Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India.
Biology Division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, 517507, India.
Mol Biol Rep. 2022 Aug;49(8):7649-7663. doi: 10.1007/s11033-022-07581-0. Epub 2022 May 25.
With the increase in population and economies of developing countries in Asia and Africa, the research towards securing future food demands is an imminent need. Among japonica and indica genotypes, indica rice varieties are largely cultivated across the globe. However, our present understanding of yield-contributing gene information stems mainly from japonica and studies on the yield potential of indica genotypes are limited.
In the present study, yield contributing orthologous genes previously characterized from japonica varieties were identified in the indica genome and analysed with binGO tool for GO biological processes categorization. Transcription factor binding site enrichment analysis in the promoters of yield-related genes of indica was performed with MEME-AME tool that revealed putative common TF regulators are enriched in flower development, two-component signalling and water deprivation biological processes. Gene regulatory networks revealed important TF-target interactions that might govern yield-related traits. Some of the identified candidate genes were validated by qRT-PCR analysis for their expression and association with yield-related traits among 16 widely cultivated popular indica genotypes. Further, SNP-metabolite-trait association analysis was performed using high-yielding indica variety Rasi. This resulted in the identification of putative SNP variations in TF regulators and targeted yield genes significantly linked with metabolite accumulation.
The study suggests some of the high yielding indica genotypes such as Ravi003, Rasi and Kavya could be used as potential donors in breeding programs based on yield gene expression analysis and SNP-metabolites associations.
随着亚洲和非洲发展中国家人口和经济的增长，保障未来粮食需求的研究迫在眉睫。在粳稻和籼稻基因型中，籼稻品种在全球范围内得到广泛种植。然而，我们目前对产量相关基因信息的了解主要来自粳稻，对籼稻基因型产量潜力的研究有限。
本研究在籼稻基因组中鉴定了先前从粳稻品种中表征的产量相关同源基因，并使用 binGO 工具进行 GO 生物过程分类分析。使用 MEME-AME 工具对与产量相关基因的启动子进行转录因子结合位点富集分析，结果表明在花发育、双组分信号和水分胁迫等生物过程中富集了潜在的常见 TF 调节剂。基因调控网络揭示了可能控制产量相关性状的重要 TF-靶标相互作用。通过 qRT-PCR 分析对一些鉴定的候选基因进行了验证，以评估它们在 16 个广泛种植的流行籼稻品种中的表达及其与产量相关性状的关联。此外，还使用高产籼稻品种 Rasi 进行了 SNP-代谢物-性状关联分析。这导致鉴定出 TF 调节剂和目标产量基因中的一些潜在 SNP 变异与代谢物积累显著相关。
该研究表明，一些高产的籼稻品种，如 Ravi003、Rasi 和 Kavya，可以根据产量基因表达分析和 SNP-代谢物关联，作为育种计划的潜在供体。
