BackgroundMADS-box genes encode a family of eukaryotic transcription factors distinguished by the presence of a highly-conserved ~58 amino acid DNA-binding and dimerization domain (the MADS-box). The central role played by MADS-box genes in peach endodormancy regulation led us to examine this large gene family in more detail. We identified the locations and sequences of 79 MADS-box genes in peach, separated them into established subfamilies, and broadly surveyed their tissue-specific and dormancy-induced expression patterns using next-generation sequencing. We then focused on the dormancy-related SVP/AGL24 and FLC subfamilies, comparing their numbers and phylogenetic relationships with those of other sequenced woody perennial genomes.ResultsWe identified 79 MADS-box genes distributed across all eight peach chromosomes and frequently located in clusters of two or more genes. They encode proteins with a mean length of 248 ± 72 amino acids and include representatives from most of the thirteen Type II (MIKC) subfamilies, as well as members of the Type I Mα, Mβ, and Mγ subfamilies. Most Type I genes were present in species-specific monophyletic lineages, and their expression in the peach sporophyte was low or absent. Most Type II genes had Arabidopsis orthologs and were expressed at much higher levels throughout vegetative and fruit tissues. During short-day-induced growth cessation, seven Type II genes from the SVP/AGL24, AGL17, and SEP subfamilies showed significant changes in expression. Phylogenetic analyses indicated that multiple, independent expansions have taken place within the SVP/AGL24 and FLC lineages in woody perennial species.ConclusionsMost Type I genes appear to have arisen through tandem duplications after the divergence of the Arabidopsis and peach lineages, whereas Type II genes appear to have increased following whole genome duplication events. An exception to the latter rule occurs in the FLC and SVP/AGL24 Type II subfamilies, in which species-specific tandem duplicates have been retained in a number of perennial species. These subfamilies comprise part of a genetic toolkit that regulates endodormancy transitions, but phylogenetic and expression data suggest that individual orthologs may not function identically across all species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0436-2) contains supplementary material, which is available to authorized users.

Environmental stress factors caused by climate change affect plant growth and crop production, and pose a growing threat to sustainable agriculture, especially for tree crops. In this context, we sought to investigate the responses to climate change of two Prunus rootstocks (GF677 and Adesoto) budded with Catherina peach cultivar. Plants were grown in 15 L pots in temperature gradient greenhouses for an 18 days acclimation period after which six treatments were applied: [CO 2 levels (400 versus 700 µmol mol-1), temperature (ambient versus ambient + 4°C), and water availability (well irrigated versus drought)]. After 23 days, the effects of stress were evaluated as changes in physiological and biochemical traits, including expression of relevant genes. Stem water potential decreased under drought stress in plants grafted on GF677 and Adesoto rootstocks; however, elevated CO 2 and temperature affected plant water content differently in both combinations. The photosynthetic rate of plants grafted on GF677 increased under high CO 2 , but decreased under high temperature and drought conditions. The photosynthetic rates of plants grafted onto Adesoto were only affected by drought treatment. Furthermore, in GF677-Catherina plants, elevated CO 2 alleviated the effect of drought, whereas in those grafted onto Adesoto, the same condition produced acclimation in the rate. Stomatal conductance decreased under high CO 2 and drought stress in both grafted rootstocks, and the combination of these conditions improved water-use efficiency. Changes in the sugar content in scion leaves and roots were significantly different under the stress conditions in both combinations. Meanwhile, the expression of most of the assessed genes was significantly affected by treatment. Regarding genotypes, GF677 rootstock showed more changes at the molecular and transcriptomic level than did Adesoto rootstock. A coordinated shift was found between the physiological status and the transcriptomic responses. This study revealed adaptive responses to climate change at the physiological, metabolic, and transcriptomic levels in two Prunus rootstocks