水稻骨干亲本桂朝2号形成的关键基因组区段定位、传递及效应分析
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摘要
桂朝2号是一个重要的水稻骨干亲本,已经衍生了超过30个的水稻核心品种。1983年至今,桂朝2号及其衍生品种的种植面积已经超过14.66百万公顷。因此,从基因组水平上认识桂朝2号及其衍生品种,能较为全面的了解桂朝2号在我国水稻育种工作中发挥的作用,对今后的育种实践,尤其是对亲本组合的选择、桂朝2号及其衍生品种的利用提供科学的理论支持。本研究以桂朝2号及其上游亲本和衍生品种作为研究对象,利用SSR分子标记进行全基因组扫描,并结合一些重要的农艺性状,希望明确桂朝2号形成的关键基因组区段、其在后代的传递规律和效应。主要研究结果概况如下：
1.利用425对多态性SSR标记对桂朝2号及其亲本、衍生品种进行遗传多样性进行分析,16个品种中检测出1095个等位变异基因,变异数目在2～7之间,平均等位基因数目为2.58；平均多态性信息含量(PIC)为0.38,变化范围为0.12～0.83；各品种间遗传相似性系数(GS)在0.72～0.93之间,平均为0.81。基于SSR分析的加权配对算术平均法(UPGMA)进行的聚类分析,桂朝2号及其亲本、衍生品种被聚为两大类,与各品种的系谱关系基本一致。
2.利用1177对SSR引物对桂朝2号及其亲本进行全基因组扫描,构建了较高密度的桂朝2号基因组区段来源图谱。由371对多态性标记形成的383个基因组区段中,有42个区段为单一亲本来源,其余为多亲本来源。单一来源区段共覆盖染色体物理距离24659.154KB,占全基因组的6.63%；其中,对桂朝2号基因组形成中贡献最大的亲本是朝阳早18和桂阳矮49,遗传贡献率分别为2.00%和1.46%。单一来源区段被确定为桂朝2号的关键基因组区段,在这些区段上定位了37个QTLs(基因),主要和产量因子相关,也含部分及病虫害抗性基因及株型基因,如已被克隆的穗实粒主效QTL Glna,矮杆基因d2等。桂朝2号自身特有区段上也定位了一些和产量性状相关的QTL,其中与千粒重相关的QTL较多。这些区段可能源自本研究中未涉及的上游亲本材料。
3.产量构成因子及品质性状在衍生品种中的传递规律：千粒重、有效穗、分蘖数、株高降低；结实率、穗实粒、单株重增加；整精米率、垩白率、垩白大小、表观直链淀粉、蛋白质含量降低,粒长、长宽比、透明度、胶稠度增加,糊化温度不变。此外桂朝2号的垩白率、垩白大小、粒长、长宽比、透明度等性状基本与朝阳早18表现一致,这些性状极可能就是遗传自朝阳早18。衍生品种继承了桂朝2号的结实率、穗实粒、分蘖数、单株重等产量性状及糊化温度与蛋白质含量；而其余品质性状整精米率、垩白率、垩白大小、粒长、长宽比、透明度、胶稠度、表观直链淀粉含量在育种过程中逐渐被淘汰掉。
4.淀粉合成相关基因的分子标记检测结果,发现基于淀粉脱支酶基因(极限糊精酶基因)Pul开发的STS标记R114/113在桂朝2号及其亲本、衍生品种中扩增出了多态性,朝阳早18、青六矮、丰青矮3个材料表现为日本晴的粳稻带型。其他标记在供试品种中的扩增结果都符合籼型带型。
5.全基因组SSR标记扫描发现348个标记在桂朝2号及其衍生品种中表现出多态性。根据SSR检测的结果,确定了桂朝2号有78个基因组区段传递给后代。各基因组区段对衍生品种的遗传贡献率变化范围是14.29～85.71%,平均47.25%。这些区段上定位了61个基因(QTLs),其中产量因子相关QTLs35个,其余基因主要与植物防御与非生物胁迫、生长发育、病虫害抗性、植株形态等性状相关。
Guichao 2, one of the most important rice core parents in China, has given rise to over thirty elite cultivars, and the total cultivation area of Guichao 2 and its derivatives amount to 14.66 million hectares since 1983. Thus, analyzing and recognizing Guichao 2 on a genomic level will definitely benefit the breeding practice, especially for core parents and for the promotion of hybrid combinations in the future.In the present study, Simple Sequence Repeat marker (SSR) based genome-wide screening and important agronomic characters investigation were performed, and combined with QTLs/gene analysis to learning the genetic structure, the effects of core genomic regions of Guichao 2 and its transfer patterns to its derivatives, and the main results were details as followed:
1. Genetic diversity of Guichao 2 and its parents, derivatives was investigated with 425 pairs of polymorphic SSR markers. A total of 1095 alleles were detected among 16 cultivals, and the number of alleles each primer pair ranged between 2-7 with an average of 2.58. The polymorphic information content (PIC) value ranged from 0.12 to 0.83 and averaged 0.38. Genetic similarity (GS) among the 16 cultivars varied from 0.72 to 0.93 with an average of 0.81, indicating that the genetic diversity is not abundant. Guichao 2 and its parents, derivatives could be clustered into two groups with UPGMA cluster analysis based on SSR analysis, and the resuls are according with their pedigrees relationships.
