水稻抗条纹叶枯病遗传分析和主基因qSTVll的精细定位
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摘要
水稻条纹叶枯病(rice stripe)是近年来危害长江中下游地区的粳稻生产的主要病害之一,传毒介体为灰飞虱(Small brown planthopper, SBPH)。水稻对条纹叶枯病的抗性分为对病毒的抗性和对介体灰飞虱的抗性,目前在生产上利用的主要抗源为来自巴基斯坦品种Modan的抗病基因Stvb-i,但该基因尚未深入研究,加之存在抗源单一的风险,因而我们需要发掘新的抗病毒基因和抗灰飞虱的基因。本研究基于上述需求开展抗条纹叶枯病的遗传学研究,从鉴定方法的建立、抗性资源的筛选、基因定位和精细定位几方面着手进行了较为系统的研究,以下为本研究的主要内容：
1、鉴定方法的建立
本研究建立了规模化灰飞虱繁殖体系,改良和优化了三种病毒接种方法(田间鉴定、集团接种和强迫饲毒),开发了12天集团接种的新方法；在灰飞虱接种方面,我们改良和优化了耐虫性测验、排驱性测验和抗生性测验的方法。
2、抗性资源的筛选和研究材料的选择
本研究共筛选出高抗品种313份,通过对广西91份地方品种的细化分析发现水稻条纹叶枯病的抗性资源主要存在籼稻中,且抗性主基因与11染色体的标记RM287连锁。
等位性分析发现三个品种(IR24、DV85和Habataki)携带的抗性基因与Stvb-i不等位,因此这三个品种作为材料进一步发掘条纹叶枯病的新抗性基因。我们还对高抗灰飞虱品种窄叶青8号和高抗的抗病对照IR36进行了相关的遗传研究。同时,我们利用籼稻品种Kasalath对其主抗基因(qSTVll)进行精细定位。
3、利用不同群体对条纹叶枯病抗性基因的发掘
利用以Asominori为遗传背景IR24为插入片段的染色体片段置换系群体(Chromosome segment substitution lines, CSSLs)验证了11染色体中抗主效基因qSTV11-i的遗传稳定性。而后我们利用2780个Asominori/CSSL62 F2:3家系将该中抗基因精细定位在与Stvb-i临近的720.6kb的区间内。同时我们利用分子标记筛选到的137份交换单株并繁殖成F3:4,完成了其中纯合株系的表型鉴定。我们的研究为分子标记辅助选择(MAS)提供了紧密连锁标记和为进一步的分离和克隆该基因提供遗传基础。
利用Sasanishiki/Habataki//Sasanishiki(BC1F8)回交重组自交系群体(Backcrossedinbred lines, BILs)进行抗条纹叶枯病基因的初步定位。利用四种接种鉴定方法共检测到了3个QTL,其中一个QTL定位于第3染色体贡献率(Phnotypic variation explained, PVE)为12.6-18.4%,第11染色体的两个加性的QTL (qSTV11.1和qSTV11.2)遗传上连锁,集团接种条件下分别表现中抗但累加后表现高抗,分别定位在标记区间G257-RM457(PVE为14.4-20.9%)和RM457-RM187(PVE为13.5-26.6%)。利用背景亲本与含有这2个QTL的片段置换系SL437杂交构建次级群体,从总共2750份F2：3中挑选出147个重组株系进行集团接种鉴定,将qSTV11.1和qSTV11.2分别定位在333.2Kb(R15-RM209)和203.9Kb(R69-R73)的区间内。本研究首次定位到了2个中抗条纹叶枯病的基因,对丰富抗水稻抗条纹叶枯病遗传资源并加速水稻抗性育种都具有重要意义。
利用来源于IR36/热研2号的重组自交系群体(Recombinant inbred lines, RILs),采用三种方法在两年不同处理中检测到抗条纹叶枯病的QTL分布在两年第1、3、4、5、7、10、11、12染色体,贡献率范围是1.2-32.9%。其中,第1染色体(区间RM488-RM128,贡献率为3.2-6.8%)和11染色体(RM332-RM287,贡献率为6.0-32.9%)检测到的QTL成簇分布,说明这两个区间存在稳定表达的QTL。上述两个QTL的抗性均来自高抗品种IR36。IR36的抗性机制的研究发现：IR36是综合了高抗病毒侵染、耐病毒、耐灰飞虱取食和排驱性等综合的高抗条纹叶枯病的特性。
另外利用窄叶青8号／京系17加倍单倍体群体在抗虫检测中采用成虫或若虫苗期集团筛选法在第1 (qSBPH1)、2(qSBPH2)和11 (qSBPH11)染色体均检测一个抗虫的QTL,两年两种处理检测到的所有QTL的贡献率为44.39-50.96。其中qSBPHl是一个抗灰飞虱新的主基因,其贡献率超过30%。
4. qSTV11的精细定位
本研究利用来源于Koshihikari和Kasalath的CSSLs验证了Kasalath的主效抗性基因及其遗传稳定性。而后,我们从7018个BC3F2单株(SL-234/Koshihikari回交次级F2群体)中筛选到372份重组的BC3F2：3株系及其后代399份重组的BC3F3：4家系。利用这些材料,我们将qSTV11定位在39.2 Kb的区间内,其中有7个侯选基因。qSTV11附近的4个多态InDel标记(R21、R25、R13和R48)可以用于抗性粳稻品种的标记辅助选择(MAS)。对应现有的表型,所有4个分子标记的选择效率>95%。
