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Successful organic farming requires crop varieties that are resilient to environmental variability. Assessing variety performance across the range of conditions represented on working farms is vital to developing such varieties; however, data collected from on-farm, participatory trials can be difficult to both collect and interpret. To assess the utility of data arising from participatory trialing efforts, we examined the performance of butternut squash (Cucurbita moschataL.), broccoli (Brassica oleraceaL.) and carrot (Daucus carotaL.) varieties grown in diverse organic production environments in participatory trials in Oregon, Washington, Wisconsin and New York using adaptability analysis (regression of variety means on environmental index). Patterns of adaptation varied across varieties, with some demonstrating broad adaptation and others showing specific adaptation to low- or high-yielding environments. Selection of varieties with broadvsspecific adaptation should be guided by farmers’ risk tolerance and on-farm environmental variation. Adaptability analysis was appropriate for continuous variables (e.g., yield traits), but less so for ordinal variables and quality traits such as flavor and appearance, which can be vitally important in organic vegetable crop variety selection. The relative advantages of adaptability analysis and additive main effects and multiplicative interactions are also discussed in relation to on-farm trial networks. This work demonstrated the unique challenges presented by extensive participatory vegetable trialing efforts, which, as compared to grain crops, require novel approaches to facilitating farmer participation as well as data collection and analysis. Efficient, precise and reliable methods for evaluating quality related traits in these crops would allow researchers to assess stability and adaptation across a wider range of traits, providing advantages for effective plant breeding and trialing activities within the organic sector.

Studies of genetic diversity among phenotypically distinct crop landraces improve our understanding of fruit evolution and genome structure under domestication. Chile peppers (Capsicum spp. L.) are economically valuable and culturally important species, and extensive phenotypic variation among landraces exists in southern Mexico, a center of C. annuum diversity. We collected 103 chile pepper seed accessions from 22 named landraces across 27 locations in southern Mexico. We genotyped these accessions with genotyping by sequencing (GBS), yielding 32,623 filtered single‐nucleotide polymorphisms. Afterward, we genotyped 32 additional C. annuum accessions from a global collection for comparison to the Mexican collection. Within the Mexican collection, genetic assignment analyses showed clear genetic differentiation between landraces and clarified the unique nature of the Tusta landrace. Further clustering analyses indicated that the largest fresh‐use Chile de Agua and dry‐use Costeño landraces were part of separate clades, indicating that these two landraces likely represent distinct populations. The global accessions showed considerable admixture and limited clustering, which may be due to the collapse of use‐type divisions outside of Central America. The separation of the Mexican landraces in part by fruit morphology related to use highlights the relevance of this use‐type morphological diversity for plant breeders and the utility of fruit development variation for evolutionary biologists.

Globally, pea (Pisum sativum L.) is an important temperate legume crop for food, feed and fodder, and many breeding programs develop cultivars adapted to these end-uses. In order to assist pea development efforts, we assembled the USDA Pea Single Plant Plus Collection (PSPPC), which contains 431 P. sativum accessions with morphological, geographic and taxonomic diversity. The collection was characterized genetically in order to maximize its value for trait mapping and genomics-assisted breeding. To that end, we used genotyping-by-sequencing-a cost-effective method for de novo single-nucleotide polymorphism (SNP) marker discovery-to generate 66 591 high-quality SNPs. These data facilitated the identification of accessions divergent from mainstream breeding germplasm that could serve as sources of novel, favorable alleles. In particular, a group of accessions from Central Asia appear nearly as diverse as a sister species, P. fulvum, and subspecies, P. sativum subsp. elatius. PSPPC genotypes can be paired with new and existing phenotype data for trait mapping; as proof-of-concept, we localized Mendel's A gene controlling flower color to its known position. We also used SNP data to define a smaller core collection of 108 accessions with similar levels of genetic diversity as the entire PSPPC, resulting in a smaller germplasm set for research screening and evaluation under limited resources. Taken together, the results presented in this study along with the release of a publicly available SNP data set comprise a valuable resource for supporting worldwide pea genetic improvement efforts.

