ArticleBMC plant biology2011
Identification of rhizome-specific genes by genome-wide differential expression analysis in Oryza longistaminata.
Article in BMC plant biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Perennials as Future Grain Crops: Opportunities and Challenges.Frontiers in plant science · 2022Pooled it
- The genetic and developmental enigma of rhizomes: crucial traits with limited understanding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Identification of Gene Regulatory Network for Nitrogen-Promoted Tiller Regrowth in Perennial Rice.Rice (New York, N.Y.) · 2026Article
- The transcriptional landscape and dynamics regulating organ differentiation and dormancy in Curcuma alismatifolia.Plant physiology · 2025Article
- Spatio-Temporal Regulation of Gibberellin Biosynthesis Contributes to Optimal Rhizome Bud Development.Rice (New York, N.Y.) · 2025Article
- Breeding Potential for Increasing Carbon Sequestration via Rhizomatous Grain Sorghum.Plants (Basel, Switzerland) · 2025Article
- Cytokinin and Metabolites Affect Rhizome Growth and Development in Kentucky Bluegrass (Biology · 2023Article
- Can the Wild Perennial, Rhizomatous Rice Species Oryza longistaminata be a Candidate for De Novo Domestication?Rice (New York, N.Y.) · 2023Review
- Functional and ecological diversification of underground organs inFrontiers in genetics · 2023Article
- Identification of LsPIN1 gene and its potential functions in rhizome turning of Leymus secalinus.BMC genomics · 2022Article
- Sucrose Facilitates Rhizome Development of Perennial Rice (International journal of molecular sciences · 2022Article
- Regeneration pattern and genome-wide transcription profile of rhizome axillary buds after perennial rice harvest.Frontiers in plant science · 2022Article
- A Genetic Network Underlying Rhizome Development inFrontiers in plant science · 2022Article
- Early stem growth mutation alters metabolic flux changes enhance sesquiterpenoids biosynthesis inPlant cell, tissue and organ culture · 2022Article
- Perennial Rye: Genetics of Perenniality and Limited Fertility.Plants (Basel, Switzerland) · 2021Article
- Article
- Transcriptome profiling unveils the mechanism of phenylpropane biosynthesis in rhizome development of Caucasian clover.PloS one · 2021Article
- Nitrogen Nutrition Promotes Rhizome Bud Outgrowth via Regulation of Cytokinin Biosynthesis Genes and anFrontiers in plant science · 2021Article
- Revealing the full-length transcriptome of caucasian clover rhizome development.BMC plant biology · 2020Article
- Differential regulatory pathways associated with drought-inhibition and post-drought recuperation of rhizome development in perennial grass.Annals of botany · 2020Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical Asia. Oryza longistaminata, a perennial wild rice with strong rhizomes, has been used as the model species for genetic and molecular dissection of rhizome development and in breeding efforts to transfer rhizome-related traits into annual rice species. In this study, an effort was taken to get insights into the genes and molecular mechanisms underlying the rhizomatous trait in O. longistaminata by comparative analysis of the genome-wide tissue-specific gene expression patterns of five different tissues of O. longistaminata using the Affymetrix GeneChip Rice Genome Array.
resultsA total of 2,566 tissue-specific genes were identified in five different tissues of O. longistaminata, including 58 and 61 unique genes that were specifically expressed in the rhizome tips (RT) and internodes (RI), respectively. In addition, 162 genes were up-regulated and 261 genes were down-regulated in RT compared to the shoot tips. Six distinct cis-regulatory elements (CGACG, GCCGCC, GAGAC, AACGG, CATGCA, and TAAAG) were found to be significantly more abundant in the promoter regions of genes differentially expressed in RT than in the promoter regions of genes uniformly expressed in all other tissues. Many of the RT and/or RI specifically or differentially expressed genes were located in the QTL regions associated with rhizome expression, rhizome abundance and rhizome growth-related traits in O. longistaminata and thus are good candidate genes for these QTLs.
conclusionThe initiation and development of the rhizomatous trait in O. longistaminata are controlled by very complex gene networks involving several plant hormones and regulatory genes, different members of gene families showing tissue specificity and their regulated pathways. Auxin/IAA appears to act as a negative regulator in rhizome development, while GA acts as the activator in rhizome development. Co-localization of the genes specifically expressed in rhizome tips and rhizome internodes with the QTLs for rhizome traits identified a large set of candidate genes for rhizome initiation and development in rice for further confirmation.
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