Rice stripe, caused by rice stripe virus (RSV), is one of the most damaging diseases in temperate regions of East Asia. In China, rice stripe is increasing in severity, particularly in Jiangsu province. The resistance to rice stripe can be divided into resistance against RSV and small brown planthopper (SBPH), so it is necessary to explore new resistant genes against RSV and resources against SBPH. Basing on the genetics of resistance to RSV and SBPH, this work was consisted of optimizing inoculation methods, scanning for resistant varieties, detetction of resistant genes/QTLs and fine mapping of major genes.The results were as follows:
1) Establishing of inoculation system of RSV and SBPH.
We optimized the inbred system of SBPH and RSV inoculation methods of field test, mass inoculation test and seedling test. Meanwhile, we innovated the 12 days inoculation test as a new method. We also optimized inoculation methods of testing resistance to SBPH. These research with be useful for later study.
2) Scanning for resistant varieties with new RSV resistant gene.
In this study, resistance to rice stripe in 735 rice landraces was scanned. According to the allelic tests with Stvb-i, two varieties (IR24 and Habataki) carrying new resistant gene were selected to construct genetic populations and map quantitative trait loci (QTL). Meanwhile, QTL for RSV resistance in'Zhaiyeqing8','IR36'and'Kasalath', and QTL for SPHB in'Zhaiyeqing8'were also scanned. Then, major QTLs detected in 'Kasalath'and'Habataki'were seletcted for fine mapping.
3) Gene mapping of rice stripe resistance with different poputions.
The partial resistant gene with main effect on chromosome 11 in IR24 was validated using chromosome segement substitution lines (CSSLs), and secondary population was constructed for fine mapping. This QTL were roughly mapped to a 720.6Kb region using 2780 F2:3 families, and 137 recombinant lines were planted to F3:4 and homogenious plants selected for fine mapping.
With four inoculation methods,85 backcross inbred lines (BILs) of Sasanishiki (japonica)×Habataki(indica) was used to map QTL conferring resistance to rice stripe virus (RSV). Two main effect QTLs (qSTVll.l and qSTV11.2) on chromosome 11 were genetically linked, and mapped in the interval G257-RM457 and RM457-RM187, respectively. Fine mapping of qSTV11.1 and qSTV11.2 was carried out using 147 recombined BC3F2:3 lines selected from 2750 BC3F2 plants of the cross Sasanishiki/SL437. The qSTV11.1 was finally localized to a 333.2Kb interval (R15-RM209), which was physically about 230 Kb away from that of the well known Stvb-i. The other locus, qSTV11.2, was delimited into a 203.9 Kb region (R69-R73).
