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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #400775
Research Project: Genetics and Breeding of Lettuce, Spinach, Melon, and Related Species to Improve Production and Consumer-related Traits

Location: Crop Improvement and Protection Research

Title: Skim resequencing finely maps the downy mildew resistance loci RPF2 and RPF3 in spinach cultivars Whale and Lazio

Author
item BHATTARAI, GEHENDRA - University Of Arkansas
item SHI, AINONG - University Of Arkansas
item Mou, Beiquan
item CORRELL, JAMES - University Of Arkansas

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/10/2023
Publication Date: 4/19/2023
Citation: Bhattarai, G., Shi, A., Mou, B., Correll, J. 2023. Skim resequencing finely maps the downy mildew resistance loci RPF2 and RPF3 in spinach cultivars Whale and Lazio. Horticulture Research. 10(6). Article uhad076. https://doi.org/10.1093/hr/uhad076.
DOI: https://doi.org/10.1093/hr/uhad076

Interpretive Summary: Spinach (Spinacia oleracea L.) is an important leafy vegetable crop, with commercial production centered in California and Arizona of the US. Downy mildew disease in spinach is the major constraint in commercial production and is caused by a fungus Peronospora effusa. Nineteen variants of the pathogen have been reported, of which 16 were documented in the last three decades. The rapid emergence of new variants of downy mildew pathogens has been continually breaking the genetic resistance in new spinach varieties. This study aimed to find the location of the resistance gene (RPF2) on the chromosome in the spinach cultivar Lazio and identify markers and candidate genes associated with the resistance. Progeny plants from a cross of varieties Lazio (Resistant) and Viroflay (Susceptible) were inoculated with a variant of the pathogen to determine disease response. DNA analysis determined the RPF2 gene location on the Chromosome #3, which is close to a gene that produces a disease-fighting protein. DNA markers close to the resistance genes were also identified. This study improved our understanding of downy mildew resistance in spinach. The markers and candidate genes identified in this study could add value to breeding downy mildew-resistant spinach varieties in the future.

Technical Abstract: Spinach (Spinacia oleracea L.) is an important leafy vegetable crop, with commercial production centered in California and Arizona of the US. Downy mildew disease in spinach is the major constraint in commercial production and is caused by an oomycete, Peronospora effusa. Nineteen races of P. effusa have been reported, of which 16 were documented in the last three decades. The rapid emergence of new races of downy mildew pathogens has been continually overcoming the genetic resistance in new varieties. This study aimed to map the RPF2 downy mildew resistance locus in the spinach cultivar Lazio and identify single nucleotide polymorphism (SNP) markers and candidate genes associated with the resistance. Progenies from a cross of Lazio (Resistant) and Viroflay (Susceptible) were inoculated with race 5 of P. effusa to determine disease response. Association analysis performed with low coverage whole genome resequencing-generated SNP markers mapped the RPF2 locus between 0.47 to 1.46 Mb with peak SNP (Chr3_1221009) showing a LOD value of 61.6 in the TASSEL GLM model, which was within 1.08 Kb from gene Spo12821 that encodes the CC-NBS-LRR disease resistance protein. The combined analysis of RPF2 and RPF3 segregating panels mapped the resistance region between 1.18-1.23 and 1.75-1.76 Mb of chromosome 3. This study improved our understanding of downy mildew resistance in the spinach cultivar Lazio and mapping of RPF2 in Lazio was compared to that of the RPF3 locus in the cultivar Whale. The SNP markers and candidate genes identified in this study could add value to breeding downy mildew-resistant varieties in the future.