National Institute of Plant Genome Research, New Delhi, India.
Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India.
BMC Biol. 2023 Apr 19;21(1):91. doi: 10.1186/s12915-023-01577-3.
Rice grain size (GS) is an essential agronomic trait. Though several genes and miRNA modules influencing GS are known and seed development transcriptomes analyzed, a comprehensive compendium connecting all possible players is lacking. This study utilizes two contrasting GS indica rice genotypes (small-grained SN and large-grained LGR). Rice seed development involves five stages (S1-S5). Comparative transcriptome and miRNome atlases, substantiated with morphological and cytological studies, from S1-S5 stages and flag leaf have been analyzed to identify GS proponents.
Histology shows prolonged endosperm development and cell enlargement in LGR. Stand-alone and comparative RNAseq analyses manifest S3 (5-10 days after pollination) stage as crucial for GS enhancement, coherently with cell cycle, endoreduplication, and programmed cell death participating genes. Seed storage protein and carbohydrate accumulation, cytologically and by RNAseq, is shown to be delayed in LGR. Fourteen transcription factor families influence GS. Pathway genes for four phytohormones display opposite patterns of higher expression. A total of 186 genes generated from the transcriptome analyses are located within GS trait-related QTLs deciphered by a cross between SN and LGR. Fourteen miRNA families express specifically in SN or LGR seeds. Eight miRNA-target modules display contrasting expressions amongst SN and LGR, while 26 (SN) and 43 (LGR) modules are differentially expressed in all stages.
Integration of all analyses concludes in a "Domino effect" model for GS regulation highlighting chronology and fruition of each event. This study delineates the essence of GS regulation, providing scope for future exploits. The rice grain development database (RGDD) ( www.nipgr.ac.in/RGDD/index.php ; https://doi.org/10.5281/zenodo.7762870 ) has been developed for easy access of data generated in this paper.
水稻粒型（GS）是一个重要的农艺性状。虽然已经知道有几个影响 GS 的基因和 miRNA 模块，并对种子发育转录组进行了分析，但缺乏一个连接所有可能参与者的综合纲要。本研究利用两个不同粒型的籼稻基因型（小粒型 SN 和大粒型 LGR）。水稻种子发育涉及五个阶段（S1-S5）。对 S1-S5 阶段和旗叶进行了比较转录组和 miRNA 图谱分析，并结合形态学和细胞学研究，以鉴定 GS 促进因子。
组织学显示 LGR 的胚乳发育和细胞增大延长。独立和比较 RNAseq 分析表明，S3（授粉后 5-10 天）阶段对于 GS 增强至关重要，与细胞周期、内多倍体化和程序性细胞死亡参与基因一致。种子贮藏蛋白和碳水化合物的积累，无论是在细胞水平上还是通过 RNAseq 分析，都显示在 LGR 中延迟。14 个转录因子家族影响 GS。四种植物激素的途径基因显示出相反的高表达模式。从转录组分析中产生的总共 186 个基因位于 SN 和 LGR 杂交鉴定的 GS 性状相关 QTL 内。14 个 miRNA 家族在 SN 或 LGR 种子中特异性表达。8 个 miRNA 靶模块在 SN 和 LGR 之间表现出不同的表达，而 26 个（SN）和 43 个（LGR）模块在所有阶段都有不同的表达。
综合所有分析得出的结论是，GS 调控的“多米诺效应”模型突出了每个事件的时间顺序和结果。本研究描绘了 GS 调控的本质，为未来的开发提供了空间。水稻粒发育数据库（RGDD）（www.nipgr.ac.in/RGDD/index.php；https://doi.org/10.5281/zenodo.7762870）已经开发出来，以便于访问本文生成的数据。
