دورية أكاديمية
أعرض في EDS

Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress.

التفاصيل البيبلوغرافية
العنوان: Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress.
المؤلفون: Hayford RK; Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA. rita.hayford@usda.gov., Haley OC; Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA., Cannon EK; Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA., Portwood JL 2nd; Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA., Gardiner JM; Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA., Andorf CM; Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA. carson.andorf@usda.gov.; Department of Computer Science, Iowa State University, Ames, IA, 50011, USA. carson.andorf@usda.gov., Woodhouse MR; Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA. margaret.woodhouse@usda.gov.
المصدر: BMC genomics [BMC Genomics] 2024 May 30; Vol. 25 (1), pp. 533. Date of Electronic Publication: 2024 May 30.
نوع المنشور: Journal Article; Meta-Analysis
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2000-
مواضيع طبية MeSH: Zea mays*/genetics , Stress, Physiological*/genetics , Transcriptome* , Molecular Sequence Annotation*, Gene Expression Regulation, Plant ; Gene Expression Profiling ; Genes, Plant
مستخلص: Background: Environmental stress factors, such as biotic and abiotic stress, are becoming more common due to climate variability, significantly affecting global maize yield. Transcriptome profiling studies provide insights into the molecular mechanisms underlying stress response in maize, though the functions of many genes are still unknown. To enhance the functional annotation of maize-specific genes, MaizeGDB has outlined a data-driven approach with an emphasis on identifying genes and traits related to biotic and abiotic stress.
Results: We mapped high-quality RNA-Seq expression reads from 24 different publicly available datasets (17 abiotic and seven biotic studies) generated from the B73 cultivar to the recent version of the reference genome B73 (B73v5) and deduced stress-related functional annotation of maize gene models. We conducted a robust meta-analysis of the transcriptome profiles from the datasets to identify maize loci responsive to stress, identifying 3,230 differentially expressed genes (DEGs): 2,555 DEGs regulated in response to abiotic stress, 408 DEGs regulated during biotic stress, and 267 common DEGs (co-DEGs) that overlap between abiotic and biotic stress. We discovered hub genes from network analyses, and among the hub genes of the co-DEGs we identified a putative NAC domain transcription factor superfamily protein (Zm00001eb369060) IDP275, which previously responded to herbivory and drought stress. IDP275 was up-regulated in our analysis in response to eight different abiotic and four different biotic stresses. A gene set enrichment and pathway analysis of hub genes of the co-DEGs revealed hormone-mediated signaling processes and phenylpropanoid biosynthesis pathways, respectively. Using phylostratigraphic analysis, we also demonstrated how abiotic and biotic stress genes differentially evolve to adapt to changing environments.
Conclusions: These results will help facilitate the functional annotation of multiple stress response gene models and annotation in maize. Data can be accessed and downloaded at the Maize Genetics and Genomics Database (MaizeGDB).
(© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)
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معلومات مُعتمدة: Project Number [5030-21000-072-00-D] US. Department of Agriculture, Agricultural Research Service; Project Number [5030-21000-072-00-D] US. Department of Agriculture, Agricultural Research Service; Project Number [5030-21000-072-00-D] US. Department of Agriculture, Agricultural Research Service; Project Number [5030-21000-072-00-D] US. Department of Agriculture, Agricultural Research Service; Project Number [5030-21000-072-00-D] US. Department of Agriculture, Agricultural Research Service; Project Number [5030-21000-072-00-D] US. Department of Agriculture, Agricultural Research Service; Project Number [5030-21000-072-00-D] US. Department of Agriculture, Agricultural Research Service
فهرسة مساهمة: Keywords: Abiotic stress; Biotic stress; Differentially expressed genes; Gene Ontology; Maize; RNA-Sequencing; Transcription factors
تواريخ الأحداث: Date Created: 20240530 Date Completed: 20240530 Latest Revision: 20240603
رمز التحديث: 20240603
مُعرف محوري في PubMed: PMC11137889
DOI: 10.1186/s12864-024-10443-7
PMID: 38816789
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2164
DOI:10.1186/s12864-024-10443-7