BACKGROUND Anaerobic germination is one of the most important traits for rice under direct-seeded conditions. The trait reduces risk of crop failure due to waterlogged conditions after seeding and allows water to be used as a means of weed control. The identification of QTLs and causal genes for anaerobic germination will facilitate breeding for improved direct-seeded rice varieties. In this study, we explored a BC1F2:3 population developed from a cross between BJ1, an indica landrace, and NSIC Rc222, a high-yielding recurrent parent. The population was phenotyped under different screening methods (anaerobic screenhouse, anaerobic tray, and aerobic screenhouse) to establish the relationship among the methods and to identify the most suitable screening method, followed by bulk segregant analysis (BSA) to identify large-effect QTLs. RESULTS The study showed high heritability for survival (SUR) under all three phenotyping conditions. Although high correlation was observed within screening environments between survival at 14 and 21 days after seeding, the correlation across environments was low. Germination under aerobic and anaerobic conditions showed very low correlation, indicating the independence of their genetic control. The results were further confirmed through AMMI analysis. Four significant markers with an effect on anaerobic germination were identified through BSA. CIM analysis revealed qAG1-2, qAG6-2, qAG7-4, and qAG10-1 having significant effects on the trait. qAG6-2 and qAG10-1 were consistent across screening conditions and seedling age while qAG1-2 and qAG7-4 were specific to screening methods. All QTLs showed an effect when survival across all screening methods was analyzed. Together, the QTLs explained 39 to 55% of the phenotypic variation for survival under anaerobic conditions. No QTL effects were observed under aerobic conditions. CONCLUSIONS The study helped us understand the effect of phenotyping method on anaerobic germination, which will lead to better phenotyping for this trait in future studies. The QTLs identified through this study will allow the improvement of breeding lines for the trait through marker-assisted selection or through forward breeding approaches such as genomic selection. The high frequency of the BJ1 allele of these QTLs will enhance the robustness of germination under anaerobic conditions in inbred and hybrid rice varieties.

中文翻译：

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基于特征的作图以鉴定水稻厌氧萌发的遗传因素：表型，GXE和QTL作图。

背景技术厌氧萌发是水稻在直接播种条件下最重要的性状之一。该性状减少了播种后因淹水而造成农作物歉收的风险，并允许将水用作杂草控制的一种手段。鉴定厌氧萌发的QTL和因果基因将有助于育种改良的直播种子水稻品种。在这项研究中，我们探讨了由印度land地方品种BJ1和高产轮回父母NSIC Rc222之间的杂交产生的BC1F2：3种群。在不同的筛选方法（厌氧筛选室，厌氧托盘和有氧筛选室）中对种群进行表型分析，以建立方法之间的关系并确定最合适的筛选方法，然后进行批量分离分析（BSA）以鉴定大影响的QTL。结果该研究显示在所有三种表型条件下的高生存力遗传力（SUR）。尽管在播种后14天和21天之间的生存期之间的筛选环境中观察到高度相关性，但跨环境的相关性很低。有氧和无氧条件下的发芽显示出很低的相关性，表明它们的遗传控制是独立的。通过AMMI分析进一步证实了结果。通过BSA鉴定了四个对厌氧萌发有影响的重要标记。CIM分析显示qAG1-2，qAG6-2，qAG7-4和qAG10-1对该性状具有显着影响。qAG6-2和qAG10-1在筛选条件和幼苗年龄之间是一致的，而qAG1-2和qAG7-4则对筛选方法具有特异性。当分析所有筛选方法的存活率时，所有QTL均显示效果。QTL共同解释了厌氧条件下生存的表型变异的39％至55％。在有氧条件下没有观察到QTL的影响。结论这项研究帮助我们了解了表型方法对厌氧萌发的影响，这将在以后的研究中为该性状带来更好的表型。通过这项研究确定的QTL将通过标记辅助选择或通过正向育种方法（例如基因组选择）来改善该性状的育种系。这些QTL的BJ1等位基因的高频率将增强自交和杂交水稻品种在厌氧条件下发芽的稳健性。QTL解释了厌氧条件下生存的表型变异的39％至55％。在有氧条件下没有观察到QTL的影响。结论这项研究帮助我们了解了表型方法对厌氧萌发的影响，这将在以后的研究中为该性状带来更好的表型。通过这项研究确定的QTL将通过标记辅助选择或通过正向育种方法（例如基因组选择）来改善该性状的育种系。这些QTL的BJ1等位基因的高频率将增强自交和杂交水稻品种在厌氧条件下发芽的稳健性。QTL解释了厌氧条件下生存的表型变异的39％至55％。在有氧条件下没有观察到QTL的影响。结论这项研究帮助我们了解了表型方法对厌氧萌发的影响，这将在以后的研究中为该性状带来更好的表型。通过这项研究确定的QTL将通过标记辅助选择或通过正向育种方法（例如基因组选择）来改善该性状的育种系。这些QTL的BJ1等位基因的高频率将增强自交和杂交水稻品种在厌氧条件下发芽的稳健性。结论这项研究帮助我们了解了表型方法对厌氧萌发的影响，这将在以后的研究中为该性状带来更好的表型。通过这项研究确定的QTL将通过标记辅助选择或通过正向育种方法（例如基因组选择）来改善该性状的育种系。这些QTL的BJ1等位基因的高频率将增强自交和杂交水稻品种在厌氧条件下发芽的稳健性。结论这项研究帮助我们了解了表型方法对厌氧萌发的影响，这将在以后的研究中为该性状带来更好的表型。通过这项研究确定的QTL将通过标记辅助选择或通过正向育种方法（例如基因组选择）来改善该性状的育种系。这些QTL的BJ1等位基因的高频率将增强自交和杂交水稻品种在厌氧条件下发芽的稳健性。