籼稻杂种优势群分析与谷壳硅含量QTL qHUS6.1的精细定位
摘要
利用384个SNP对737份来源广泛的现代优良籼稻品种或广泛用于籼稻育种的优良亲本进行遗传多样性分析，基于模型的遗传结构分析表明此群体分为两个大群或六个亚群；有超过一半的供试材料（51.8%）被划分为“混合型”，表明由于育种过程中发生的种质交流与渗透以及有限资源的重复利用,世界各水稻种植区水稻种质遗传背景日趋复杂；基于遗传距离的聚类分析表明，来自于拉丁美洲的材料聚成一个单独的生态群，尽管与来自亚洲的材料的亲缘关系仍然很近，但它们是杂交籼稻育种潜在的优势生态群。
根据737份材料的遗传多样性和遗传结构分析结果，挑选17份代表亲本材料采用半双列杂交获得136个杂交种，在热带地区五个环境下（季节和地点）进行农艺性状鉴定，分析热带地区杂交籼稻的杂种表现及其杂种优势水平、组内与组间配组的杂种优势及亲本遗传距离与杂种优势的相关性。结果表明：1）杂交组合产量优势明显，平均比亲本增产20.4%；2）基因型与环境互作效应对杂交种产量影响极显著，表明选育在热带地区具有广适应性的优良杂交组合是极其困难的；3）群间配组的平均产量、产量杂种优势和产量配合力都明显高于群内配组，表明基于分子标记遗传距离的群体分组结果，可以进一步用于杂种优势群的构建；4）基于随机挑选SNP的遗传距离与杂种产量、杂种优势和配合力之间没有相关性，或相关性非常弱，表明基于随机挑选分子标记的遗传距离不能用于杂种产量、杂种优势和配合力的预测。
全基因组重测序分析了优良三系杂交稻汕优10号双亲（珍汕97和密阳46）的全基因组SNP、短片段InDel和SV变异。与参考序列9311比较，珍汕97中检测到364488个SNP、61181个InDel和6298个SV变异，密阳46中检测到364179个SNP、61984个InDel和6408个SV。珍汕97和密阳46之间比对出181737个SNP和1205个InDel；将其中180个3-8bp的InDel转化成PCR标记，其中160（88.9%）个能够扩增出稳定的PCR产物且在6%PAGE中呈现明显多态性。
利用从珍汕97/密阳46重组自交系群体筛选出的一个剩余杂合体（RH），通过连续自交发展3套目标区间相互交迭的近等基因系（NIL），利用小样本量群体将一个控制谷壳硅含量的QTLqHUS6.1定位在仅含有一个开放阅读框的区间内，同时构建了一套仅针对目标QTL qHUS6.1的单基因NIL。采用剩余杂合体定位策略，共检测了源自RH6自交7代所衍生的2441个单株，平均每代筛选348株，就筛选到了3个分离区间缩小并相互交迭的sub-RH，通过对3个sub-RH所发展的3套NIL的分析，将qHUS6.1定位到一个单基因区间内。
Seven hundred and thirty seven improved indica varieties/lines developed recently and/or widelyused by present indica breeding programs worldwide, were genotyped with384single nucleotidepolymorphism (SNP) assay. Model-based population structure analysis revealed the presence of twomajor groups with six subgroups. Over half of the accessions (51.8%) appeared to have less than0.6memberships assigned to any one of the six model-based groups, highlighting the wide range of geneflow within improved indica varieties/lines and the genetic integration of valuable alleles shared byancestries among improved high-yielding varieties/lines through germplasm exchanges and theincreasingly complex genetic background among improved high-yielding varieties/lines. Distance-basedclustering analysis showed Latin American cultivated indica lines have tended to form their ownecological cline, which could serve as a potential heterotic ecotype for hybrid rice breeding althoughthey are still closely related to Asian indica lines.
