Todd C. Wehner

Genetic diversity among watermelon (Citrullus lanatus and Citrullus colocynthis) accessions

Genetic diversity was estimated among 42 U.S. PlantIntroduction (PI) accessions of the genusCitrullus (of these, 34 PIs are reported tohave disease resistance), and 5 watermelon cultivars, using 30RAPD primers. These primers produced 662 RAPD markers that could berated with high confidence. Based on these markers, geneticsimilarity coefficients were calculated and a dendrogram wasconstructed using the unweighted pair-group method witharithmetic average (UPGMA). The analysis delineated threemajor clusters. The first cluster consisted of a group of fivewatermelon cultivars, a group of C.lanatus var. lanatusaccessions, and a group of C.lanatus var. lanatusaccessions that contained some C.lanatus var. citroidesgenes. The second cluster consisted of the C.lanatus var. citroidesaccessions, while the third cluster consisted of theC. colocynthis accessions.The two C. lanatus clustersdifferentiated from each other and from the C.colocynthis cluster at the level of 58.8%and 38.9% genetic similarity, respectively. Assessment ofgenetic diversity among accessions that have been reported to havedisease resistance indicated that resistance to either anthracnose,downy mildew, powdery mildew, or watermelon mosaic virus is foundamong all major groups of Citrullus PIs.Additionally, resistance to gummy stem blight or Fusarium wilt mayexist among C. lanatus var.citroides PIs. This study demonstrates thatmolecular markers can be useful in assessing genetic diversity, andin sorting Citrullus PIs into phylogeneticgroups prior to their evaluation for disease or pestresistance.

Evidence for downy mildew races in cucumber tested in Asia, Europe, and North America.

Abstract Downy mildew ( Pseudoperonospora cubensis (Berk. and Curt.) Rostov.) is an important disease in most cucumber ( Cucumis sativus L.) production areas worldwide. A set of cucumber cultivars and breeding lines (hereafter referred to collectively as cultigens) resistant to downy mildew in particular regions of the world were tested for resistance in geographical regions thought to differ in pathogen virulence or race (US, Poland, China, and India). Cucumber cultigens used in the study were developed in the US, Poland or China, and differed in their resistance to downy mildew. These cultigens were evaluated against local isolates of P. cubensis under field conditions (North Carolina and India) or greenhouse conditions (South Carolina and Poland). Significant differences were observed among cultigens for resistance to P. cubensis at all locations. Individual cultigens differed in their resistance to the pathogen at different geographic locations, providing evidence that the different local isolates represented different races of the pathogen. Cultigens from PR China that were resistant to downy mildew in that country were also resistant in India. However, those same cultigens were intermediate in resistance in the US and Poland. Cultigens from the US and Poland that were resistant in those countries were intermediate in resistance in India. The most resistant cultigens over all locations were ‘Nongchen #4’ (PR China) and M 21 (NC State University).

Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon

BackgroundA large single nucleotide polymorphism (SNP) dataset was used to analyze genome-wide diversity in a diverse collection of watermelon cultivars representing globally cultivated, watermelon genetic diversity. The marker density required for conducting successful association mapping depends on the extent of linkage disequilibrium (LD) within a population. Use of genotyping by sequencing reveals large numbers of SNPs that in turn generate opportunities in genome-wide association mapping and marker-assisted selection, even in crops such as watermelon for which few genomic resources are available. In this paper, we used genome-wide genetic diversity to study LD, selective sweeps, and pairwise FST distributions among worldwide cultivated watermelons to track signals of domestication.ResultsWe examined 183 Citrullus lanatus var. lanatus accessions representing domesticated watermelon and generated a set of 11,485 SNP markers using genotyping by sequencing. With a diverse panel of worldwide cultivated watermelons, we identified a set of 5,254 SNPs with a minor allele frequency of ≥ 0.05, distributed across the genome. All ancestries were traced to Africa and an admixture of various ancestries constituted secondary gene pools across various continents. A sliding window analysis using pairwise FST values was used to resolve selective sweeps. We identified strong selection on chromosomes 3 and 9 that might have contributed to the domestication process. Pairwise analysis of adjacent SNPs within a chromosome as well as within a haplotype allowed us to estimate genome-wide LD decay. LD was also detected within individual genes on various chromosomes. Principal component and ancestry analyses were used to account for population structure in a genome-wide association study. We further mapped important genes for soluble solid content using a mixed linear model.ConclusionsInformation concerning the SNP resources, population structure, and LD developed in this study will help in identifying agronomically important candidate genes from the genomic regions underlying selection and for mapping quantitative trait loci using a genome-wide association study in sweet watermelon.

Resurgence of Pseudoperonospora cubensis: The Causal Agent of Cucurbit Downy Mildew

The downy mildew pathogen, Pseudoperonospora cubensis, which infects plant species in the family Cucurbitaceae, has undergone major changes during the last decade. Disease severity and epidemics are far more destructive than previously reported, and new genotypes, races, pathotypes, and mating types of the pathogen have been discovered in populations from around the globe as a result of the resurgence of the disease. Consequently, disease control through host plant resistance and fungicide applications has become more complex. This resurgence of P. cubensis offers challenges to scientists in many research areas including pathogen biology, epidemiology and dispersal, population structure and population genetics, host preference, host-pathogen interactions and gene expression, genetic host plant resistance, inheritance of host and fungicide resistance, and chemical disease control. This review serves to summarize the current status of this major pathogen and to guide future management and research efforts within this pathosystem.

