Phosphorus (P) deficiency is one of the major limiting factors for rice productivity with only one locus (PSTOL1) available for field based application. A biparental mapping population (F₆) derived from two P deficiency tolerant genotypes (Sahbhagi Dhan (SD) (PSTOL1⁺) and Chakhao Poreiton (CP) (PSTOL1⁻)), in which, transcriptome data generated from our lab had previously shown existence of diverse mechanisms was used to identify novel regions for better yield under lowland acidic soils. Phenotyping at F₄, F₅ and F₆ generations revealed significant correlation between traits like tiller number at 30 days (TN 30), tiller number at 60 days (TN 60), filled grains (FG), percent spikelet fertility (SF%), panicle number (PN) and grain yield per panicle (GYPP) and also association with better yield/performance under low P acidic soil conditions. Through selected genotyping on a set of forty superior and inferior lines using SSR, candidate gene–based and SNP polymorphic markers, 5 genomic regions associated with various yield-related traits were identified. Marker trait association studies revealed 13 markers significantly associated with yield attributing traits and PUE under lowland acidic field conditions. Chi-square and regression analyses of markers run on the entire population identified seven and six markers for SF% and GYPP, respectively, and two for biological yield with positive allele derived from SD which constitute a novel 1.847-Mb region on chromosome 2 flanked by two markers RM12550 and PR9-2. Expression analysis of 7 candidate genes lying within this region across SD, CP and two low P susceptible rice genotypes has revealed that expression of four genes including SPL4, SPL5, ACA9 and MLO8 is significantly upregulated only in SD under low P conditions. In CP, there is low expression of MLO8 under low P conditions, whereas SPL4, SPL5 and Os02g08120 are downregulated. In the case of the two susceptible genotypes, there is no expression of Os02g08120 either in optimum or limiting conditions. Sequence data across a panel of 3024 rice genotypes also suggests that there is polymorphism for these differentially expressed genes. The genes and underlying markers identified on chromosome 2 will be key to imparting tolerance to low P in diverse genetic backgrounds and for marker-assisted selection for higher yield under lowland acidic conditions.

磷 (P) 缺乏是水稻生产力的主要限制因素之一，只有一个基因座 (PSTOL1) 可用于田间应用。双亲作图群体 (F ₆ ) 源自两种 P 缺乏耐受基因型 (Sahbhagi Dhan (SD) (PSTOL1 ⁺ ) 和 Chakhao Poreiton (CP) (PSTOL1 ^- ))，其中，我们实验室生成的转录组数据先前已显示存在多种机制被用于确定在低地酸性土壤下提高产量的新区域。F ₄、F ₅和 F _{6 的}表型分析世代揭示了 30 天分蘖数 (TN 30)、60 天分蘖数 (TN 60)、饱满谷粒 (FG)、小穗肥力百分比 (SF%)、穗数 (PN) 和每粒产量等性状之间的显着相关性。穗（GYPP），并且在低磷酸性土壤条件下与更好的产量/性能相关。通过使用 SSR、基于候选基因和 SNP 多态性标记对一组 40 个优劣品系进行选择性基因分型，确定了与各种产量相关性状相关的 5 个基因组区域。标记性状关联研究显示，在低地酸性田间条件下，有 13 个标记与产量归因性状和 PUE 显着相关。在整个群体上运行的标记的卡方和回归分析分别确定了 SF% 和 GYPP 的七个和六个标记，和两个来自 SD 的阳性等位基因的生物学产量，它们在染色体 2 上构成一个新的 1.847-Mb 区域，两侧是两个标记 RM12550 和 PR9-2。位于该区域内的 7 个候选基因的表达分析表明，包括SPL4、SPL5、ACA9和MLO8仅在低磷条件下在 SD 中显着上调。在 CP 中，低 P 条件下MLO8 的表达较低，而SPL4、SPL5和Os02g08120则下调。在两个易感基因型的情况下，没有Os02g08120的表达无论是在最佳条件还是极限条件下。一组 3024 个水稻基因型的序列数据也表明这些差异表达的基因存在多态性。在 2 号染色体上鉴定的基因和潜在标记将是在不同遗传背景下赋予对低磷的耐受性以及标记辅助选择以在低地酸性条件下获得更高产量的关键。