A sample of17parents was selected from the panel of737improved cultivated elite varieties/lines,the parents represent the original genetic structure with6groups.17parents were crossed following adiallel mating design without reciprocals resulting136hybrids that were evaluated at five environments(Seasons and locations) in tropics, with the objectives of evaluating the magnitude of hybridperformance, yield heterosis, the consistency between marker-based group and heterotic performance ofhybrids, as well as the correlation between genetic distance (GD) with hybrid performance, yieldheterosis and combining ability. The analysis showed that1) the hybrids yielded20.4%higher than theparents;2) significant genotype environment effect for hybrid yield represented a challenge todevelop high yield hybrid rice with widespread for multi-environments in tropics;3) significant yield,yield heterosis and combining ability of inter-groups versus intra-group crosses suggested that groupsidentified by GD based on molecular marker could be a practical starting point for further breedingwork to develop useful heterotic groups;4) the correlations between the GD based on random molecularmarkers with hybrid yield, heterosis, SCA were insignificant or weak, GD cannot be used for hybridyield, heterosis and SCA prediction.
Genome analysis based on re-sequencing of two indica accessions Zhenshan97(ZS97) andMilyang46(MY46), the parents of an elite three-line indica hybrid Shanyou10, has led to discovercomprehensive SNPs, short InDels and SVs variations. Compared with reference9311, a total of364488SNPs,61181InDels and6298SVs were detected in ZS97;364179SNPs,61984InDels and6408SVs were detected in MY46. Meanwhile,181737different SNPs,1205different short InDels wereobserved between ZS97and MY46. Out of1205different short InDels between ZS97and MY46,180InDels with3to8bp length were converted into PCR-based markers,160(88.9%) validated InDelmarkers can be amplified and showed significant plolymorphism between ZS97and MY46run in6%PAGE.
A fine mapping strategy were used in the fine mapping of qHUS6.1for the silicon content in rice hull: a residual heterozygous plant (RH) was identified from RILs of ZS97/MY46; develop three sets ofNILs with overlapping target segregating chromosome segment; qHUS6.1was narrowed into an intervalwith only one ORF, as well as one set of single gene NILs (qHUS6.1) was developed using smallpopulation. Base one the fine mapping strategy with RH, totally,2441plants derived from selfedprogenies with seven generations from RH6were genotyped. Three sub-RHs with overlappingheterozygous segments were obtained by genoytyping only averaged348plants in every generation.Based on analyses of the phenotypic distribution and variance among the three sets of NILs derivedfrom the three sub-RHs, qHUS6.1was delimited to a region with only a single gene.
根据737份材料的遗传多样性和遗传结构分析结果，挑选17份代表亲本材料采用半双列杂交获得136个杂交种，在热带地区五个环境下（季节和地点）进行农艺性状鉴定，分析热带地区杂交籼稻的杂种表现及其杂种优势水平、组内与组间配组的杂种优势及亲本遗传距离与杂种优势的相关性。结果表明：1）杂交组合产量优势明显，平均比亲本增产20.4%；2）基因型与环境互作效应对杂交种产量影响极显著，表明选育在热带地区具有广适应性的优良杂交组合是极其困难的；3）群间配组的平均产量、产量杂种优势和产量配合力都明显高于群内配组，表明基于分子标记遗传距离的群体分组结果，可以进一步用于杂种优势群的构建；4）基于随机挑选SNP的遗传距离与杂种产量、杂种优势和配合力之间没有相关性，或相关性非常弱，表明基于随机挑选分子标记的遗传距离不能用于杂种产量、杂种优势和配合力的预测。
全基因组重测序分析了优良三系杂交稻汕优10号双亲（珍汕97和密阳46）的全基因组SNP、短片段InDel和SV变异。与参考序列9311比较，珍汕97中检测到364488个SNP、61181个InDel和6298个SV变异，密阳46中检测到364179个SNP、61984个InDel和6408个SV。珍汕97和密阳46之间比对出181737个SNP和1205个InDel；将其中180个3-8bp的InDel转化成PCR标记，其中160（88.9%）个能够扩增出稳定的PCR产物且在6%PAGE中呈现明显多态性。
利用从珍汕97/密阳46重组自交系群体筛选出的一个剩余杂合体（RH），通过连续自交发展3套目标区间相互交迭的近等基因系（NIL），利用小样本量群体将一个控制谷壳硅含量的QTLqHUS6.1定位在仅含有一个开放阅读框的区间内，同时构建了一套仅针对目标QTL qHUS6.1的单基因NIL。采用剩余杂合体定位策略，共检测了源自RH6自交7代所衍生的2441个单株，平均每代筛选348株，就筛选到了3个分离区间缩小并相互交迭的sub-RH，通过对3个sub-RH所发展的3套NIL的分析，将qHUS6.1定位到一个单基因区间内。