IR36 is highly resistant to rice stripe disease. QTLs against RSV were detected on chromosomes 1,3,4,5,7,10,11 and 12 across two years. Of these QTLs, three were repeatedly detected, they were:one on chromosome 1 (interval RM488-RM128, PVE of 3.2-6.8%) and two on chromosome 11 (interval RM332-RM202, PVE of 11.8-32.9% and interval RM202-RM287, PVE of 6.0-24.8%, respectively). And the QTL of interval RM332-RM202 was allelic with the well known Stvb-i. The resistance mechanism in IR36 was consisted of resistance to virus infection, tolerance to virus, tolerance to feeding of vector and antixenosis.
Using a doubled haploid lines (DHs) bred from the cross ZYQ8 x JX17 and four separate inoculation methods to genetically dissect the rice stripe resistance present in ZYQ8. Two linked RSV resistance QTLs were located on chromosome 1, and one on chromosome 11, jointly explaining 30-44% of the trait variance. The main-effect qSTV11 was mapped close to the established RSV resistance gene Stvb-i. For resistance to SBPH, three QTLs were located, mapping to chromosomes 1,2 and 11 and jointly explaining 44-51% of the trait variance. The large-effect qSBPHl (PVE>30%) appears to be a novel QTL conferring a degree of tolerance and antibiosis against SBPH. Analysis of a set of chromosome segment substitution lines showed rice stripe resistance genes/QTLs are commonly exsisted on the long arm of chromosome 1.
4) Fine mapping of a main effect qSTV11 in Kasalath
The stability of was validated using 39 established chromosome segment substitution lines. Fine mapping of qSTV11 was carried out using 372 recombinant BC3F2:3 and 399 BC3F3:4 lines selected from 7018 BC3F2 plants of the cross SL-234/Koshihikari.Four SSR (Simple Sequence Repeat), ten InDel and one CAPS markers were developed to narrow qSTVll locus. The qSTV11 was finally localized to a 39.2 Kb region that contains seven annotated genes. Marker-resistance association analysis suggested qSTV11 was distributed in diverse landraces coming from different regions. These results will provide a basis for map-based cloning of qSTV11,and benefit for the improvement of RSV resistance in rice varieties.
1、鉴定方法的建立
本研究建立了规模化灰飞虱繁殖体系,改良和优化了三种病毒接种方法(田间鉴定、集团接种和强迫饲毒),开发了12天集团接种的新方法；在灰飞虱接种方面,我们改良和优化了耐虫性测验、排驱性测验和抗生性测验的方法。
2、抗性资源的筛选和研究材料的选择
本研究共筛选出高抗品种313份,通过对广西91份地方品种的细化分析发现水稻条纹叶枯病的抗性资源主要存在籼稻中,且抗性主基因与11染色体的标记RM287连锁。
等位性分析发现三个品种(IR24、DV85和Habataki)携带的抗性基因与Stvb-i不等位,因此这三个品种作为材料进一步发掘条纹叶枯病的新抗性基因。我们还对高抗灰飞虱品种窄叶青8号和高抗的抗病对照IR36进行了相关的遗传研究。同时,我们利用籼稻品种Kasalath对其主抗基因(qSTVll)进行精细定位。
3、利用不同群体对条纹叶枯病抗性基因的发掘
