Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the AP2-ERF genes in the common bean genome. In this study, a comprehensive genome-wide in silico analysis identified 180 AP2-ERF superfamily genes in common bean (Phaseolus vulgaris). Based on the amino acid alignment and phylogenetic analyses, superfamily members were classified into four subfamilies: DREB (54), ERF (95), AP2 (27) and RAV (3), as well as one soloist. The physical and chemical characteristics of amino acids, interaction between AP2-ERF proteins, cis elements of promoter region of AP2-ERF genes and phylogenetic trees were predicted and analyzed. Additionally, expression levels of AP2-ERF genes were evaluated by in silico and qRT-PCR analyses. In silico micro-RNA target transcript analyses identified nearly all PvAP2-ERF genes as targets of by 44 different plant species' miRNAs were identified in this study. The most abundant target genes were PvAP2/ERF-20-25-62-78-113-173. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST analyses. Interactome analysis revealed that the transcription factor PvAP2-ERF78, an ortholog of Arabidopsis At2G28550, was potentially interacted with at least 15 proteins, indicating that it was very important in transcriptional regulation. Here we present the first study to identify and characterize the AP2-ERF transcription factors in common bean using whole-genome analysis, and the findings may serve as a references for future functional research on the transcription factors in common bean.

Current cultivation and breeding strategy based on selections from local and wild vegetation does not meet the hazelnut demand. This situation would benefit from the development of high-yielding cultivars with greater tolerance to abiotic and biotic stress conditions. Molecular markers are useful tools to support these breeding efforts. In the current study, EST-SSR markers were developed from RNA-sequencing data obtained from three hazelnut varieties. The transcriptome sequences contained 86,542 unigenes and a total of 25,391 SSRs, most of which (50.9%) were di-nucleotide repeats. A set of 40 primer pairs were randomly selected to validate their usefulness for investigating genetic diversity in 19 C. avellana cultivars and one accession of Corylus colurna. Of the 40, 28 were highly polymorphic with average values of observed heterozygosity, polymorphism information content and number of alleles per locus of 0.45, 0.67 and 6.11, respectively. The principal coordinate and dendrogram analysis separated the C. colurna accession from the C. avellana cultivars, and separated the cultivars for date of leaf bud burst. These new EST-SSRs and others that could be developed from the transcriptome sequences increase the number of markers for cultivar fingerprinting and may be useful for identifying marker-trait associations and further genetic diversity analyses.