Mapping and selection of downy mildew resistance in spinach cv. Whale by low coverage whole genome sequencing

Authors: BHATTARAI, GEHENDRA - University Of Arkansas; DOTUN, OLAOYE - Syngenta, Inc; Mou, Beiquan; CORRELL, JAMES - University Of Arkansas; SHI, AINONG - University Of Arkansas

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2022
Publication Date: 10/6/2022
Citation: Bhattarai, G., Dotun, O., Mou, B., Correll, J., Shi, A. 2022. Mapping and selection of downy mildew resistance in spinach cv. Whale by low coverage whole genome sequencing. Frontiers in Plant Science. 13. Article 1012923. https://doi.org/10.3389/fpls.2022.1012923.
DOI: https://doi.org/10.3389/fpls.2022.1012923

Interpretive Summary: Spinach (Spinacia oleracea) is a popular leafy vegetable crop and its commercial production is centered in California and Arizona in the US. A fungus pathogen, Peronospora effuse, causes one of the most important disease in spinach, downy mildew. A total of nineteen forms of the pathogen are known, with more than 15 documented in the last three decades, and the regular emergence of new forms is continually overcoming the genetic resistance of the spinach cultivars to the pathogen. This study aimed to study a downy mildew resistance gene (RPF3) in spinach, identify DNA markers associated with the resistance, and predict the disease resistance using genetic models. Progeny population developed from a cross of resistant cultivar Whale and susceptible cultivar Viroflay was inoculated under greenhouse conditions with a form of the pathogen (race 5) to determine their downy mildew disease response. The DNA sequences of the plants were determined and analyzed. The resistance gene (RPF3) was found to be located on the chromosome 3. Three DNA markers were identified, which can be efficiently used to select plants with downy mildew resistance based on multiple genetic models. The results from this study have added new genetic resources, generated an informed basis of the RPF3 gene resistant to the spinach downy mildew pathogen, and developed markers and prediction methods to select resistant plants and develop resistant cultivars.

Technical Abstract: Spinach (Spinacia oleracea) is a popular leafy vegetable crop and its commercial production is centered in California and Arizona in the US. The oomycete Peronospora effusa causes one of the most important disease in spinach, downy mildew. A total of nineteen races of P. effusa are known, with more than 15 documented in the last three decades, and the regular emergence of new races is continually overcoming the genetic resistance to the pathogen. This study aimed to finely map the downy mildew resistance locus RPF3 in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, refine the candidate genes responsible for the resistance, and evaluate the prediction performance using multiple machine learning genomic prediction (GP) methods. A segregating progeny population developed from a cross of the resistant cultivar Whale and the susceptible cultivar Viroflay to race 5 of P. effusa was inoculated under greenhouse conditions to determine the downy mildew disease response across the panel. The progeny panel and the parents were whole genome re-sequenced at low coverage (1x) to identify genome wide SNP markers. Association analysis was performed using disease response phenotype data and SNP markers in TASSEL, GAPIT, and GENESIS programs and mapped the race 5 resistance loci (RPF3) to 1.25 and 2.73 Mb of chromosome 3. The associated SNP in the 1.25 Mb region was 0.9 Kb from the NBS-LRR gene SOV3g001250. This study extended our understanding of the genetic basis of downy mildew resistance in spinach cultivar Whale and mapped the RPF3 resistance loci close to the NBS-LRR gene, providing a target to pursue functional validation. Three SNP markers efficiently selected resistance based on multiple genomic selection (GS) models. The results from this study have added new genomic resources, generated an informed basis of the RPF3 locus resistant to the spinach downy mildew pathogen, P. effusa, and developed markers and prediction methods to select resistant lines.