利用以Asominori为遗传背景IR24为插入片段的染色体片段置换系群体(Chromosome segment substitution lines, CSSLs)验证了11染色体中抗主效基因qSTV11-i的遗传稳定性。而后我们利用2780个Asominori/CSSL62 F2:3家系将该中抗基因精细定位在与Stvb-i临近的720.6kb的区间内。同时我们利用分子标记筛选到的137份交换单株并繁殖成F3:4,完成了其中纯合株系的表型鉴定。我们的研究为分子标记辅助选择(MAS)提供了紧密连锁标记和为进一步的分离和克隆该基因提供遗传基础。
利用Sasanishiki/Habataki//Sasanishiki(BC1F8)回交重组自交系群体(Backcrossedinbred lines, BILs)进行抗条纹叶枯病基因的初步定位。利用四种接种鉴定方法共检测到了3个QTL,其中一个QTL定位于第3染色体贡献率(Phnotypic variation explained, PVE)为12.6-18.4%,第11染色体的两个加性的QTL (qSTV11.1和qSTV11.2)遗传上连锁,集团接种条件下分别表现中抗但累加后表现高抗,分别定位在标记区间G257-RM457(PVE为14.4-20.9%)和RM457-RM187(PVE为13.5-26.6%)。利用背景亲本与含有这2个QTL的片段置换系SL437杂交构建次级群体,从总共2750份F2：3中挑选出147个重组株系进行集团接种鉴定,将qSTV11.1和qSTV11.2分别定位在333.2Kb(R15-RM209)和203.9Kb(R69-R73)的区间内。本研究首次定位到了2个中抗条纹叶枯病的基因,对丰富抗水稻抗条纹叶枯病遗传资源并加速水稻抗性育种都具有重要意义。
利用来源于IR36/热研2号的重组自交系群体(Recombinant inbred lines, RILs),采用三种方法在两年不同处理中检测到抗条纹叶枯病的QTL分布在两年第1、3、4、5、7、10、11、12染色体,贡献率范围是1.2-32.9%。其中,第1染色体(区间RM488-RM128,贡献率为3.2-6.8%)和11染色体(RM332-RM287,贡献率为6.0-32.9%)检测到的QTL成簇分布,说明这两个区间存在稳定表达的QTL。上述两个QTL的抗性均来自高抗品种IR36。IR36的抗性机制的研究发现：IR36是综合了高抗病毒侵染、耐病毒、耐灰飞虱取食和排驱性等综合的高抗条纹叶枯病的特性。
另外利用窄叶青8号／京系17加倍单倍体群体在抗虫检测中采用成虫或若虫苗期集团筛选法在第1 (qSBPH1)、2(qSBPH2)和11 (qSBPH11)染色体均检测一个抗虫的QTL,两年两种处理检测到的所有QTL的贡献率为44.39-50.96。其中qSBPHl是一个抗灰飞虱新的主基因,其贡献率超过30%。
4. qSTV11的精细定位
本研究利用来源于Koshihikari和Kasalath的CSSLs验证了Kasalath的主效抗性基因及其遗传稳定性。而后,我们从7018个BC3F2单株(SL-234/Koshihikari回交次级F2群体)中筛选到372份重组的BC3F2：3株系及其后代399份重组的BC3F3：4家系。利用这些材料,我们将qSTV11定位在39.2 Kb的区间内,其中有7个侯选基因。qSTV11附近的4个多态InDel标记(R21、R25、R13和R48)可以用于抗性粳稻品种的标记辅助选择(MAS)。对应现有的表型,所有4个分子标记的选择效率>95%。
Rice stripe, caused by rice stripe virus (RSV), is one of the most damaging diseases in temperate regions of East Asia. In China, rice stripe is increasing in severity, particularly in Jiangsu province. The resistance to rice stripe can be divided into resistance against RSV and small brown planthopper (SBPH), so it is necessary to explore new resistant genes against RSV and resources against SBPH. Basing on the genetics of resistance to RSV and SBPH, this work was consisted of optimizing inoculation methods, scanning for resistant varieties, detetction of resistant genes/QTLs and fine mapping of major genes.The results were as follows:
1) Establishing of inoculation system of RSV and SBPH.
We optimized the inbred system of SBPH and RSV inoculation methods of field test, mass inoculation test and seedling test. Meanwhile, we innovated the 12 days inoculation test as a new method. We also optimized inoculation methods of testing resistance to SBPH. These research with be useful for later study.
