Combined use of bulked segregant analysis and microarrays reveals SNP markers pinpointing a major QTL for resistance to Phytophthora capsici in pepper

• Published in: Theoretical and applied genetics Vol. 127; no. 11; pp. 2503 - 2513
• Main Authors: Liu, Wing-Yee, Kang, Jin-Ho, Jeong, Hyeon-Seok, Choi, Hye-Jeong, Yang, Hee-Bum, Kim, Ki-Taek, Choi, Doil, Choi, Gyung Ja, Jahn, Molly, Kang, Byoung-Cheorl
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01-11-2014; Springer Berlin Heidelberg; Springer; Springer Nature B.V
• Subjects: Agriculture; Base Sequence; Biochemistry; Biomedical and Life Sciences; Biotechnology; Capsicum; Capsicum - genetics; Capsicum - microbiology; Chromosome Mapping; Chromosomes; Chromosomes, Plant; Cultivars; disease resistance; Disease Resistance - genetics; DNA, Plant - genetics; dominant genes; Drug resistance in microorganisms; Genes; Genetic Linkage; Genetic Markers; Genomics; inbred lines; Life Sciences; Medical screening; microarray technology; Models, Genetic; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis; Original Paper; Pathogens; pepper; Phenotype; Phytophthora; Phytophthora capsici; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Diseases - genetics; Plant Diseases - microbiology; Plant Genetics and Genomics; Polymorphism, Single Nucleotide; prediction; Quantitative genetics; Quantitative Trait Loci; Sequence Analysis, DNA; single nucleotide polymorphism; Virulence; zoospores; South Korea; Israel; Canada; Major Quantitative Trait Locus; Single Nucleotide Polymorphism; Phytophthora; Quantitative Trait Locus; Quantitative Trait Locus Analysis
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-014-2394-8

KEY MESSAGE : Bulked segregant analysis (BSA) using Affymetrix GeneChips revealed candidate genes underlying the major QTL for Phytophthora capsici resistance in Capsicum . Using the candidate genes, reliable markers for Phytophthora resistance were developed and validated. Phytophthora capsici L. is one of the most destructive pathogens of pepper (Capsicum spp.). Resistance of pepper 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 × 10³/mL). Resistance phenotype segregation ratios for the populations fit a 3:1 and 1:1 (resistant:susceptible) segregation model, 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 was 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 P. capsici 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 P. capsici isolate. These results suggest that Phyto5NBS1 is a reliable marker for P. capsici resistance and can be used for identification of a gene(s) underlying the major QTL on chromosome 5.