Salinity is one of the important abiotic stress factors that limit crop production. Common bean, Phaseolus vulgaris L., a major protein source in developing countries, is highly affected by soil salinity and the information on genes that play a role in salt tolerance is scarce. We aimed to identify differentially expressed genes (DEGs) and related pathways by comprehensive analysis of transcriptomes of both root and leaf tissues of the tolerant genotype grown under saline and control conditions in hydroponic system. We have generated a total of 158 million high-quality reads which were assembled into 83,774 all-unigenes with a mean length of 813 bp and N50 of 1,449 bp. Among the all-unigenes, 58,171 were assigned with Nr annotations after homology analyses. It was revealed that 6,422 and 4,555 all-unigenes were differentially expressed upon salt stress in leaf and root tissues respectively. Validation of the RNA-seq quantifications (RPKM values) was performed by qRT-PCR (Quantitative Reverse Transcription PCR) analyses. Enrichment analyses of DEGs based on GO and KEGG databases have shown that both leaf and root tissues regulate energy metabolism, transmembrane transport activity, and secondary metabolites to cope with salinity. A total of 2,678 putative common bean transcription factors were identified and classified under 59 transcription factor families; among them 441 were salt responsive. The data generated in this study will help in understanding the fundamentals of salt tolerance in common bean and will provide resources for functional genomic studies.

The Wnt signaling pathway is involved in many differentiation events during embryonic development and can lead to tumor formation after aberrant activation of its components. beta-catenin, a cytoplasmic component, plays a major role in the transduction of canonical Wnt signaling. The aim of this study was to identify novel genes that are regulated by active beta-catenin/TCF signaling in hepatocellular carcinoma-derived Huh7 cells with high (transfected) and low beta-catenin/TCF activities. High TCF activity Huh7 cells led to earlier and larger tumor formation when xenografted into nude mice. SAGE (Serial Analysis of Gene Expression), genome-wide microarray and in silico promoter analysis were performed in parallel, to compare gene expression between low and high beta-catenin/TCF activity clones, and also those that had been rescued from the xenograft tumors. SAGE and genome-wide microarray data were compared and contrasted. BRI3 and HSF2 were identified as novel targets of Wnt/beta-catenin signaling after combined analysis and confirming experiments including qRT-PCR, ChIP, luciferase assay and lithium treatment.

Anthracnose disease, caused by the fungal pathogen Colletotricum lindemuthianum brings about great yield losses in the Blacksea Region of Turkey. The present study is carried out to start the resistance breeding program against anthracnose disease. Five pathogenic strains (2175, 3071, 3303, 3321, 4071) identified previously from Blacksea Region were inoculated on seven foreign anthracnose resistant varieties of fresh bean (MDRK, PM, Kaboon, Widusa, Machinac, Isles and Chinook) as well as on nine breeding lines (T23, TK57, TK1, Ç31, Ç28, T7, T26, TK15 and T21) which were developed as Ayşe kadın type by pure-line selection, a method used for self-pollinated crops. Results indicated that while all the foreign varieties were resistant to these pathogen strains, the pure-lines were all susceptible. Thus foreign varieties and pure-lines were selected as parents to perform 63 combinations of genetic cross with the intention to start anthracnose resistance breeding program, only 18 of which produced seed. Through self fertilization of 360 F 1 plants an F 2 population of 4365 plants were obtained which were phenotyped for resistance both by inoculation with five pathogen strains as well as using resistance gene (Co-1) linked molecular marker (SEactMcca). Since Ayşe Kadın type lines are of Andean origin and Co-1 locus controls resistance against Andean pathogens additional confirmation of Co-1 presence in the resistant F 2 lines is of great importance. Marker screening results indicated the presence of Co-1 gene in 6 out of 18 hybrid lines. Confirmation of resistance trait inheritance on 6 F 2 lines both by inoculations as well as molecular marker screening for Co-1 gene have given us the opportunity to continue with the backcross studies with high confidence. With this study anthracnose resistance breeding has been initiated in Turkey for the first time and molecular marker assisted selection has been integrated into the breeding program.