The common bean is one of the most important staples in many areas of the world. Extensive phenotypic and genetic characterization of unexplored bean germplasm are still needed to unlock the breeding potential of this crop. Dissecting genetic control of flowering time is of pivotal importance to foster common bean breeding and to develop new varieties able to adapt to changing climatic conditions. Indeed, flowering time strongly affects yield and plant adaptation ability. The aim of this study was to investigate the genetic control of days to flowering using a whole genome association approach on a panel of 192 highly homozygous common bean genotypes purposely developed from landraces using Single Seed Descent. The phenotypic characterization was carried out at two experimental sites throughout two growing seasons, using a randomized partially replicated experimental design. The same plant material was genotyped using double digest Restriction-site Associated DNA sequencing producing, after a strict quality control, a dataset of about 50 k Single Nucleotide Polymorphisms (SNPs). The Genome-Wide Association Study revealed significant and meaningful associations between days to flowering and several SNP markers; seven genes are proposed as the best candidates to explain the detected associations.

Excessive soil salinity is a major ecological and agronomical problem, the adverse effects of which are becoming a serious issue in regions where saline water is used for irrigation. Plants can employ regulatory strategies, such as DNA methylation, to enable relatively rapid adaptation to new conditions. In this regard, cytosine methylation might play an integral role in the regulation of gene expression at both the transcriptional and post-transcriptional levels. Rapeseed, which is the most important oilseed crop in Europe, is classified as being tolerant of salinity, although cultivars can vary substantially in their levels of tolerance. In this study, the Methylation Sensitive Amplified Polymorphism (MSAP) approach was used to assess the extent of cytosine methylation under salinity stress in salinity-tolerant (Exagone) and salinity-sensitive (Toccata) rapeseed cultivars. Our data show that salinity affected the level of DNA methylation. In particular methylation decreased in Exagone and increased in Toccata. Nineteen DNA fragments showing polymorphisms related to differences in methylation were sequenced. In particular, two of these were highly similar to genes involved in stress responses (Lacerata and trehalose-6-phosphatase synthase S4) and were chosen to further characterization. Bisulfite sequencing and quantitative RT-PCR analysis of selected MSAP loci showed that cytosine methylation changes under salinity as well as gene expression varied. In particular, our data show that salinity stress influences the expression of the two stress-related genes. Moreover, we quantified the level of trehalose in Exagone shoots and found that it was correlated to TPS4 expression and, therefore, to DNA methylation. In conclusion, we found that salinity could induce genome-wide changes in DNA methylation status, and that these changes, when averaged across different genotypes and developmental stages, accounted for 16.8% of the total site-specific methylation differences in the rapeseed genome, as detected by MSAP analysis.

Truffles (Tuber spp.) and other ectomycorrhizal species form species-rich assemblages in the wild as well as in cultivated ecosystems. We aimed to in