Seven hundred and thirty seven improved indica varieties/lines developed recently and/or widelyused by present indica breeding programs worldwide, were genotyped with384single nucleotidepolymorphism (SNP) assay. Model-based population structure analysis revealed the presence of twomajor groups with six subgroups. Over half of the accessions (51.8%) appeared to have less than0.6memberships assigned to any one of the six model-based groups, highlighting the wide range of geneflow within improved indica varieties/lines and the genetic integration of valuable alleles shared byancestries among improved high-yielding varieties/lines through germplasm exchanges and theincreasingly complex genetic background among improved high-yielding varieties/lines. Distance-basedclustering analysis showed Latin American cultivated indica lines have tended to form their ownecological cline, which could serve as a potential heterotic ecotype for hybrid rice breeding althoughthey are still closely related to Asian indica lines.
A sample of17parents was selected from the panel of737improved cultivated elite varieties/lines,the parents represent the original genetic structure with6groups.17parents were crossed following adiallel mating design without reciprocals resulting136hybrids that were evaluated at five environments(Seasons and locations) in tropics, with the objectives of evaluating the magnitude of hybridperformance, yield heterosis, the consistency between marker-based group and heterotic performance ofhybrids, as well as the correlation between genetic distance (GD) with hybrid performance, yieldheterosis and combining ability. The analysis showed that1) the hybrids yielded20.4%higher than theparents;2) significant genotype environment effect for hybrid yield represented a challenge todevelop high yield hybrid rice with widespread for multi-environments in tropics;3) significant yield,yield heterosis and combining ability of inter-groups versus intra-group crosses suggested that groupsidentified by GD based on molecular marker could be a practical starting point for further breedingwork to develop useful heterotic groups;4) the correlations between the GD based on random molecularmarkers with hybrid yield, heterosis, SCA were insignificant or weak, GD cannot be used for hybridyield, heterosis and SCA prediction.
Genome analysis based on re-sequencing of two indica accessions Zhenshan97(ZS97) andMilyang46(MY46), the parents of an elite three-line indica hybrid Shanyou10, has led to discovercomprehensive SNPs, short InDels and SVs variations. Compared with reference9311, a total of364488SNPs,61181InDels and6298SVs were detected in ZS97;364179SNPs,61984InDels and6408SVs were detected in MY46. Meanwhile,181737different SNPs,1205different short InDels wereobserved between ZS97and MY46. Out of1205different short InDels between ZS97and MY46,180InDels with3to8bp length were converted into PCR-based markers,160(88.9%) validated InDelmarkers can be amplified and showed significant plolymorphism between ZS97and MY46run in6%PAGE.
A fine mapping strategy were used in the fine mapping of qHUS6.1for the silicon content in rice hull: a residual heterozygous plant (RH) was identified from RILs of ZS97/MY46; develop three sets ofNILs with overlapping target segregating chromosome segment; qHUS6.1was narrowed into an intervalwith only one ORF, as well as one set of single gene NILs (qHUS6.1) was developed using smallpopulation. Base one the fine mapping strategy with RH, totally,2441plants derived from selfedprogenies with seven generations from RH6were genotyped. Three sub-RHs with overlappingheterozygous segments were obtained by genoytyping only averaged348plants in every generation.Based on analyses of the phenotypic distribution and variance among the three sets of NILs derivedfrom the three sub-RHs, qHUS6.1was delimited to a region with only a single gene.
引文
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