Identification of Genes Showing Differential Methylation and Expression Patterns in Flowers of Apomictic and Sexual Paspalum Spp.

Apomixis is a reproduction mode described in numerous genera, which allows the generation of viable clonal seeds by circumventing meiosis and fertilization. Successful harnessing of apomixis in agriculture would not only facilitate the clonal propagation of any hybrid combination through seeds by an indefinite number of generations, but also alter the current plant breeding paradigm, by simplifying and reducing the costs of the programs aimed at improving varieties of major crops. The genus Paspalum is an attractive biological system for the study of this trait. Particularly in Paspalum notatum, apomixis is associated with a single genomic region with a distorted segregation ratio, showing a dominant behaviour. This “apospory-controlling region” (ACR) is a large non-recombinant chromosomal sector, plagged with retrotransposons and heavily methylated. Its demethylation was associated with a depression of parthenogenesis, which suggests that the trait could be under epigenetic control. The aim of this work was to identify genes displaying differences in gene methylation profiles between sexual and apomictic P. notatum genotypes, by using the Methylation-Sensitive Amplification Polymorphisms (MSAP) technique. In MSAP assays, a total of 547 clear and reproducible bands were amplified by using 12 primer combinations. There were no statistically significant differences in the total quantity of methylated cytosines between plants with contrasting mode of reproduction, but a total of 12 DNA fragments showing differential methylation between apomictic and sexual individuals were recovered from the gels, cloned and sequenced. The resulting sequences were used to look for similarities in 454 cDNA libraries of sexual and apomictic P. notatum. Five sequences were found to be part of genes expressed in the libraries showing the same bias as predicted from the methylation analysis. While two of them corresponded to retrotransposon sequences, the remaining three were functional protein-coding genes. qPCRs revealed quantitative overexpression in florets of apomictic plants for the three candidates. The results of this work, carried out within the MSCA-RISE PROCROP project (project number 645674), will be reported and discussed.