Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves
| Autor: | Frederico P. de Matta, Ana Luisa Sousa Azevedo, B. B. Z. Vigna, Alessandra Pereira Fávero, Carla Cristina da Silva, Fernanda Oliveira, Anete Pereira de Souza |
|---|---|
| Přispěvatelé: | Fernanda A. de Oliveira, UNICAMP, BIANCA BACCILI ZANOTTO VIGNA, CPPSE, Carla C. da Silva, UNICAMP, ALESSANDRA PEREIRA FAVERO, CPPSE, FREDERICO DE PINA MATTA, CPPSE, ANA LUISA SOUSA AZEVEDO, CNPGL, Anete P. de Souza, UNICAMP. |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Candidate gene
DNA Plant lcsh:QH426-470 lcsh:Biotechnology Transcriptome Differential expression Gene Expression Regulation Plant lcsh:TP248.13-248.65 Apomixis Genetics Paspalum Gene Plant Proteins biology Gene Expression Profiling Computational Biology High-Throughput Nucleotide Sequencing Reproducibility of Results Molecular Sequence Annotation RNA sequencing Gene coexpression network biology.organism_classification Plant Leaves lcsh:Genetics Inflorescence DNA microarray Paspalum notatum Research Article Biotechnology |
| Zdroj: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA-Alice) Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA BMC Genomics, Vol 21, Iss 1, Pp 1-15 (2020) BMC Genomics |
| Popis: | Background Paspalum notatum exhibits both sexual and apomictic cytotypes and, thus, is considered a good model for studies of apomixis because it facilitates comparative approaches. In this work, transcriptome sequencing was used to compare contrasting P. notatum cytotypes to identify differential expression patterns and candidate genes involved in the regulation of expression of this trait. Results We built a comprehensive transcriptome using leaf and inflorescence from apomictic tetraploids and sexual diploids/tetraploids and a coexpression network based on pairwise correlations between transcript expression profiles. We identified genes exclusively expressed in each cytotype and genes differentially expressed between pairs of cytotypes. Gene Ontology enrichment analyses were performed to better interpret the data. We de novo assembled 114,306 reference transcripts. In total, 536 candidate genes possibly associated with apomixis were detected through statistical analyses of the differential expression data, and several interacting genes potentially linked to the apomixis-controlling region, genes that have already been reported in the literature, and their neighbors were transcriptionally related in the coexpression network. Conclusions Apomixis is a highly desirable trait in modern agriculture due to the maintenance of the characteristics of the mother plant in the progeny. The reference transcriptome, candidate genes and their coexpression network identified in this work represent rich resources for future grass breeding programs. |
| Databáze: | OpenAIRE |
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