Both the fruit mesocarp and the seeds of winter squash can be used for consumption, although the focus of breeding efforts varies by cultivar. Cultivars bred for fruit consumption are selected for fruit mesocarp quality traits such as carotenoid content, percent dry matter, and percent soluble solids, while these traits are essentially ignored in oilseed pumpkins. To compare fruit development in these two types of squash, we sequenced the fruit transcriptome of two cultivars bred for different purposes: an acorn squash, 'Sweet REBA', and an oilseed pumpkin, 'Lady Godiva'. Putative metabolic pathways were developed for carotenoid, starch, and sucrose synthesis in winter squash fruit and squash homologs were identified for each of the structural genes in the pathways. Gene expression, especially of known rate-limiting and branch point genes, corresponded with metabolite accumulation both across development and between the two cultivars. Thus, developmental regulation of metabolite genes is an important factor in winter squash fruit quality.

Domestication of crop plants had effects on human lifestyle and agriculture. However, little is known about the underlying molecular mechanisms accompanying the changes in fruit appearance as a consequence of selection by early farmers. We report the fine mapping and cloning of a tomato (Solanum lycopersicum) fruit mass gene encoding the ortholog of KLUH, SlKLUH, a P450 enzyme of the CYP78A subfamily. The increase in fruit mass is predominantly the result of enlarged pericarp and septum tissues caused by increased cell number in the large fruited lines. SlKLUH also modulates plant architecture by regulating number and length of the side shoots, and ripening time, and these effects are particularly strong in plants that transgenically down-regulate SlKLUH expression carrying fruits of a dramatically reduced mass. Association mapping followed by segregation analyses revealed that a single nucleotide polymorphism in the promoter of the gene is highly associated with fruit mass. This single polymorphism may potentially underlie a regulatory mutation resulting in increased SlKLUH expression concomitant with increased fruit mass. Our findings suggest that the allele giving rise to large fruit arose in the early domesticates of tomato and becoming progressively more abundant upon further selections. We also detected association of fruit weight with CaKLUH in chile pepper (Capsicum annuum) suggesting that selection of the orthologous gene may have occurred independently in a separate domestication event. Altogether, our findings shed light on the molecular basis of fruit mass, a key domestication trait in tomato and other fruit and vegetable crops., We thank Dr. D. Choi (Seoul National University) for providing DNA sequence of chile pepper CaKLUH region; and Molecular and Cellular Imaging Center, The Ohio State University, for assistance with microscopy. This work was supported by National Science Foundation Grant IOS-0922661 (to E.v.d.K.).

Acorn squash (Cucurbita pepo) is an iconic fall vegetable in the United States, known for its unique fruit shape and also prized for its culinary properties. Little is known about the metabolism that underlies the development of fruit quality attributes such as color, sweetness, texture and nutritional qualities in acorn squash, or any other winter squash grown worldwide. To provide insight into winter squash fruit and seed development and add to the genomic resources in the Cucurbita genus, RNA sequencing was used to generate an acorn squash fruit and seed transcriptome from the cultivar Sweet REBA at critical points throughout fruit development. 141 838 600 high-quality paired-end Illumina reads were assembled into 55 949 unigenes. 85% of unigenes with predicted open reading frames had homology with previously identified genes and over 62% could be functionally annotated. Comparison with the watermelon and cucumber genomes provided confirmation that the unigenes are full-length and comprehensive, covering an average of 90% of the coding sequence of their homologs and 72% of the cucumber and watermelon exomes. Key candidate genes associated with carotenoid and carbohydrate metabolism were identified toward a resource for winter squash fruit quality trait dissection. This transcriptome represents a major advance in C. pepo genomics, providing significant new sequence information and revealing the repertoire of genes expressed throughout winter squash fruit and seed development. Future studies on the genetic basis of fruit quality and future breeding efforts will be enhanced by tools and insights developed from this resource.