Luo Wei, Sun Min, Zhang Ailing, Lin Chuang, Jin Yarong, Wang Xiaoshan, Huang Linkai
College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Institute of Advanced Study, Chengdu University, Chengdu, 610106, China.
BMC Genomics. 2024 Dec 18;25(1):1199. doi: 10.1186/s12864-024-11114-3.
Pearl millet (Pennisetum glaucum (L.) R. Br.) is a vital cereal crop, predominantly cultivated in arid and semi-arid regions of Asia and Africa. It serves as a staple food for millions, while also being utilized as forage and an energy crop. The crop's resistance to heat and drought, coupled with its high biomass, positions it as a promising candidate for climate-resilient agriculture. A detailed understanding of its gene expression patterns across various tissues and developmental stages is essential for enhancing its yield and quality. This study aims to fill this knowledge gap by employing RNA-seq to identify housekeeping genes (HKGs) and tissue-specific genes (TSGs) in pearl millet.
Our analysis of RNA-seq data from nine tissues (seed, germ, radicle, leaf, root, tillering tissue, stem, spike, and grain) across eight developmental stages in pearl millet accession Tifleaf3 revealed a comprehensive gene expression profile. We identified 461 HKGs that exhibited stable expression across all tissues and stages, providing robust internal references for RT-qPCR. Additionally, 8091 TSGs were discovered, many of which showed distinctive expression patterns in tissues such as spike, stem, and leaf. Functional enrichment analysis of these genes using GO and KEGG pathways highlighted their roles in key biological processes and pathways, indicating their potential in crop trait enhancement. Protein-protein interaction networks constructed for stem and leaf tissues further illuminated the regulatory mechanisms underlying the transition from vegetative to reproductive growth stages.
This study presents a detailed transcriptomic landscape of pearl millet, identifying a set of HKGs and TSGs that are crucial for understanding the molecular basis of its growth and development. We provided valuable options for transcript normalization and crucial targets for exploring gene function for the plant growth and development in pearl millet. The insights gained from this work are instrumental for breeding programs aimed at enhancing the productivity of pearl millet, thereby contributing to food and energy security.
珍珠粟（Pennisetum glaucum (L.) R. Br.）是一种重要的谷类作物，主要种植于亚洲和非洲的干旱及半干旱地区。它是数百万人的主食，同时也用作饲料和能源作物。该作物耐热耐旱，生物量高，是气候适应型农业的一个有潜力的候选品种。详细了解其在不同组织和发育阶段的基因表达模式对于提高其产量和品质至关重要。本研究旨在通过RNA测序来鉴定珍珠粟中的管家基因（HKGs）和组织特异性基因（TSGs），以填补这一知识空白。
我们对珍珠粟品种Tifleaf3八个发育阶段的九个组织（种子、胚、胚根、叶、根、分蘖组织、茎、穗和籽粒）的RNA测序数据进行分析，揭示了一个全面的基因表达谱。我们鉴定出461个在所有组织和阶段均表现出稳定表达的管家基因，为RT-qPCR提供了可靠的内部参照。此外，还发现了8091个组织特异性基因，其中许多在穗、茎和叶等组织中表现出独特的表达模式。利用基因本体（GO）和京都基因与基因组百科全书（KEGG）通路对这些基因进行功能富集分析，突出了它们在关键生物学过程和通路中的作用，表明它们在改善作物性状方面的潜力。为茎和叶组织构建的蛋白质-蛋白质相互作用网络进一步阐明了从营养生长阶段向生殖生长阶段转变的调控机制。
本研究展示了珍珠粟详细的转录组图谱，鉴定出了一组对于理解其生长和发育分子基础至关重要的管家基因和组织特异性基因。我们为转录本标准化提供了有价值的选择，并为探索珍珠粟植物生长和发育的基因功能提供了关键靶点。这项工作获得的见解有助于旨在提高珍珠粟生产力的育种计划，从而促进粮食和能源安全。
