported the dual origin of cultivated rice.2common wild rice specific genes were also indentified and one of them was suggested plays a role in high salt tolerance of plant in this study. All these results will deepen our understanding of genetic diversity of common wild rice and provide therotical support for genetic improvement of cultivated rice. Meanwhile, according to the cpDNA genetic diversity,17different CMS lines were classified in to3types:CMS-WA, CMS-HL and CMS-BT, and a corresponding DNA fingerprinting system for them was preliminarily established.
1.普通野生稻与栽培稻叶绿体分子遗传多样性的研究
供试的12个普通野生稻和18个栽培稻在9个cpDNA多变区共计9080个碱基中,共检测到多态性碱基144个。其中普通野生稻间具多态性碱基117个表明分布在不同区域的普通野生稻间存在遗传分化。典型籼稻与典型粳稻之间有131个具亚种特征性差异碱基；爪哇稻在这些特征性位点的碱基序列与粳稻完全一致,说明爪哇稻的cpDNA与粳稻有更近的遗传关系。ORF29-TrnCGCA和ORF100两个扩增片段是快速区分籼粳两种类型cpDNA的分子标记,用这2个分子标记也可将12个普通野生稻cpDNA分成籼粳两种类型,但在9个cpDNA序列中,同一个普通野生稻在不同位点的籼粳属性不同,由此说明普通野生稻cpDNA具有一定籼粳分化趋势,但不能仅凭几对分子标记结果将普通野生稻像栽培稻一样分为型籼型或粳型。本研究支持籼型亚洲栽培稻和粳型亚洲栽培稻分别由具有一定籼粳分化趋势的普通野生稻演化而来的二元起源学说。
2.不同类型三系不育系材料cpDNA遗传多态性的比较
对17个不同细胞质来源的三系不育系材料cpDNA的遗传多态性进行比较表明,17个三系不育系可分为三种细胞质类型,即野败型、红莲型和BT型。生产中所称的印水型、冈型、K型不育系cpDNA的9个多变区序列与野败型完全一致,因此都应为野败型细胞质。野败型、红莲型细胞质虽然都来自于海南野生稻,但野败型叶绿体rps16内含子的第220-225位点具独有GTTGAG碱基序列,红莲型在rps16内含子的第595位具特有的碱基G,而其他材料都为T；所谓籼稻质源的BT型不育系cpDNA序列却仅在ccsA基因的540-543位点的碱基与籼稻相同,其余序列均与典型粳稻完全一致,因此本文结果认为BT型不育系的细胞质应为粳型,而粳稻cpDNA背景的ccsA基因的540-543位点的籼型特征性GCTT序列可作为BT型不育系cpDNA特征性分子标记。雄性不育系cpDNA的这些特征性碱基可作为相应不育细胞质类型的分子标记。推测这些特征性碱基是细胞质发生了遗传变异导致的,但这些突变序列与花粉不育有否关系有待于进-步研究。
3.普通野生稻与栽培稻第四染色体的分子遗传多样性分析
本研究选用471对SSR标记,对供试普通野生稻和栽培稻第四染色体的遗传多态性进行研究。供试普通野生稻在第四染色体上也呈现出丰富的遗传多态性,遗传距离分析显示普通野生稻内的遗传多样性远大于栽培稻内的遗传多样性,且普通野生稻中含有一些栽培稻中不具有的等位基因,说明从普通野生稻中发掘用于栽培稻品种改良的新基因具有巨大的潜力。通过比对典型籼稻、粳稻亚种间的遗传差异,在第四染色体上建立了141个籼粳亚种间的特征性分子标记。不同纬度来源的普通野生稻在141个籼粳特征性分子标记位点也出现了不同程度的籼粳分化趋势,聚类分析也显示一部分普通野生稻材料归为籼稻一支,另一部分归为粳稻一支。因此,本研究从水稻第四染色体的水平上再次为水稻二元起源学说提供了分子遗传学证据。与cpDNA不同,供试爪哇稻材料在第四染色体上出现了籼粳分化。因此,本文认为基于爪哇稻cpDNA与粳亚种一致性程度高,将爪哇稻归为粳亚种是适合的,但根据第四染色体以及前人关于ITS和IGS序列的遗传多态性分析的综合结果,将爪哇稻归为独立籼稻、粳稻亚种间的一个中间型亚种也有一定遗传基础。
4.普通野生稻第四染色体特有基因的筛选及其功能初步分析
本研究筛选得到2个位于第四染色体上的普通野生稻特有基因,并将这两个基因遗传转化到栽培稻中,对其中一个基因遗传转化植株的叶绿素和脯氨酸含量进行了测定,发现其叶绿素和脯氨酸含量均高于野生型对照。同时对此转基因植株进行了各种非生物逆境处理中,初步认为此基因可能与水稻耐高盐胁迫有关。
综上所述,通过对普通野生稻cpDNA和第四染色体的遗传多态性分析,发现普通野生稻具有丰富的遗传多态性,并且具有一定的籼粳分化趋势。这为亚洲栽培稻的二元起源学说提供了分子遗传证据。同时,本研究还筛选到普通野生稻特有的基因,并认为其中一个基因可能与水稻耐高盐胁迫有关,为加速对普通野生稻资源的认识并进一步挖掘应用普通野生稻种质资源提供了一定的理论参考。另外cpDNA序列差异为基础,将三系不育系材料分为野败型、红莲型和BT型,并首次提出区分3种细胞质的分子标记。
Cultivated rice (Oryza sativa L.) is a major source of nutrition for more than half the global population. Asian common wild rice(Oryza rufipogon Griff.) has long been believed to be the direct ancestor of Asian cultivated rice. It serves as a valuable gene pool for the improvement of cultivated rice because of its many extraordinary traits, therefore, a better understanding of the genetic diversity of Asian common wild rice will be beneficial for the efficient use of the Oryza gene pool and will certainly have significant impact on rice production. In the present study,12different common wild rice distributed from18.73N to28.14N in China were studied, and six indica cultivars, four japonica cultivars were used as controls. A more comprehensive comparison of nine highly variable cpDNA regions and471SSR markers on chromosome4were performed to elucidate the genetic diversity of common wild rice.The results will deepen our understanding of the genetic diversity of common wild rice and ultimately accelerate the efficient use of the extraordinary genes of common wild rice for the genetic improvement of cultivated rice. Meanwhile, the cpDNA genetic diversity of17different cytoplasm male sterile (CMS) lines was also studied in this research. The main results are as follows:
1. CpDNA genetic diversity analysis of common wild rice and cultivated rice The chloroplast DNA (cpDNA) polymorphism among18cultivated rice and12Asian common wild rice were analyzed by comparing the polymorphic sites in nine highly variable regions. A total of144polymorphic bases were detected. O. rufipogon from different distributions, with117polymorphic bases, showed rich genetic diversity. The131bases in13sites were identified with indica/japonica characteristics, as they showed differences between the indica and japonica subspecies at these sites. The javanica strains and japonica shared similar bases at these131polymorphic sites, suggesting that javanica has a close relationship with japonica. Using the amplified fragment length analysis of ORF100and ORF29-TrnCGCA can simply and rapidly identify the indica/japonica types of O. sativa cytoplasm. Based on the results of the length analyses of the ORF100and the ORF29-TrnCGCA fragments, the O. rufipogon strains can also be classified into indica/japonica subgroups, which indicate that differences in indica and japonica also exist in the cpDNA genome of the O. rufipogon strains. However, these differences showed certain primitiveness and incompleteness, as an O. rufipogon line may show different indica/japonica attributes at different sites. Consequently, the O. rufipogon cannot be simply classified into the indica/japonica types according one or several molecular markers. Our data support the hypothesis that Asian cultivated rice, indica and japonica, separately evolved from different Asian common wild rice strains, which have different indica-japonica differentiation trends.
