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Alfin-like (AL) transcription factor family in Oryza sativa L.: Genome-wide analysis and expression profiling under different stresses.

ABSTRACT: Oryza sativa L. is the world's most essential and economically important food crop. Climate change and ecological imbalances make rice plants vulnerable to abiotic and biotic stresses, threatening global food security. The Alfin-like (AL) transcription factor family plays a crucial role in plant development and stress responses. This study comprehensively analyzed this gene family and their expression profiles in rice, revealing nine AL genes, classifying them into three distinct groups based on phylogenetic analysis and identifying four segmental duplication events. RNA-seq data analysis revealed high expression levels of OsALs in different tissues, growth stages, and their responsiveness to stresses. RT-qPCR data showed significant expression of OsALs in different abiotic stresses. Identification of potential cis-regulatory elements in promoter regions has also unveiled their involvement. Tertiary structures of the proteins were predicted. These findings would lay the groundwork for future research to reveal their molecular mechanism in stress tolerance and plant development.

SUBMITTER: Rahman JF

PROVIDER: S-EPMC11217604 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature

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Alfin-like (AL) transcription factor family in <i>Oryza sativa</i> L.: Genome-wide analysis and expression profiling under different stresses.

Rahman Jeba Faizah JF Hoque Hammadul H Jubayer Abdullah-Al- AA Jewel Nurnabi Azad NA Hasan Md Nazmul MN Chowdhury Aniqua Tasnim AT Prodhan Shamsul H SH

Biotechnology reports (Amsterdam, Netherlands) 20240529

<i>Oryza sativa</i> L. is the world's most essential and economically important food crop. Climate change and ecological imbalances make rice plants vulnerable to abiotic and biotic stresses, threatening global food security. The Alfin-like (AL) transcription factor family plays a crucial role in plant development and stress responses. This study comprehensively analyzed this gene family and their expression profiles in rice, revealing nine AL genes, classifying them into three distinct groups b ...[more]

PMID: 38962072

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Project description:BackgroundMedicago sativa, often referred to as the "king of forage", is prized for its high content of protein, minerals, carbohydrates, and digestible nutrients. However, various abiotic stresses can hinder its growth and development, ultimately resulting in reduced yield and quality, including water deficiency, high salinity, and low temperature. The ethylene-insensitive 3 (EIN3)/ethylene-insensitive 3-like (EIL) transcription factors are key regulators in the ethylene signaling pathway in plants, playing crucial roles in development and in the response to abiotic stresses. Research on the EIN3/EIL gene family has been reported for several species, but minimal information is available for M. sativa.ResultsIn this study, we identified 10 MsEIN3/EIL genes from the M. sativa genome (cv. Zhongmu No.1), which were classified into three clades based on phylogenetic analysis. The conserved structural domains of the MsEIN3/EIL genes include motifs 1, 2, 3, 4, and 9. Gene duplication analyses suggest that segmental duplication (SD) has played a significant role in the expansion of the MsEIN3/EIL gene family throughout evolution. Analysis of the cis-acting elements in the promoters of MsEIN3/EIL genes indicates their potential to respond to various hormones and environmental stresses. We conducted a further analysis of the tissue-specific expression of the MsEIN3/EIL genes and assessed the gene expression profiles of MsEIN3/EIL under various stresses using transcriptome data, including cold, drought, salt and abscisic acid treatments. The results showed that MsEIL1, MsEIL4, and MsEIL5 may act as positive regulatory factors involved in M. sativa's response to abiotic stress, providing important genetic resources for molecular design breeding.ConclusionThis study investigated MsEIN3/EIL genes in M. sativa and identified three candidate transcription factors involved in the regulation of abiotic stresses. These findings will offer valuable insights into uncovering the molecular mechanisms underlying various stress responses in M. sativa.

Project description:BackgroundAlfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. Its survival and production are often hampered by environmental changes. However, there are few studies on stress-resistance genes in alfalfa because of its incomplete genomic information and rare expression profile data. The MYB proteins are characterized by a highly conserved DNA-binding domain, which is large, functionally diverse, and represented in all eukaryotes. The role of MYB proteins in plant development is essential; they function in diverse biological processes, including stress and defense responses, and seed and floral development. Studies on the MYB gene family have been reported in several species, but they have not been comprehensively analyzed in alfalfa.MethodsTo identify more comprehensive MYB transcription factor family genes, the sequences of 168 Arabidopsis thaliana, 430 Glycine max, 185 Medicago truncatula, and 130 Oryza sativa MYB proteins were downloaded from the Plant Transcription Factor Database. These sequences were used as queries in a BLAST search against the M. sativa proteome sequences provided by the Noble Research Institute.ResultsIn the present study, a total of 265 MsMYB proteins were obtained, including 50 R1-MYB, 186 R2R3-MYB, 26 R1R2R3-MYB, and three atypical-MYB proteins. These predicted MsMYB proteins were divided into 12 subgroups by phylogenetic analysis, and gene ontology (GO) analysis indicated that most of the MsMYB genes are involved in various biological processes. The expression profiles and quantitative real-time PCR analysis indicated that some MsMYB genes might play a crucial role in the response to abiotic stresses. Additionally, a total of 170 and 914 predicted protein-protein and protein-DNA interactions were obtained, respectively. The interactions between MsMYB043 and MSAD320162, MsMYB253 and MSAD320162, and MsMYB253 and MSAD308489 were confirmed by a yeast two-hybrid system. This work provides information on the MYB family in alfalfa that was previously lacking and might promote the cultivation of stress-resistant alfalfa.

Project description:BackgroundThe trihelix gene family is a plant-specific transcription factor family that plays important roles in plant growth, development, and responses to abiotic stresses. However, to date, no systemic characterization of the trihelix genes has yet been conducted in wheat and its close relatives.ResultsWe identified a total of 94 trihelix genes in wheat, as well as 22 trihelix genes in Triticum urartu, 29 in Aegilops tauschii, and 31 in Brachypodium distachyon. We analyzed the chromosomal locations and orthology relations of the identified trihelix genes, and no trihelix gene was found to be located on chromosome 7A, 7B, or 7D of wheat, thereby reflecting the uneven distributions of wheat trihelix genes. Phylogenetic analysis indicated that the 186 identified trihelix proteins in wheat, rice, B. distachyon, and Arabidopsis were clustered into five major clades. The trihelix genes belonging to the same clades usually shared similar motif compositions and exon/intron structural patterns. Five pairs of tandem duplication genes and three pairs of segmental duplication genes were identified in the wheat trihelix gene family, thereby validating the supposition that more intrachromosomal gene duplication events occur in the genome of wheat than in that of other grass species. The tissue-specific expression and differential expression profiling of the identified genes under cold and drought stresses were analyzed by using RNA-seq data. qRT-PCR was also used to confirm the expression profiles of ten selected wheat trihelix genes under multiple abiotic stresses, and we found that these genes mainly responded to salt and cold stresses.ConclusionsIn this study, we identified trihelix genes in wheat and its close relatives and found that gene duplication events are the main driving force for trihelix gene evolution in wheat. Our expression profiling analysis demonstrated that wheat trihelix genes responded to multiple abiotic stresses, especially salt and cold stresses. The results of our study built a basis for further investigation of the functions of wheat trihelix genes and provided candidate genes for stress-resistant wheat breeding programs.

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Alfin-like (AL) transcription factor family in Oryza sativa L.: Genome-wide analysis and expression profiling under different stresses.

Publications

Alfin-like (AL) transcription factor family in <i>Oryza sativa</i> L.: Genome-wide analysis and expression profiling under different stresses.

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