2. Origins map of Guichao 2's genetic regions was drawn based on genome-wide screening.371 polymorphic makers constitute 383 genetice regions,42 of them have single origin, and others have multiple origins.42 genetic regions cover chromosome physical distance 24659.154kb,6.63% of whole genome size. For the 42 single origin regions, Chaoyangzaol8 and Guichao 2 contribute more genetic components to Guichao 2 than other parents, and their genetic contribution ratio were 2.00% and 1.46%, respectively. The 42 single origin genetic regions inherited from a given parent or characteristic by Guichao 2, and be thought of important genetic regions of Guichao 2. There were 37 QTLs/gene mapped on these important genetic regions, most of them associated with yield factors, and some of them are related to plant type morphogenesis and resistance to diseases. For example, Glna, a main QTL associated with filled seeds per panicle, which can explain 44% of variation. A drawft gene, d2 mapped on important genetic regions too, and both of them had been cloned successifully. Moreover, some QTLs/gene related to yield factors, espcically associated with thousand grains weight, mapped on the genetic regions characteristic of Guichao 2, and these genetic regions uniquled by Guichao 2 might inherited from the parents dose not be involved in this study.
3.3. Results of deliver rules of yield factors and quality traits from Guichao 2 to its derivatives indicates that:thousand grains weight, effective panicle number, tillers number and plant height decrease, while seed setting ratio, filled seeds per panicle and plant weight are increased; as for quality characters, head rice ratio, chalky ratio, chalk size, apparent amylase content and protein content decline, while grain length, length-width ratio, transparency and gel consistency rise, and gelatinization temperature is constant. Otherwise, chalky ratio, chalk size, grain length, length-width ratio and transparency of Guichao 2 are similer to Chaoyangzao 18's, indicating these characters might be inherited from Chaoyangzao 18. Furthermore, some yield factors, seed setting ratio, filled seeds per panicle, tillers number and plant weight for instance, gelatinization temperature and protein content inherits by derivatives from Guichao 2, while most of quality characters of Guichao 2's, such as head rice ratio, chalky ratio, chalk size, rain length, length-width ratio, transparency, gel consistency and apparent amylase content are sifted out in breeding programs due to hardly reach high quality standards.
4. Markers developed from starch-synthesis genes were using to test genotype of Guichao 2 and its parents Chaoyangzao 18、Guiyangai 49 and its derivatives. Only 114/113, developed from Pul (gene encoding pullulanase), amplified polymorphic bands among ten cultivars, Chaoyangzao 18-. Qingliuai and Fengqingai are classied into Nipponbare genotype, others are classied into Indica genotype. Other markers did not amplified polymorphism among the ten cultivars, which are grouped into Indica genotype.
