Genome-wide association analysis of resistance to Pseudoperonospora cubensis in citron watermelon

Cultivated sweet watermelon (Citrullus lanatus) is an important vegetable crop for millions of people around the world. There are limited sources of resistance to economically important diseases within C. lanatus, whereas Citrullus amarus has a reservoir of traits that can be exploited to improve C. lanatus for resistance to biotic and abiotic stresses. Cucurbit downy mildew (CDM), caused by Pseudoperonospora cubensis, is an emerging threat to watermelon production. We screened 122 C. amarus accessions for resistance to CDM over two tests (environments). The accessions were genotyped by whole-genome resequencing to generate 2,126,759 single nucleotide polymorphic (SNP) markers. A genome-wide association study was deployed to uncover marker-trait associations and identify candidate genes underlying resistance to CDM. Our results indicate the presence of wide phenotypic variability (1.1 - 57.8%) for leaf area infection, representing a 50.7-fold variation for CDM resistance across the C. amarus germplasm collection. Broad-sense heritability estimate was 0.55, implying the presence of moderate genetic effects for resistance to CDM. The peak SNP markers associated with resistance to P. cubensis were located on chromosomes Ca03, Ca05, Ca07, and Ca11. The significant SNP markers accounted for up to 30% of the phenotypic variation and were associated with promising candidate genes encoding disease resistance proteins, leucine-rich repeat receptor-like protein kinase, and WRKY transcription factor. This information will be useful in understanding the genetic architecture of the P. cubensis-Citrullus spp. patho-system as well as development of resources for genomics-assisted breeding for resistance to CDM in watermelon.

Efficacy of Fungicides for Pseudoperonospora cubensis Determined using Bioassays over Multiple Years in the Mid-Atlantic and Northeastern United States

In the United States, fungicides are the primary management option for cucumber growers to protect their crops from Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew. Pathogen resistance to some fungicides can quickly develop with the repeated applications needed to protect yield. In order to determine fungicide efficacy and monitor it over time, bioassays were conducted from 2016-2019 in Delaware, Maryland, Pennsylvania, and New York. Potted cucumber plants were either sprayed with fungicides or not treated, placed next to field-grown plants with cucurbit downy mildew for up to two days, then kept in a greenhouse until symptoms developed. Severity of symptoms or number of lesions on leaves was recorded 6-14 days after exposure started and used to determine fungicide efficacy. Quadris (azoxystrobin) was ineffective in seven of the nine bioassays, while Revus (mandipropamid) was ineffective in six of seven bioassays. Forum (dimethomorph) and Presidio (fluopicolide) were ineffective in three of eight and four of nine bioassays, respectively. The most effective fungicides were Bravo (chlorothalonil), Zing! (zoxamide + chlorothalonil), and Orondis (oxathiapiprolin), all of which consistently suppressed disease severity more than 90% when compared with the untreated control. Previcur Flex (propamocarb hydrochloride) and Ranman (cyazofamid) were also effective in every bioassay.

“Jumping Jack”: Genomic Microsatellites Underscore the Distinctiveness of Closely Related Pseudoperonospora cubensis and Pseudoperonospora humuli and Provide New Insights Into Their Evolutionary Past

Downy mildews caused by obligate biotrophic oomycetes result in severe crop losses worldwide. Among these pathogens, Pseudoperonospora cubensis and P. humuli, two closely related oomycetes, adversely affect cucurbits and hop, respectively. Discordant hypotheses concerning their taxonomic relationships have been proposed based on host–pathogen interactions and specificity evidence and gene sequences of a few individuals, but population genetics evidence supporting these scenarios is missing. Furthermore, nuclear and mitochondrial regions of both pathogens have been analyzed using microsatellites and phylogenetically informative molecular markers, but extensive comparative population genetics research has not been done. Here, we genotyped 138 current and historical herbarium specimens of those two taxa using microsatellites (SSRs). Our goals were to assess genetic diversity and spatial distribution, to infer the evolutionary history of P. cubensis and P. humuli, and to visualize genome-scale organizational relationship between both pathogens. High genetic diversity, modest gene flow, and presence of population structure, particularly in P. cubensis, were observed. When tested for cross-amplification, 20 out of 27 P. cubensis-derived gSSRs cross-amplified DNA of P. humuli individuals, but few amplified DNA of downy mildew pathogens from related genera. Collectively, our analyses provided a definite argument for the hypothesis that both pathogens are distinct species, and suggested further speciation in the P. cubensis complex.

Major cucumber diseases and the crop immunity

In Ukraine, cucumber (Cucumis sativus Linneus) annually occupies about 20 % of the total area of all vegetable crops sown in the open ground or 52.6 thousand hectares. The main reason that significantly reduces the quantitative and qualitative indicators of this vegetable crop's main valuable economic traits is the high incidence of commercial crops with diseases, especially downy mildew (Pseudoperonospora cubensis (Berk and M.A. Curtis) Rostovtsev). Since 1985 in Ukraine, this cucumber disease in the open ground on nonresistant varieties has continuously had intense development, in some years the development – by the type of epiphytotic. Simultaneously, the shortage of commercial yield of this vegetable crop due to the defeat of this disease under the field conditions can reach the level of 50–80 % or more, seed loss – 25–70 %. One of the main reasons for significant losses of commercial yield and seeds of gherkin cucumber under the conditions of its cultivation in the open ground is recognized as the high susceptibility of samples to some diseases, particularly downy mildew (Pseudoperonospora cubensis (Berk. and M.A. Curtis) Rostovtsev). Unfortunately, this problem has remained relevant for Ukraine over the past few decades. So, obtaining the initial material of a gherkin cucumber with a harmonious combination in the genotypes of a complex of various valuable economic characteristics (yield, quality, resistance to diseases, chemical substances content, suitability for various types of processing) and creating a modern competitive, innovative product (variety, hybrid) on its basis remains a relevant and priority task for domestic agricultural science at present. At the same time, scientists have proved that introducing complex (integrated) systems into production, which expect the biologization of protection with its transfer to an ecological and economic basis, is recognized as the most promising today. We suggested using resistant varieties (hybrids) in such integrated systems that provide the highest economic effect.