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Apomixis-related genes identified from a coexpression network in Paspalum notatum, a Neotropical grass

Apomixis is a highly desirable trait in modern agriculture, due to the maintenance of characteristics of the mother plant in the progeny. However, incorporating it into breeding programs requires a deeper knowledge of its regulatory mechanisms. Paspalum notatum is considered a good model for such studies because it exhibits both sexual and apomictic cytotypes, facilitating the performance of comparative approaches. Therefore, we used comparative transcriptomics between contrasting P. notatum cytotypes to identify novel candidate genes involved in the regulation of the expression of this phenotype. We assembled and characterized a transcriptome from leaf and inflorescence from apomictic tetraploids and sexual diploids/tetraploids of P. notatum accessions, and then assembled a coexpression network based on pairwise correlation between transcripts expression profiles. We identified genes exclusively expressed in each cytotype and differentially expressed genes between pairs of cytotypes. Gene ontology enrichment analyses were performed for the interpretation of data. We de novo assembled 114,306 of reference transcripts. 536 novel candidate genes for the control of apomixis were detected through statistical analyses of expression data, contains in this set, the interactions among genes potentially linked to the apomixis-controlling region, differentially expressed, several genes also already reported in the literature and their neighbors transcriptionally related in the coexpression network. The reference transcriptome obtained in this study represents a robust set of expression data for P. notatum. Additionally, novel candidate genes identified in this work represent a valuable resource for future grass breeding programs. Author Summary Clonal mode of reproduction by seeds is termed apomixis, which results from the failure of gamete formation (meiosis) and fertilization in the sexual female reproductive pathway. The manipulation of seeds production genetically identical to the mother plant bears great promise for agricultural applications, however clarification regarding gene interactions involved in reproductive process is needed. Paspalum is considered a model genus for the analysis of apomixis mechanisms. Here, we describe an overall analysis of the expression profiles of Paspalum notatum transcripts in response to changes in reproductive mode (sexual to apomictic), which allowed us to identify several candidate apomixis genes. Among these, we found genes potentially associated with the apomixis control region, in addition to genes already described in the literature for Paspalum, which highlights the representativeness of assembled transcriptome. For the first time in the literature, we explored the main biological processes involved in controlling the expression of apomictic reproduction based on co-regulatory networks of candidate apomixis genes.