5 A total of 348 polymorphic markers and 833 polymorphic alleles were detected. In addition,78 genomic regions of Guichao 2 are identified inherited by these derivatives, their contribution ratios ranging from 14.29% to 85.71%, with an average of 41.25%. Moreover,61 genes and quantitative trait loci (QTLs) were found to be located on these genomic regions,35 of them are associated with yield factors, and others mainly involve in stress response, growth and development, resistance to diseases and plant type.
1.利用425对多态性SSR标记对桂朝2号及其亲本、衍生品种进行遗传多样性进行分析,16个品种中检测出1095个等位变异基因,变异数目在2～7之间,平均等位基因数目为2.58；平均多态性信息含量(PIC)为0.38,变化范围为0.12～0.83；各品种间遗传相似性系数(GS)在0.72～0.93之间,平均为0.81。基于SSR分析的加权配对算术平均法(UPGMA)进行的聚类分析,桂朝2号及其亲本、衍生品种被聚为两大类,与各品种的系谱关系基本一致。
2.利用1177对SSR引物对桂朝2号及其亲本进行全基因组扫描,构建了较高密度的桂朝2号基因组区段来源图谱。由371对多态性标记形成的383个基因组区段中,有42个区段为单一亲本来源,其余为多亲本来源。单一来源区段共覆盖染色体物理距离24659.154KB,占全基因组的6.63%；其中,对桂朝2号基因组形成中贡献最大的亲本是朝阳早18和桂阳矮49,遗传贡献率分别为2.00%和1.46%。单一来源区段被确定为桂朝2号的关键基因组区段,在这些区段上定位了37个QTLs(基因),主要和产量因子相关,也含部分及病虫害抗性基因及株型基因,如已被克隆的穗实粒主效QTL Glna,矮杆基因d2等。桂朝2号自身特有区段上也定位了一些和产量性状相关的QTL,其中与千粒重相关的QTL较多。这些区段可能源自本研究中未涉及的上游亲本材料。
3.产量构成因子及品质性状在衍生品种中的传递规律：千粒重、有效穗、分蘖数、株高降低；结实率、穗实粒、单株重增加；整精米率、垩白率、垩白大小、表观直链淀粉、蛋白质含量降低,粒长、长宽比、透明度、胶稠度增加,糊化温度不变。此外桂朝2号的垩白率、垩白大小、粒长、长宽比、透明度等性状基本与朝阳早18表现一致,这些性状极可能就是遗传自朝阳早18。衍生品种继承了桂朝2号的结实率、穗实粒、分蘖数、单株重等产量性状及糊化温度与蛋白质含量；而其余品质性状整精米率、垩白率、垩白大小、粒长、长宽比、透明度、胶稠度、表观直链淀粉含量在育种过程中逐渐被淘汰掉。
4.淀粉合成相关基因的分子标记检测结果,发现基于淀粉脱支酶基因(极限糊精酶基因)Pul开发的STS标记R114/113在桂朝2号及其亲本、衍生品种中扩增出了多态性,朝阳早18、青六矮、丰青矮3个材料表现为日本晴的粳稻带型。其他标记在供试品种中的扩增结果都符合籼型带型。
5.全基因组SSR标记扫描发现348个标记在桂朝2号及其衍生品种中表现出多态性。根据SSR检测的结果,确定了桂朝2号有78个基因组区段传递给后代。各基因组区段对衍生品种的遗传贡献率变化范围是14.29～85.71%,平均47.25%。这些区段上定位了61个基因(QTLs),其中产量因子相关QTLs35个,其余基因主要与植物防御与非生物胁迫、生长发育、病虫害抗性、植株形态等性状相关。
Guichao 2, one of the most important rice core parents in China, has given rise to over thirty elite cultivars, and the total cultivation area of Guichao 2 and its derivatives amount to 14.66 million hectares since 1983. Thus, analyzing and recognizing Guichao 2 on a genomic level will definitely benefit the breeding practice, especially for core parents and for the promotion of hybrid combinations in the future.In the present study, Simple Sequence Repeat marker (SSR) based genome-wide screening and important agronomic characters investigation were performed, and combined with QTLs/gene analysis to learning the genetic structure, the effects of core genomic regions of Guichao 2 and its transfer patterns to its derivatives, and the main results were details as followed:
1. Genetic diversity of Guichao 2 and its parents, derivatives was investigated with 425 pairs of polymorphic SSR markers. A total of 1095 alleles were detected among 16 cultivals, and the number of alleles each primer pair ranged between 2-7 with an average of 2.58. The polymorphic information content (PIC) value ranged from 0.12 to 0.83 and averaged 0.38. Genetic similarity (GS) among the 16 cultivars varied from 0.72 to 0.93 with an average of 0.81, indicating that the genetic diversity is not abundant. Guichao 2 and its parents, derivatives could be clustered into two groups with UPGMA cluster analysis based on SSR analysis, and the resuls are according with their pedigrees relationships.
2. Origins map of Guichao 2's genetic regions was drawn based on genome-wide screening.371 polymorphic makers constitute 383 genetice regions,42 of them have single origin, and others have multiple origins.42 genetic regions cover chromosome physical distance 24659.154kb,6.63% of whole genome size. For the 42 single origin regions, Chaoyangzaol8 and Guichao 2 contribute more genetic components to Guichao 2 than other parents, and their genetic contribution ratio were 2.00% and 1.46%, respectively. The 42 single origin genetic regions inherited from a given parent or characteristic by Guichao 2, and be thought of important genetic regions of Guichao 2. There were 37 QTLs/gene mapped on these important genetic regions, most of them associated with yield factors, and some of them are related to plant type morphogenesis and resistance to diseases. For example, Glna, a main QTL associated with filled seeds per panicle, which can explain 44% of variation. A drawft gene, d2 mapped on important genetic regions too, and both of them had been cloned successifully. Moreover, some QTLs/gene related to yield factors, espcically associated with thousand grains weight, mapped on the genetic regions characteristic of Guichao 2, and these genetic regions uniquled by Guichao 2 might inherited from the parents dose not be involved in this study.
3.3. Results of deliver rules of yield factors and quality traits from Guichao 2 to its derivatives indicates that:thousand grains weight, effective panicle number, tillers number and plant height decrease, while seed setting ratio, filled seeds per panicle and plant weight are increased; as for quality characters, head rice ratio, chalky ratio, chalk size, apparent amylase content and protein content decline, while grain length, length-width ratio, transparency and gel consistency rise, and gelatinization temperature is constant. Otherwise, chalky ratio, chalk size, grain length, length-width ratio and transparency of Guichao 2 are similer to Chaoyangzao 18's, indicating these characters might be inherited from Chaoyangzao 18. Furthermore, some yield factors, seed setting ratio, filled seeds per panicle, tillers number and plant weight for instance, gelatinization temperature and protein content inherits by derivatives from Guichao 2, while most of quality characters of Guichao 2's, such as head rice ratio, chalky ratio, chalk size, rain length, length-width ratio, transparency, gel consistency and apparent amylase content are sifted out in breeding programs due to hardly reach high quality standards.
4. Markers developed from starch-synthesis genes were using to test genotype of Guichao 2 and its parents Chaoyangzao 18、Guiyangai 49 and its derivatives. Only 114/113, developed from Pul (gene encoding pullulanase), amplified polymorphic bands among ten cultivars, Chaoyangzao 18-. Qingliuai and Fengqingai are classied into Nipponbare genotype, others are classied into Indica genotype. Other markers did not amplified polymorphism among the ten cultivars, which are grouped into Indica genotype.
5 A total of 348 polymorphic markers and 833 polymorphic alleles were detected. In addition,78 genomic regions of Guichao 2 are identified inherited by these derivatives, their contribution ratios ranging from 14.29% to 85.71%, with an average of 41.25%. Moreover,61 genes and quantitative trait loci (QTLs) were found to be located on these genomic regions,35 of them are associated with yield factors, and others mainly involve in stress response, growth and development, resistance to diseases and plant type.
引文
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