Coexpression and transcriptome analyses identify active apomixis-related genes in paspalum notatum leaves

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. 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. 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 programs211CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP2018/18527-9Não tem2008/52197-4; 2013/20447-0; 2015/24346-9This work was supported by grants from the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP 2008/52197–4) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, Computational Biology Program). FAO received a PhD fellowship from FAPESP (2013/20447–0), CAPES-Computational Biology Program, and CAPES-EMBRAPA Program, and a PD fellowship (2018/18527–9) from FAPESP. CCS received a PD fellowship from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and FAPESP (2015/24346–9). APS is the recipient of a research fellowship from CNPq. The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscrip