Bacterial spot of tomato (Solanum lycopersicum L.) is caused by at least four species of Xanthomonas with multiple physiological races. In this study, we developed a mapping population for association analysis of bacterial spot resistance. For this population, six advanced breeding lines with distinct sources of resistance were first crossed in all combinations and their F1 hybrids were intercrossed. The 1,100 segregating progeny from these crosses were evaluated in the field against T1 strains. Based on this individual evaluation, we selected 5% of the most resistant and 5% of the most susceptible progeny for evaluation as plots in two subsequent replicate field trials inoculated with T1 and T3 strains. A total of 461 markers across 12 chromosomes were used for genotyping these selections. Of these markers, an optimized subset of 384 SNPs was derived from the 7,720 SNP Infinium array developed by the Solanaceae Coordinated Agricultural Project (SolCAP). For association analysis to detect known resistance loci and additional novel loci, we used the mixed models with correction for population structure, and found that accounting for kinship appeared to be sufficient. Detection of known loci was not improved by adding a correction for structure using either a Q matrix from model-based clustering or covariate matrix from Principal Component Analysis. Both single-point and haplotype analyses identified strong associations in the region of the genome known to carry Rx-3 (chromosome 5) and Rx-4/Xv3 (chromosome 11). Additional QTL associated with resistance were detected on chromosomes 1, 3, 4, 6 and 7 for T1 resistance and chromosomes 2, 4, and 6 for T3 resistance. Haplotype analysis improved our ability to trace the origin of positive alleles. These results demonstrate that both known and novel associations can be identified using complex breeding populations that have experienced directional selection.

Recently whole genome SNP genotyping has been used to do association analysis and to map a gene of interest. Here we report application of bulked segregant analysis(BSA) using Infinium HD assay with ‘BARC Bean6K_3’, a SNP genotyping beadchip containing 5,399 SNPs for common bean to locate a target gene. We used BSA using Infinium HD assay was performed to find the candidate region of a single dominant rust resistant gene in PI310762, a common bean cultivar. And SSR markers were identified and mapped on the candidate region using F2 population derived from the cross of susceptible Pinto114 x resistant PI310762. BSA revealed the candidate region of the resistant gene is on chromosome 4 where we developed nine SSR markers. Three SSR markers (beanssr1170, beanssr1168, and beanssr1167) of them appeared closely linked to the resistant gene which is located between beanssr1167 at 0.1cM and beanssr1170 at 0.5cM on chromosome 4. This study showed BSA using high-throughput whole genome SNP genotyping is a very fast and efficient method to locate a gene of interest on chromosome.

Tsw, a single dominant resistant gene against Tomato spotted wilt virus (TSWV), has been mapped on chromosome 10 in Capsicum chinense species. Previously reported molecular markers linked to the Tsw gene are not transferable for all pepper breeding materials. To develop additional markers and do genome-based fine mapping of the Tsw gene, approaches of mapping comparison, pooled transcriptome analysis, and genome walking were applied. Eleven additional SNP molecular markers tightly linked to the Tsw gene were developed using tomato and pepper whole genome sequencing databases. Among them, four SNP markers, SNP7715-1, SNP68-1, SNP17918-1, and SNP1072-1, showed no recombination in two segregating populations of F2 ‘Telmo’ (210 individuals) and ‘SP’ (843 individuals). Three scaffold sequences from the C. annuum BAC database and two BAC clones from the BAC library of C. annuum ‘CM334’ covering the Tsw gene were identified by transcriptome analysis and genome walking. A pepper scaffold sequence covering three pepper scaffold sequences was identified from a final version of the C. annuum BAC database. The Tsw gene was delimited within 149 kb by alignment analysis of two BAC clone sequences and the pepper scaffold sequence. A total of 22 predicted genes were resided in the target region between SNP7715-1 and SNP1072-1 co-segregating markers. Among them, five predicted genes showing annotations of CC/TIR-NBS-LRR resistance proteins, mRNA-6, mRNA-7, mRNA-11, mRNA-12, and mRNA-13, were identified. The transcriptome analysis and gene expression study showed that the mRNA-13 was expressed in ‘PI152225’ but was absent in ‘Special’, demonstrating the mRNA-13 could be a strong candidate gene for the Tsw gene. This result will be favorable for cloning the Tsw gene and developing cultivars which carry the TSWV-resistance gene.