Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet
Abstract Background 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 drou...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-12-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-024-11114-3 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850133682195529728 |
|---|---|
| author | Wei Luo Min Sun Ailing Zhang Chuang Lin Yarong Jin Xiaoshan Wang Linkai Huang |
| author_facet | Wei Luo Min Sun Ailing Zhang Chuang Lin Yarong Jin Xiaoshan Wang Linkai Huang |
| author_sort | Wei Luo |
| collection | DOAJ |
| description | Abstract Background 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. Results 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. Conclusion 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. |
| format | Article |
| id | doaj-art-5e4929dcf04b4681a648c507a0b78867 |
| institution | OA Journals |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-5e4929dcf04b4681a648c507a0b788672025-08-20T02:31:54ZengBMCBMC Genomics1471-21642024-12-0125111710.1186/s12864-024-11114-3Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl milletWei Luo0Min Sun1Ailing Zhang2Chuang Lin3Yarong Jin4Xiaoshan Wang5Linkai Huang6College of Grassland Science and Technology, Sichuan Agricultural UniversityCollege of Grassland Science and Technology, Sichuan Agricultural UniversityCollege of Grassland Science and Technology, Sichuan Agricultural UniversityCollege of Grassland Science and Technology, Sichuan Agricultural UniversityCollege of Grassland Science and Technology, Sichuan Agricultural UniversityCollege of Grassland Science and Technology, Sichuan Agricultural UniversityCollege of Grassland Science and Technology, Sichuan Agricultural UniversityAbstract Background 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. Results 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. Conclusion 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.https://doi.org/10.1186/s12864-024-11114-3Pearl milletHousekeeping geneTissue-specific geneRNA-seqDevelopment |
| spellingShingle | Wei Luo Min Sun Ailing Zhang Chuang Lin Yarong Jin Xiaoshan Wang Linkai Huang Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet BMC Genomics Pearl millet Housekeeping gene Tissue-specific gene RNA-seq Development |
| title | Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet |
| title_full | Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet |
| title_fullStr | Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet |
| title_full_unstemmed | Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet |
| title_short | Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet |
| title_sort | comprehensive analysis of housekeeping genes tissue specific genes and dynamic regulation across developmental stages in pearl millet |
| topic | Pearl millet Housekeeping gene Tissue-specific gene RNA-seq Development |
| url | https://doi.org/10.1186/s12864-024-11114-3 |
| work_keys_str_mv | AT weiluo comprehensiveanalysisofhousekeepinggenestissuespecificgenesanddynamicregulationacrossdevelopmentalstagesinpearlmillet AT minsun comprehensiveanalysisofhousekeepinggenestissuespecificgenesanddynamicregulationacrossdevelopmentalstagesinpearlmillet AT ailingzhang comprehensiveanalysisofhousekeepinggenestissuespecificgenesanddynamicregulationacrossdevelopmentalstagesinpearlmillet AT chuanglin comprehensiveanalysisofhousekeepinggenestissuespecificgenesanddynamicregulationacrossdevelopmentalstagesinpearlmillet AT yarongjin comprehensiveanalysisofhousekeepinggenestissuespecificgenesanddynamicregulationacrossdevelopmentalstagesinpearlmillet AT xiaoshanwang comprehensiveanalysisofhousekeepinggenestissuespecificgenesanddynamicregulationacrossdevelopmentalstagesinpearlmillet AT linkaihuang comprehensiveanalysisofhousekeepinggenestissuespecificgenesanddynamicregulationacrossdevelopmentalstagesinpearlmillet |