2) Scanning for resistant varieties with new RSV resistant gene.
In this study, resistance to rice stripe in 735 rice landraces was scanned. According to the allelic tests with Stvb-i, two varieties (IR24 and Habataki) carrying new resistant gene were selected to construct genetic populations and map quantitative trait loci (QTL). Meanwhile, QTL for RSV resistance in'Zhaiyeqing8','IR36'and'Kasalath', and QTL for SPHB in'Zhaiyeqing8'were also scanned. Then, major QTLs detected in 'Kasalath'and'Habataki'were seletcted for fine mapping.
3) Gene mapping of rice stripe resistance with different poputions.
The partial resistant gene with main effect on chromosome 11 in IR24 was validated using chromosome segement substitution lines (CSSLs), and secondary population was constructed for fine mapping. This QTL were roughly mapped to a 720.6Kb region using 2780 F2:3 families, and 137 recombinant lines were planted to F3:4 and homogenious plants selected for fine mapping.
With four inoculation methods,85 backcross inbred lines (BILs) of Sasanishiki (japonica)×Habataki(indica) was used to map QTL conferring resistance to rice stripe virus (RSV). Two main effect QTLs (qSTVll.l and qSTV11.2) on chromosome 11 were genetically linked, and mapped in the interval G257-RM457 and RM457-RM187, respectively. Fine mapping of qSTV11.1 and qSTV11.2 was carried out using 147 recombined BC3F2:3 lines selected from 2750 BC3F2 plants of the cross Sasanishiki/SL437. The qSTV11.1 was finally localized to a 333.2Kb interval (R15-RM209), which was physically about 230 Kb away from that of the well known Stvb-i. The other locus, qSTV11.2, was delimited into a 203.9 Kb region (R69-R73).
IR36 is highly resistant to rice stripe disease. QTLs against RSV were detected on chromosomes 1,3,4,5,7,10,11 and 12 across two years. Of these QTLs, three were repeatedly detected, they were:one on chromosome 1 (interval RM488-RM128, PVE of 3.2-6.8%) and two on chromosome 11 (interval RM332-RM202, PVE of 11.8-32.9% and interval RM202-RM287, PVE of 6.0-24.8%, respectively). And the QTL of interval RM332-RM202 was allelic with the well known Stvb-i. The resistance mechanism in IR36 was consisted of resistance to virus infection, tolerance to virus, tolerance to feeding of vector and antixenosis.
Using a doubled haploid lines (DHs) bred from the cross ZYQ8 x JX17 and four separate inoculation methods to genetically dissect the rice stripe resistance present in ZYQ8. Two linked RSV resistance QTLs were located on chromosome 1, and one on chromosome 11, jointly explaining 30-44% of the trait variance. The main-effect qSTV11 was mapped close to the established RSV resistance gene Stvb-i. For resistance to SBPH, three QTLs were located, mapping to chromosomes 1,2 and 11 and jointly explaining 44-51% of the trait variance. The large-effect qSBPHl (PVE>30%) appears to be a novel QTL conferring a degree of tolerance and antibiosis against SBPH. Analysis of a set of chromosome segment substitution lines showed rice stripe resistance genes/QTLs are commonly exsisted on the long arm of chromosome 1.
4) Fine mapping of a main effect qSTV11 in Kasalath
The stability of was validated using 39 established chromosome segment substitution lines. Fine mapping of qSTV11 was carried out using 372 recombinant BC3F2:3 and 399 BC3F3:4 lines selected from 7018 BC3F2 plants of the cross SL-234/Koshihikari.Four SSR (Simple Sequence Repeat), ten InDel and one CAPS markers were developed to narrow qSTVll locus. The qSTV11 was finally localized to a 39.2 Kb region that contains seven annotated genes. Marker-resistance association analysis suggested qSTV11 was distributed in diverse landraces coming from different regions. These results will provide a basis for map-based cloning of qSTV11,and benefit for the improvement of RSV resistance in rice varieties.
引文
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