Genome wide association studies in multiple spinach breeding populations refine downy mildew Race 13 resistance genes

Authors: BHATTARAI, GEHENDRA - University Of Arkansas; SHI, AINONG - University Of Arkansas; FENG, CHUNDA - University Of Arkansas; DHILLON, BRAHAM - University Of Arkansas; Mou, Beiquan; CORRELL, JAMES - University Of Arkansas

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2020
Publication Date: 10/21/2020
Citation: Bhattarai, G., Shi, A., Feng, C., Dhillon, B., Mou, B., Correll, J.C. 2020. Genome wide association studies in multiple spinach breeding populations refine downy mildew Race 13 resistance genes. Frontiers in Plant Science. 11. https://doi.org/10.3389/fpls.2020.563187.
DOI: https://doi.org/10.3389/fpls.2020.563187

Interpretive Summary: Downy mildew, caused by the fungus Peronospora effuse, is the economically most important disease in spinach. Fourteen new races of the pathogen were identified in the last three decades. The regular emergence of new downy mildew races has continually broken the genetic resistances in spinach. The objectives of this research were to provide the spinach chromosome location of the genes that govern the resistance to Race 13 of the pathogen and to identify DNA markers associated with the resistance. Populations were generated from crosses of Race 13-resistant cultivars Swan, T-Bird, Squirrel, Tonga with susceptible cultivars Whale and Polka. Plants were inoculated with Race 13 pathogen and downy mildew disease responses were recorded. DNA sequencing was used to identify molecular markers associated with the resistance. Association analysis mapped the Race 13 resistance genes to positions of spinach chromosome 3. Molecular markers closely linked to the Race 13 resistance genes were also identified. This study extended our understanding of the genetic basis of downy mildew resistance in spinach and provided the most promising candidate genes to pursue further functional validation. The molecular markers may be used to select for the resistant plants to improve genetic resistance against the downy mildew pathogen and to develop durably resistant cultivars.

Technical Abstract: Downy mildew, caused by the oomycete Peronospora effuse, is the economically most important disease in spinach. Fourteen new races were identified in the last three decades. The regular emergence of new P. effusa races has continually broken the genetic resistances in spinach. The objectives of this research were to map downy mildew resistance loci in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, and refine the candidate genes providing resistance. Populations generated from crosses of P. effusa race 13-resistant cultivars Swan, T-Bird, Squirrel, Tonga with susceptible cultivars Whale and Polka were inoculated with P. effusa race 13 and downy mildew disease responses were recorded. Genotyping by sequencing (GBS) was used to identify SNP markers and association analyses were performed in multiple programs to identify significantly associated SNPs. Association analysis mapped the P. effusa race 13 resistance locus to 0.39, 0.69, 0.94-0.98, and 1.2 Mb position of chromosome 3. The associated SNPs were within 1-7 kb of the disease resistance genes Spo12784, Spo12719, Spo12905, and Spo12821, and 11-18 Kb from Spo12903. This study extended our understanding of the genetic basis of downy mildew resistance in spinach and provided the most promising candidate genes, Spo12784 and Spo12903, to pursue functional validation. The SNP markers may be used to select for the resistant lines to improve genetic resistance against the downy mildew pathogen and in developing durably resistant cultivars.