Little heterosis for yield and yield components in hybrids of six cucumber inbreds

Heterosis and inbreeding depression for fruit yield has been reported for pickling cucumber (Cucumis sativus L.). However, cucumber inbreds often perform as well as hybrids, and there is little inbreeding depression. The objectives of this study were to reexamine the amount of heterosis and inbreeding depression for fruit yield and yield components in pickling cucumber, and to determine the relationship between yield components and yield for heterosis. Two pickling cucumber inbreds (M 12, M 20) and inbreds from four open-pollinated monoecious cultivars (‘Addis’, ‘Clinton’, ‘Wisconsin SMR 18’, ‘Tiny Dill’) were hybridized to form four F1 hybrids (‘Addis’ × M 20, ‘Addis’ × ‘Wis. SMR 18’, ‘Clinton’ × M 12, M 20 × ‘Tiny Dill’). F1 hybrids were then self-pollinated or backcrossed to generate F2, BC1A, and BC1B progeny. Thirty plants of each generation within each hybrid family were grown in plots 3.1 m long with four replications in each of two seasons. Data were collected from once-over harvest for vegetative, reproductive, yield, and fruit quality traits. Heterosis and inbreeding depression for fruit yield and yield components were not observed in three of the hybrids. Only ‘Addis’ × ‘Wis. SMR 18’ exhibited high-parent heterosis and inbreeding depression for total, marketable, and early fruit weight. For ‘Addis’ × ‘Wis. SMR 18’, heterosis for fruit yield was associated with a decreased correlation between percentage of fruit set and fruit weight, an increased negative correlation between percentage of fruit set and both the number of branches per plant and the percentage of pistillate nodes, and an increased negative correlation between the number of nodes per branch and total fruit weight. Inbreeding depression was associated with a weakening of the strong negative correlations between percentage of fruit set and the number of branches per plant, and between the number of nodes per branch and total fruit weight. Those correlations were associated with high-parent heterosis and inbreeding depression only for one cross, and do not necessarily apply to future crosses in which heterosis may be observed for yield. We did not observe the heterosis or inbreeding depression for yield in cucumber in most of the crosses as was reported by Ghaderi & Lower (1979a; 1979c).

OPTIMUM PLOT SIZE DETERMINATION AND ITS APPLICATION TO CUCUMBER YIELD TRIALS

SummaryMethods of estimating Smiths b and, thereby, optimum plot size are compared from a theoretical viewpoint. For estimating b, generalized least squares is recommended over Smiths (1938) original method and other methods because the points used to fit the required regression are correlated and have unequal variances.Optimum plot size for once-over-harvest trials measuring yield (as number of fruits per plot) of pickling and frest-market cucumbers (Cucumis sativus L.) was estimated to be 0.7 to 3.8 m2 (0.5 to 2.5 m of row for rows 1.5 m apart) for conventional harvesting, and 1.0 to 5.6 m2 (0.7 to 3.7 m of row) for simulated harvesting using paraquat to defoliate plots before evaluation. Estimates of optimum plot size were calculated from a number of uniformity trials differing in year (1982 or 1983), planting date (early or late), and field. The estimates were sufficiently stable to suggest that they have useful generality.For multiple-harvest yield trials, optimum plot sizes for determining yield of pickling (expressed in

High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon.

/ha or q/ha) or fresh-market cucumbers (i.e. USDA Fancy and No. 1 grade fruit combined or USDA Fancy, No. 1, and No. 2 grade fruit combined, in q/ha) were estimated from experimental data to be 6.4 to 10.3 m2 (4.3 to 6.8 m of row).

Effect of inbreeding on horticultural performance of lines developed from an open-pollinated pickling cucumber population

We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Collinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD), and selective sweep for wild, semi-wild, and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1563 SNPs obtained after LD pruning with minor allele frequency of 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild, and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima’s D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication.

Eight isolates of Didymella bryoniae from geographically diverse areas exhibit variation in virulence but not isolate by cultivar interaction on Cucumis sativus

SummaryThe effect of self-pollination of cucumber (Cucumis sativus L.) for 6 generations in lines developed from the North Carolina Medium Base Pickle population was determined by regression of trait expression for each generation on Wrights coefficient of inbreeding. Two yield traits (total and marketable), earliness and 3 fruit quality traits (shape, color and seedcell size) were evaluated in 2 environments (spring and summer, 1983). The regression did not result in significant negative slopes, indicating that inbreeding depression was not important in the population for the traits studied. Midparent heterosis was found for most traits in many hybrids obtained from crossing S6 lines with the gynoecious inbred line, Gy 14A.

Environmental effects on genetic variation of chilling resistance in cucumber

Eight isolates of Didymella bryoniae from geographically diverse areas were tested for differences in virulence on nine genotypes of cucumber (Cucumis sativus) in two greenhouse experiments. Cucumber genotypes tested represent the range of resistance currently available. Isolates were collected in Arizona, California, The Netherlands, North Carolina, South Carolina, Sweden, and Wisconsin. The original host for one isolate was unknown, six were from cucumber, and one from muskmelon (C. melo). No significant isolate by cultivar interaction was detected in either experiment. Ranks of isolates were usually consistent across cultivars and experiments, and ranks of cultivars were usually consistent across isolates and experiments. Thus, resistance in cucumber to D. bryoniae appears to be nonspecific in nature. Single degree of freedom contrasts showed that the two foreign isolates (from The Netherlands and Sweden) were significantly more virulent than the U.S. isolates. Regression analysis indicated that the variance among cultivar ratings was not significantly correlated with mean isolate rating and that the variance among isolate ratings was not correlated with mean cultivar rating, indicating that an additive model of host-pathogen interaction may control resistance. The finding that resistance to D. bryoniae in cucumber is nonspecific suggests that breeders can use a single virulent isolate of D. bryoniae to screen for resistance.