In order to screen for putative candidate genes linked to tomato fruit weight and to sugar or acid content, genes and QTLs involved in fruit size and composition were mapped. Genes were selected among EST clones in the TIGR tomato EST database (http://www.tigr.org/tdb/tgi/lgi/) or corresponded to genes preferentially expressed in the early stages of fruit development. These clones were located on the tomato map using a population of introgression lines (ILs) having one segment of Lycopersicon pennellii (LA716) in a L. esculentum (M82) background. The 75 ILs allowed the genome to be segmented into 107 bins. Sixty-three genes involved in carbon metabolism revealed 79 loci. They represented enzymes involved in the Calvin cycle, glycolysis, the TCA cycle, sugar and starch metabolism, transport, and a few other functions. In addition, seven cell-cycle-specific genes mapped into nine loci. Fourteen genes, primarily expressed during the cell division stage, and 23 genes primarily expressed during the cell expansion stage, revealed 24 and 26 loci, respectively. The fruit weight, sugars, and organic acids content of each IL was measured and several QTLs controlling these traits were mapped. Comparison between map location of QTLs and candidate gene loci indicated a few candidate genes that may influence the variation of sugar or acid contents. Furthermore, the gene/QTL locations could be compared with the loci mapped in other tomato populations.

BackgroundExpressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs), to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes.ResultsA set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 × G19833 recombinant inbred line (RIL) population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 × 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes.ConclusionThe SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction of a transcript map and given their high conservation between species allowed synteny comparisons to be made to sequenced genomes. This synteny analysis may support positional cloning of target genes in common bean through the use of genomic information from these other legumes.

Single nucleotide polymorphisms (SNPs) are the most common sequence difference found in plant genomes, yet they have not been widely exploited for producing molecular markers in common bean (Phaseolus vulgaris L.). The objective of this study was to develop a SNP assay based on a type of heteroduplex mismatch cleavage called EcoTILLING for molecular marker development in this important legume, and apply the assay (i) to the conversion of a sequence‐characterized amplified region (SCAR) marker useful for selecting virus resistance (SR2) and (ii) to the screening of SNP polymorphisms in newly developed expressed sequence tag (EST)–based markers. The SNP assay involved heteroduplex mismatch cleavage by a single‐strand specific nuclease ‘CEL I’ which was used to uncover two SNPs in the SR2 fragment and 22 SNPs in 37 candidate ESTs, some of which were used in segregation analysis. While developing the SNP techniques we tested several platforms, including LI‐COR, nondenaturing polyacrylamide, and agarose gel detection. The agarose gel system was used for SNP genetic mapping in two common bean mapping populations, showing that heteroduplex cleavage is a useful technique for increasing molecular marker number for the crop. Examples are given of mapped SNP markers for the phytic acid pathway gene for myo‐inositol‐1‐phosphate synthase and a drought tolerance–related gene, S‐adenosylmethionine decarboxylase.