Genome of 'Charleston Gray', the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection.

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.

Floral primordia-targeted ACS (1-aminocyclopropane-1-carboxylate synthase) expression in transgenic Cucumis melo implicates fine tuning of ethylene production mediating unisexual flower development.

MAIN CONCLUSION: 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.

Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection.

Melon (C. melo L.) is an economically important vegetable crop cultivated worldwide. The melon collection in the U.S. National Plant Germplasm System (NPGS) is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding. Here we use the genotyping-by-sequencing (GBS) technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist. Population structure and genetic diversity analyses suggested that C. melo ssp. melo was firstly introduced from the centers of origin, Indian and Pakistan, to Central and West Asia, and then brought to Europe and Americas. C. melo ssp. melo from East Asia was likely derived from C. melo ssp. agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp. melo accessions from other geographic regions. We developed a core collection of 383 accessions capturing more than 98% of genetic variation in the germplasm, providing a publicly accessible collection for future research and genomics-assisted breeding of melon. Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection. Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits. This study provides insights into melon origin and domestication, and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.

The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development.

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.