Development of molecular markers linked to three spinach downy mildew resistance loci

Abstract

Downy mildew, caused by the obligate oomycete pathogen Peronospora effusa, is the most important disease of spinach. Growing resistant cultivars is the most economical way to manage the disease, particularly for organic spinach production. Therefore, the tools that assist and expedite the development of resistant cultivars are urgently needed. Resistance to P. effusa is typically controlled by major qualitative dominant genes, and at least six resistance loci are known to exist in spinach. Three of these resistant loci, RPF1, RPF2 and RPF3 have been genetically characterized and each locus controls resistance to more than nine of the 17 described races of P. effusa. However, as downy mildew is an obligate pathogen, the bioassays used to evaluate resistance are especially challenging. Thus, having robust molecular markers closely linked to resistance loci would greatly expedite genetic selections. In this study, multiple approaches, including bulked segregant analysis (BSA) using genotyping-by-sequencing, were deployed to develop thirteen, two, and seven markers linked to the RPF1, RPF2, and RPF3 resistance loci, respectively. One marker, RPF3-3, was linked to RPF2 and RPF3, and three markers, RPF3-1, RPF3-2, and RPF3-6, were linked to all three loci, indicating that the three resistance loci are closely linked. In blind tests, the markers effectively discriminated the presence of RPF1, RPF2, and RPF3 in diverse spinach germplasm. Thus, the markers developed in this study accurately predict the presence of RPF1, RPF2, and RPF3 loci, and can accelerate the development of downy mildew resistance in spinach breeding programs.