2. CpDNA genetic diversity analysis of cytoplasm male sterile (CMS) lines The cpDNA genetic diversity of different types of CMS lines was elucidated by comparing the polymorphic sites in nine highly variable regions, taking cultivated rice and common wild rice as controls. According to the cpDNA polymorphism, the17CMS lines were divided into three cytoplasmic types:CMS-WA (wild-abortive), CMS-HL (Honglian) and CMS-BT (Boro II). So-called CMS-Yinshui, CMS-GA and CMS-K types had the same sequences with CMS-WA lines, so they were redefined as CMS-WA cytoplasmic type. Each CMS type had specific bases:CMS-WA lines uniquely had a "GTTGAG" sequence at position220-225of rps16intron, CMS-HL lines contained a specific "G" base at position595of rps16intron, and CMS-BT lines were distinguishable by their indica specific sequences "GCTT" in the ccsA gene under a japonica cpDNA background. All of these specific sequences can be used as DNA fingerprinting for them. On the other hand, it was proved that some genetic variations occurred in cpDNA of CMS lines. However, further study is needed to reveal the correlationship between these variations and pollen sterility.
3. Genetic diversity analysis on chromosome4of common wild rice and cultivated rice471pairs of SSR markers were used in this study to explore the genetic diversity on chromosome4in common wild rice and cultivated rice. O. rufipogon from different distributions showed rich genetic diversity which is much higher than that of cultivated rice. And there also exists some allelic genes that cannot be found in cultivated rice, which indicated that common wild rice contains many extraordinary genes used for genetic improvement of cultivated rice.141indica-japonica characteristic SSR markers were identified, and O. rufipogon strains showed different indica-japonica differentiation at these sites. So it proved again that there exists an indica-japonica differentiation trend in genome of the O. rufipogon strains. The constructed dendrogram of these materials also showed this result. Thus, these results provided evidence for dual origin of cultivated rice on the level of molecular genetics. However, javanica rices in this study showed different indica-jaopnica differentiations, which was inconsistent with the results showed by using cpDNA sequences. So it is reasonable to classified javanica in to japonica subspecies based on the cpDNA sequences characteristic of them, while it also seems have a lag to stand on to regard javanica as an independent subspecies of cultivated rice according to the complex analysis results of IGS and ITS sequences (studied by the other researcher of our lab) and chromosome4.
4. Identification of specific genes in common wild rice and the functional analysis of these genes Two common wild rice specific genes located on chromosome4were identified, cloned and transferred into cultivated rice in this study. And the chlorophyll content and proline of one transgenic line were higer than wild type, which suggested this common wild rice specific gene might be related to the stress tolerance of plant. According to the primary results of abiotic stress treatment of this transgenic line, it was suuggetted that this gene might play a role in high salt tolerance of plant. Generally, common wild rice showed rich genentic diversity in both cpDNA and chromosome4. And there also exist indica-japonica differentiation trend in common wild rice which supported the dual origin of cultivated rice.2common wild rice specific genes were also indentified and one of them was suggested plays a role in high salt tolerance of plant in this study. All these results will deepen our understanding of genetic diversity of common wild rice and provide therotical support for genetic improvement of cultivated rice. Meanwhile, according to the cpDNA genetic diversity,17different CMS lines were classified in to3types:CMS-WA, CMS-HL and CMS-BT, and a corresponding DNA fingerprinting system for them was preliminarily established.
引文
[1]Vaughan DA, Morishima H and Kadowaki K. Diversity in the Oryza genus [J]. Curr Opi Plant Biol,2003 (6):139-146.
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