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Genome-assisted marker development for disease resistance in pepper
The last decade has witnessed tremendous progress in genome sequencing and explosion of genome sequence information. This remarkable advancement in genomics provides unprecedented opportunities for crop improvement. Pepper (Capsicum spp.) is an important vegetable crop worldwide. Pepper production is constantly challenged by various pathogens and developing cultivars harnessing multiple disease resistance genes are ever increasing. Molecular markers linked to disease resistance genes will expedite the gene pyramiding. Here, I introduce genome-assisted development of molecular markers linked to resistance genes, in pepper. Phytophthora capsici L. is one of the most destructive pathogens of pepper (Capsicum spp.). Resistance of Capsicum annuum against P. capsici is controlled by quantitative trait loci (QTL), including a major QTL on chromosome 5 that is the predominant contributor to resistance. Here, to maximize the effect of this QTL and study its underlying genes, an F2 population and recombinant inbred lines were inoculated with P. capsici strain JHAI1-7 zoospores at a low concentration (3 x 103 /mL). Resistance phenotype segregation ratios for the populations were close to 3:1 and 1:1 (resistant:susceptible), respectively, consistent with a single dominant gene model. Bulked segregant analysis (BSA) using Affymetrix GeneChips revealed a single position polymorphism (SPP) marker mapping to the major QTL. When this SPP marker (Phyto5SAR) together with other SNP markers located on chromosome 5 were used to confirm the position of the major QTL, Phyto5SAR showed the highest LOD value at the QTL. A scaffold sequence (scaffold194) containing Phyto5SAR was identified from the C. annuum genome database. The scaffold contained two putative NBS-LRR genes and one SAR 8.2A gene as candidates for contributing to Phytophthora resistance. Markers linked to these genes were developed and validated by testing 100 F1 commercial cultivars. Among the markers, Phyto5NBS1 showed about 90% accuracy in predicting resistance phenotypes to a low-virulence Phytophthora isolate. These results suggest that Phyto5NBS1 is a reliable marker for Phytophthora resistance and can be used for identification of a gene(s) underlying the major QTL on chromosome 5
