Background

Aerobic rice production (AP) may be a solution to the looming water crisis by utilising less water compared to traditional flooded culture. As such, development of genotypes with narrow root cone angle (RCA) is considered a key AP adaptation trait as it could lead to deeper rooting and ensure water uptake at depth. Quantitative trait loci (QTL) and genes associated with rooting angle have been identified in rice, but usually in conventional transplanted systems or in upland and drought conditions. This study aimed to identify QTL associated with RCA in AP systems using a recombinant inbred line population derived from IRAT109.

Results

Four experiments conducted in glasshouse and aerobic field conditions revealed significant genotypic variation existed for RCA in the population. Single and multiple QTL models identified the presence of eight QTL distributed in chromosomes 1, 2, 3, 4, and 11. Combined, these QTL explained 36.7–51.2% of the genotypic variance in RCA present in the population. Two QTL, qRCA1.1 and qRCA1.3, were novel and may be new targets for improvement of RCA. Genotypes with higher number of favourable QTL alleles tended to have narrower RCA. qRCA4 was shown to be a major and stable QTL explaining up to 24.3% of the genotypic variation, and the presence of the target allele resulted in as much as 8.6° narrower RCA. Several genes related to abiotic stress stimulus response were found in the qRCA4 region.

Conclusion

Stable and novel genomic regions associated with RCA have been identified. Genotypes which had combinations of these QTL, resulted in a narrower RCA phenotype. Allele mining, gene cloning, and physiological dissection should aid in understanding the molecular function and mechanisms underlying RCA and these QTL. Ultimately, our work provides an opportunity for breeding programs to develop genotypes with narrow RCA and deep roots for improved adaptation in an AP system for sustainable rice production.

中文翻译：

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稳定和新颖的定量性状位点（QTL）在有氧水稻（Oryza sativa L.）生产系统中赋予窄根锥角

背景

与传统的淹水养殖相比，有氧稻米生产（AP）可以通过使用更少的水来解决迫在眉睫的水危机。因此，具有窄根锥角（RCA）的基因型的发育被认为是关键的AP适应性状，因为它可能导致更深的生根并确保深处的水分吸收。已经在水稻中鉴定了数量性状基因座（QTL）和与生根角相关的基因，但通常在常规移植系统中或在旱地和干旱条件下均已鉴定。这项研究旨在使用衍生自IRAT109的重组自交系群体鉴定AP系统中与RCA相关的QTL。

结果

在温室和有氧田间条件下进行的四个实验表明，人群中RCA存在明显的基因型变异。单个和多个QTL模型确定了8个QTL分布在1、2、3、4和11号染色体中。这些QTL共同解释了人群中RCA基因型变异的36.7-51.2％。qRCA1.1和qRCA1.3这两个QTL是新颖的，可能是改善RCA的新目标。QTL等位基因数量较多的基因型往往具有较窄的RCA。qRCA4结果显示，这是一个主要且稳定的QTL，解释了高达24.3％的基因型变异，并且目标等位基因的存在导致RCA缩小了8.6°。在qRCA4区发现了几个与非生物胁迫刺激反应相关的基因。

结论

已经鉴定出与RCA相关的稳定和新颖的基因组区域。结合了这些QTL的基因型导致了更窄的RCA表型。等位基因挖掘，基因克隆和生理解剖应有助于理解RCA和这些QTL的分子功能和机制。最终，我们的工作为育种计划提供了一个机会，以开发具有窄RCA和深根的基因型，从而改善AP系统中水稻可持续可持续生产的适应性。