Summary Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high‐quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping‐by‐sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high‐quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome‐wide association studies. The high‐quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.

Germplasm collections are a crucial resource to conserve natural genetic diversity and provide a source of novel traits essential for sustained crop improvement. Optimal collection, preservation and utilization of these materials depends upon knowledge of the genetic variation present within the collection. Here we use the high-throughput genotyping-by-sequencing (GBS) technology to characterize the United States National Plant Germplasm System (NPGS) collection of cucumber (Cucumis sativus L.). The GBS data, derived from 1234 cucumber accessions, provided more than 23 K high-quality single-nucleotide polymorphisms (SNPs) that are well distributed at high density in the genome (~1 SNP/10.6 kb). The SNP markers were used to characterize genetic diversity, population structure, phylogenetic relationships, linkage disequilibrium, and population differentiation of the NPGS cucumber collection. These results, providing detailed genetic analysis of the U.S. cucumber collection, complement NPGS descriptive information regarding geographic origin and phenotypic characterization. We also identified genome regions significantly associated with 13 horticulturally important traits through genome-wide association studies (GWAS). Finally, we developed a molecularly informed, publicly accessible core collection of 395 accessions that represents at least 96% of the genetic variation present in the NPGS. Collectively, the information obtained from the GBS data enabled deep insight into the diversity present and genetic relationships among accessions within the collection, and will provide a valuable resource for genetic analyses, gene discovery, crop improvement, and germplasm preservation.

Linkage maps of the sweet cherry cultivar 'Emperor Francis' (EF) and the wild forest cherry 'New York 54' (NY) were constructed using primarily simple sequence repeat (SSR) markers and gene-derived markers with known positions on the Prunus reference map. The success rate for identifying SSR markers that could be placed on either the EF or NY maps was only 26% due to two factors: a reduced transferability of other Prunusspecies-derived markers and a low level of polymorphism in the mapping parents. To increase marker density, we developed four cleaved amplified polymorphic sequence markers (CAPS), 19 derived CAPS markers, and four insertion-deletion markers for cherry based on 101 Prunus expressed sequence tags. In addition, four gene-derived markers representing orthologs of a tomato vacuolar invertase and fruit size gene and two sour cherry sorbitol transporters were developed. To complete the linkage analysis, 61 amplified fragment length polymorphism and seven sequence-related amplified polymorphism markers were also used for map construction. This analysis resulted in the expected eight linkage groups for both parents. The EF and NY maps were 711.1 cM and 565.8 cM, respectively, with the average distance between markers of 4.94 cM and 6.22 cM. A total of 82 shared markers between the EF and NY maps and the Prunus reference map showed that the majority of the marker orders were the same with the Prunus reference map suggesting that the cherry genome is colinear with that of the other diploid Prunus species.

Phytophthora capsici causes severe losses in vegetable production, including many cucurbit crops. Our previous work showed that cucumber (Cucumis sativus) fruit are most susceptible to P. capsici when they are very young and rapidly elongating, but develop resistance as they approach full length at 10 to 12 days postpollination (DPP). In this study, fruit from seven additional cucurbit crops representing four species, melon (Cucumis melo), butternut squash (Cucurbita moschata), watermelon (Citrullus lanatus), and zucchini, yellow summer squash, acorn squash, and pumpkin (Cucurbita pepo), were tested for the effect of fruit development on susceptibility to P. capsici. Field-grown fruit of the different crops varied in overall susceptibility. Zucchini and yellow summer squash were the most susceptible, with the majority of fruit exhibiting water-soaking symptoms within 24 hours postinoculation. Fruit from all of the crops exhibited size-related decrease in susceptibility, but to varying degrees. Cucumber had the most pronounced effect. In infested fields, cucumber fruit were found to be most frequently infected at the blossom end. Comparison of the peduncle and blossom end showed a difference in susceptibility along the length of the fruit for cucumber, butternut squash, and zucchini. Greenhouse-grown, hand-pollinated pumpkin, acorn squash, and butternut squash showed an age-related decrease in susceptibility similar to field-grown fruit. For all of these fruit, a pronounced reduction in susceptibility accompanied the transition from the waxy green to green stage at ≈3 to 8 DPP.

