QTLs for Downy Mildew Resistance and Their Association with LRR-RLK Resistance Gene Analogs in Cucumber

Downy mildew (DM) caused by the obligate oomycete Pseudoperonospora cubensis is an important disease of cucumber and other cucurbit crops. In the United States, for more than 50 years, DM was effectively controlled in cucumber through host resistance conferred mainly by the dm-1 derived from PI 197087, which was overcome in 2004 due to the appearance of a new pathotype. Resistance sources (for example, K8, PI 197088 and PI 330628) against the new DM strain have been identified and QTL mapping studies have revealed the recessive and quantitative nature of DM resistance in these materials. QTLs for DM resistance in K8, PI 197088 and PI 330628 were detected in five (1, 2, 4, 5, and 6) of the seven cucumber chromosomes. Previous studies in other plant species suggested that the leucine-rich repeat (LRR)-receptor-like kinases (RLKs) or proteins (RLPs) may be responsible for recessively inherited host resistance against oomycete pathogens. To better understand the molecular basis of DM resistance in cucumber, we performed genome-wide identification of LRR-RLK and LRR-RLP type resistant gene homologs (RGHs) in the cucumber genome, aiming for possible association of these RGHs with DM resistance QTLs. From the Gy14 and 9930 draft genome assemblies, we identified 192 and 178 LRR-RLK, and 42 and 56 LRR-RLP RGHs respectively. Several LRR-RLKs in chromosomes 4 and 5 were co-localized or near major-effect DM resistance QTLs, but further evidence is needed to establish true association of these RGHs with the QTLs for DM resistance. Cucumber (Cucumis sativus L.) is an important vegetable crop and is widely grown in the world with total harvest of more than two million hectares in 2012 after tomato, onion, and cabbage (FAOSTAT, 2014). Downy mildew (DM hereinafter), caused by the obligate oomycete Pseudoperonospora cubensis [(Berkeley & M. A. Curtis) Rostoyzev] has a host range of more than 60 species in the Cucurbitaceae family including several economically important cucurbit crops such as cucumber, melon (C. melo L.), watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai], and squash/pumpkin (Cucurbita spp.) (Whitaker and Davis, 1962; Palti and Cohen, 1980). In the U.S., in the past, cucumber DM was well managed with deployment of resistant cultivars such as ‘Polaris’, ‘Poinsett’, and ‘Chipper’. Most of these varieties carried the DM resistance gene dm-1 from PI 197087 which, however, became less effective in 2004 due to the appearance of a new pathotype. Fortunately, large scale screening tests have identified resistant lines to this new DM strain (Criswell, 2008; Klosinska et al., 2010; Call et al., 2012a, b; Holdsworth et al., 2014). The inheritance of DM resistance in cucumber has been investigated in a number of studies with varying results. Classical genetic analysis suggested that the resistance in cucumber line Gy14 was controlled by polygenes (McFerson, 1978), while three genes, dm1, dm2, and dm3 derived from PI 197087 were reported to present in resistant cultivars ‘Aojihai’ and ‘Poinsett’ (Van Vliet and Meysing, 1974; Doruchowski and Lakowska-Ryk, 1992). One or two incompletely dominant genes were reported in the cucumber variety J-13, a derivative of Wisc 2843 (Petrov et al., 2000). Among more than 1,300 Plant Introduction (PI) lines, Call et al. (2012b) identified Ames 2353, PI 197088, PI 330628, and PI 197085 as the four most resistant cultigens to DM. Genetic variance study for Ames 353 revealed a small number of genes controlling DM resistance, and one of them seems to be allelic to dm-1(Kozik et al., 2013). In a QTL mapping study for DM resistance in the cucumber line CS-PMR1 derived from PI 197088, Yoshioka et al. (2014) identified nine DM resistance QTLs, six of which were from PI 197088. On the other hand, Caldwell et al. (2011) reported three DM resistance QTLs contributed by PI 197088, which were located in cucumber chromosomes (Chr) 2, 4, and 5, respectively, and there was epistasis effect between the two QTLs in Chr4 and Chr5. In a north Chinese type cucumber (Chinese Long) inbred line K8, Zhang et al. (2013) mapped three DM resistance QTLs in Chr5 (dm5.1, dm5.2 and dm5.3). While a number of DM resistance QTLs have been identified, the molecular basis of DM resistance in cucumber is not known. So far most simply inherited dominant disease resistant (R) genes cloned in crop plants belong to the NB-LRR (nucleotide binding leucine rich repeats) type R genes. NB-LRR type resistant gene homologs (RGHs) have been well characterized in the cucumber *Corresponding author; email: [email protected].