Ariharasutharsan Gunasekaran, Karthikeyan Adhimoolam, Geetha Seshadri, Raveendran Muthurajan, Lalitha Ravi, Ananda-Lekshmi Latha, Akilan Manoharan, Sushmitharaj Dhanalakshmi Veeraraj, Dhasarathan Manickam, Saraswathi Ramasamy, Arunachalam Paramasivam
Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India.
Subtropical Horticulture Research Institute, Jeju National University, Jeju, 63243, South Korea.
Funct Integr Genomics. 2025 Jan 20;25(1):19. doi: 10.1007/s10142-025-01532-1.
Dwarfism is a major trait for developing lodging-resistant rice cultivars. Gamma irradiation-induced mutagenesis has proven to be an effective method for generating dwarf rice mutants. In this research, we isolated a dwarf mutant from Anna R (4) in the M generation and subsequently stabilized the trait through successive selfing of progeny across the M-M generations. We then employed whole-genome re-sequencing (WGRS) and RNA sequencing (RNA-seq) analyses of Anna R (4) and the mutant (designated as ACM-20001) to elucidate the underlying mechanisms and identify candidate genes associated with dwarfness. Numerous genetic variations were identified between Anna (R) 4 and ACM-20001 through WGRS. In total, 2049 genetic variants, including 343 InDels and 1706 nonsynonymous SNPs, were identified across 697 genes. Additionally, RNA-seq analysis revealed 2,881 differentially expressed genes between the wild-type Anna (R) 4 and the mutant ACM-20001, with 1,451 genes up-regulated and 1,430 genes down-regulated in ACM-20001 compared to Anna (R) 4. By integrating WGRS and RNA-seq data with functional annotation analysis, we identified the most likely candidate genes (i.e., Os02g0506400, Os05g0515200, Os06g0154200 and Os08g0250900) related to dwarfness. Quantitative real-time PCR analysis verified the expression of these genes. Collectively, our study provides valuable insights in to the genes and mechanisms underlying dwarfness in rice. Further studies are required to elucidate the roles of these candidate genes in dwarfness, which contribute to advancements rice breeding programs.
矮化是培育抗倒伏水稻品种的一个主要性状。γ射线辐照诱变已被证明是产生矮化水稻突变体的有效方法。在本研究中，我们从M代的安娜R(4)中分离出一个矮化突变体，随后通过M-M代子代的连续自交使该性状稳定。然后，我们对安娜R(4)和突变体（命名为ACM-20001）进行了全基因组重测序（WGRS）和RNA测序（RNA-seq）分析，以阐明潜在机制并鉴定与矮化相关的候选基因。通过WGRS在安娜(R)4和ACM-20001之间鉴定出许多遗传变异。总共在697个基因中鉴定出2049个遗传变异，包括343个插入缺失和1706个非同义单核苷酸多态性。此外，RNA-seq分析显示野生型安娜(R)4和突变体ACM-20001之间有2881个差异表达基因，与安娜(R)4相比，ACM-20001中有1451个基因上调，1430个基因下调。通过将WGRS和RNA-seq数据与功能注释分析相结合，我们确定了最有可能与矮化相关的候选基因（即Os02g0506400、Os05g0515200、Os06g0154200和Os08g0250900）。定量实时PCR分析验证了这些基因的表达。总的来说，我们的研究为水稻矮化的基因和机制提供了有价值的见解。需要进一步研究来阐明这些候选基因在矮化中的作用，这将有助于推进水稻育种计划。
