title: Prunus transcription factors: breeding perspectives.
abstract: Many plant processes depend on differential gene expression, which is generally controlled by complex proteins called transcription factors (TFs). In peach, 1533 TFs have been identified, accounting for about 5.5% of the 27,852 protein-coding genes. These TFs are the reference for the rest of the Prunus species. TF studies in Prunus have been performed on the gene expression analysis of different agronomic traits, including control of the flowering process, fruit quality, and biotic and abiotic stress resistance. These studies, using quantitative RT-PCR, have mainly been performed in peach, and to a lesser extent in other species, including almond, apricot, black cherry, Fuji cherry, Japanese apricot, plum, and sour and sweet cherry. Other tools have also been used in TF studies, including cDNA-AFLP, LC-ESI-MS, RNA, and DNA blotting or mapping. More recently, new tools assayed include microarray and high-throughput DNA sequencing (DNA-Seq) and RNA sequencing (RNA-Seq). New functional genomics opportunities include genome resequencing and the well-known synteny among Prunus genomes and transcriptomes. These new functional studies should be applied in breeding programs in the development of molecular markers. With the genome sequences available, some strategies that have been used in model systems (such as SNP genotyping assays and genotyping-by-sequencing) may be applicable in the functional analysis of Prunus TFs as well. In addition, the knowledge of the gene functions and position in the peach reference genome of the TFs represents an additional advantage. These facts could greatly facilitate the isolation of genes via QTL (quantitative trait loci) map-based cloning in the different Prunus species, following the association of these TFs with the identified QTLs using the peach reference genome.
authors.affiliation: Department of Plant Physiology, Instituto de Biologia, Universidade Federal de Pelotas Pelotas-RS, Brazil.
authors.forename: Valmor J
authors.initials: VJ
authors.lastname: Bianchi
authors.affiliation: Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas Murcia, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Rubio
authors.affiliation: Department of Biology, University of Padua Padova, Italy.
authors.forename: Livio
authors.initials: L
authors.lastname: Trainotti
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CRA) - Centro di ricerca per la frutticoltura Roma, Italy.
authors.forename: Ignazio
authors.initials: I
authors.lastname: Verde
authors.affiliation: Department of Agronomy, Food, Natural Resources, and Environment (DAFNAE). University of Padua Padova, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Bonghi
authors.affiliation: Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas Murcia, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Martínez-Gómez
keywords: Prunus spp.; abiotic stress; biotic stress; breeding; flowering time; fruit quality; gene regulation; transcription factors