Complete panicle exsertion (CPE) in rice is an important determinant of yield and a desirable trait in breeding. However, the genetic basis of CPE in rice still remains to be completely characterized. An ethyl methane sulfonate (EMS) mutant line of an elite cultivar Samba Mahsuri (BPT 5204), displaying stable and consistent CPE, was identified and named as CPE-110. MutMap and RNA-seq were deployed for unraveling the genomic regions, genes, and markers associated with CPE. Two major genomic intervals, on chromosome 8 (25668481-25750456) and on chromosome 11 (20147154-20190400), were identified to be linked to CPE through MutMap. A non-synonymous SNP (G/A; Chr8:25683828) in the gene LOC_Os08g40570 encoding pyridoxamine 5′-phosphate oxidase with the SNP index 1 was converted to Kompetitive allele-specific PCR (KASP) marker. This SNP (KASP 8-1) exhibited significant association with CPE and further validated through assay in the F₂ mapping population, released varieties and CPE exhibiting BPT 5204 mutant lines. RNA-seq of the flag leaves at the booting stage, 1100 genes were upregulated and 1305 downregulated differentially in CPE-110 and BPT 5204. Metabolic pathway analysis indicated an enrichment of genes involved in photosynthesis, glyoxylate, dicarboxylate, porphyrin, pyruvate, chlorophyll, carotenoid, and carbon metabolism. Further molecular and functional studies of the candidate genes could reveal the mechanistic aspects of CPE.

水稻的穗完全外露（CPE）是产量的重要决定因素，也是育种中的理想性状。然而，水稻 CPE 的遗传基础仍有待完全阐明。优良品种 Samba Mahsuri (BPT 5204) 的甲磺酸乙酯 (EMS) 突变系表现出稳定且一致的 CPE，经鉴定并命名为 CPE-110。MutMap 和 RNA-seq 用于解开与 CPE 相关的基因组区域、基因和标记。通过 MutMap 确定 8 号染色体上的两个主要基因组区间 (25668481-25750456) 和 11 号染色体上的 (20147154-20190400) 与 CPE 相关。将编码吡哆胺 5'-磷酸氧化酶的基因LOC_Os08g40570中具有 SNP 索引 1 的非同义 SNP (G/A; Chr8:25683828)转换为竞争性等位基因特异性 PCR (KASP) 标记。_{该 SNP (KASP 8-1) 表现出与 CPE 显着相关性，并通过 F 2}作图群体、发布的品种和表现出 BPT 5204 突变系的 CPE中的测定进一步得到验证。孕穗期旗叶的RNA-seq显示，CPE-110和BPT 5204中有1100个基因差异上调，1305个基因下调。代谢途径分析表明参与光合作用、乙醛酸、二羧酸、卟啉、丙酮酸、叶绿素、类胡萝卜素和碳代谢。对候选基因的进一步分子和功能研究可以揭示 CPE 的机制。