Members of the Cucurbitaceae family display a range of sexual phenotypes including various combinations of male, female, or bisexual flowers. Ethylene appears to be a key hormone regulating the sex determination process. Application of ethylene, or inhibition of ethylene action, increases or decreases the number of pistil-bearing buds, respectively. Elevated levels of ethylene production and expression of genes for ethylene biosynthesis, have been correlated with pistillate flower production. In this study, we sought to determine the effect of modified endogenous ethylene production on sex expression by constitutively expressing ACS (1-aminocyclopropane-1-carboxylate synthase), the first committed enzyme for ethylene biosynthesis, in transgenic melons (Cucumis melo L.). Most melon genotypes are andromonoecious, where an initial phase of male flowers is followed by a mixture of bisexual and male flowers. ACS melon plants showed increased ethylene production by leaves and flower buds, and increased femaleness as measured by earlier and increased number of bisexual buds. ACS melons also had earlier and increased number of bisexual buds that matured to anthesis, suggesting that ethylene is important not only for sex determination, but also for development of the bisexual bud to maturity. Field studies showed that ACS melons had earlier mature bisexual flowers, earlier fruit set, and increased number of fruit set on closely spaced nodes on the main stem. These results provide a direct demonstration of the importance of endogenous ethylene production for female reproductive processes in melon.

Floral primordia-targeted expression of the ethylene biosynthetic gene, ACS , in melon suggests that differential timing and ethylene response thresholds combine to promote carpels, inhibit stamens, and prevent asexual bud formation. Typical angiosperm flowers produce both male and female reproductive organs. However, numerous species have evolved unisexuality. Melons (Cucumis melo L.) can produce varying combinations of male, female or bisexual flowers. Regardless of final sex, floral development begins with sequential initiation of all four floral whorls; unisexuality results from carpel or stamen primordia arrest regulated by the G and A loci, respectively. Ethylene, which promotes femaleness, is a key factor regulating sex expression. We sought to further understand the location, timing, level, and relationship to sex gene expression required for ethylene to promote carpel development or inhibit stamen development. Andromonoecious melons (GGaa) were transformed with the ethylene biosynthetic enzyme gene, ACS (1-aminocyclopropane-1-carboxylate synthase), targeted for expression in stamen and petal, or carpel and nectary, primordia using Arabidopsis APETALA3 (AP3) or CRABSCLAW (CRC) promoters, respectively. CRC::ACS plants did not exhibit altered sex phenotype. AP3::ACS melons showed increased femaleness manifested by gain of a bisexual-only phase not seen in wild type, decreased male buds and flowers, and loss of the initial male-only phase. In extreme cases, plants became phenotypically hermaphrodite, rather than andromonoecious. A reduced portion of buds progressed beyond initial whorl formation. Both the ACS transgene and exogenous ethylene reduced the expression of the native carpel-suppressing gene, G, while elevating expression of the stamen-suppressing gene, A. These results show ethylene-mediated regulation of key sex expression genes and suggest a mechanism by which temporally regulated ethylene production and differential ethylene response thresholds can promote carpels, inhibit stamens, and prevent the formation of asexual buds.

Sexual diversity expressed by Curcurbitaceae species is a primary example of developmental plasticity in plants. Ethylene, which promotes femaleness (carpel development), plays a key role in sex determination. We sought to determine the critical location for ethylene perception in developing floral primodia. The dominant negative Arabidopsis ethylene response mutant gene, etr1-1, was introduced into melon (Cucumis melo L.) plants under control of the constitutive cauliflower mosaic virus (CaMV) 35S promoter, or floral-targeted Apetela3 (AP3) and Crab's Claw (CRC) promoters, which in Arabidopsis, promote expression in petal and stamen, and carpel and nectary primordia, respectively. Based on effects of exogenous ethylene, it was predicted that inhibition of ethylene perception by carpel primordia would inhibit carpel development. Constitutive expression of etr1-1 caused several phenotypes associated with ethylene insensitivity, verifying that etr1-1 inhibits ethylene perception in the heterologous melon system. Carpel-bearing bud production was essentially abolished in 35S::etr1-1 melons, providing direct demonstration of the requirement for ethylene perception for carpel development. CRC::etr1-1 plants, however, showed enhanced femaleness as manifested by earlier and increased number of carpel-bearing buds, and production of female (rather than bisexual) buds. Despite increased carpel-bearing bud formation, a greater proportion of the CRC::etr1-1 carpel-bearing buds aborted before anthesis. AP3::etr1-1 plants showed increased maleness by nearly exclusive staminate flower production, and poorly developed carpels in the rare bisexual flowers. These results indicate that ethylene perception by the stamen (or petal) primordia plays a critical role in promoting carpel development at the time of sex determination, while ethylene perception by the carpel is important for maturation of carpel-bearing flowers to anthesis.

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