Cucurbits (Cucurbitaceae; Cucumis spp., Cucurbita spp., Citrullus spp.)

The Cucurbitaceae is a remarkable plant family, deserving of attention because of its economic, aesthetic, cultural, medicinal, and botanical significance. In the Old and New Worlds, cucurbits have been associated with human nutrition and culture for more than 12,000 years (Brothwell and Brothwell 1969; Lira-Saade 1995). Thus, the Cucurbitaceae, along with the Brassicaceae and Asteraceae, can be considered families of extraordinary importance to humans, and they follow cereals and legumes in their economic significance to human economy (Whitaker and Davis 1962; Nayar and More 1998)

Toward integrated conservation of North America's crop wild relatives

North America harbors a rich native flora of crop wild relatives—the progenitors and closely related species of domesticated plants—as well as a range of culturally significant wild utilized plants. Despite their current and potential future value, they are rarely prioritized for conservation efforts; thus many species are threatened in their natural habitats, and most are underrepresented in plant genebanks and botanical gardens. Further coordination of efforts among land management, botanical, and agricultural science organizations will improve conservation and general public awareness with regard to these species. We present examples of productive collaborations focused on wild cranberries (Vaccinium macrocarpon and Vaccinium oxycoccos) and chile peppers (Capsicum annuum var. glabriusculum). We then discuss five shared priorities for further action: (1) understand and document North America's crop wild relatives and wild utilized plants, (2) protect threatened species in their natural habitats, (3) collect and conserve ex situ the diversity of prioritized species, (4) make this diversity accessible and attractive for plant breeding, research, and education, and (5) raise public awareness of their value and the threats to their persistence

A Survey of key methods, traits, parameters, and conditions for measuring texture in cranberry (Vaccinium macrocarpon Ait.)

In the cranberry (Vaccinium macrocarpon Ait.) industry, the textural properties and firmness of the fruit are priority traits for producing processed products, such as sweetened dried cranberry (SDC), which have gained popularity in recent years. However, there is currently no reliable methodology for screening these traits in breeding programs. In this study, we examine the key methodologies, textural traits, parameters, and conditions that are necessary to accurately and efficiently measure the texture of cranberry fruit. Double compression, single compression, puncture, shearing and Kramer shear cell methodologies were successfully implemented in cranberry, resulting in a total of 47 textural features. These features allowed the evaluation of the texture of the cranberry fruit based on key factors such as flesh, structure, and skin. This study also examined factors than can affect the performance of texture measurements, including the optimal sample size, storage time, fruit texture-size correlation, fruit temperature and orientation, optimal speed/strain combinations, and the effect of probe diameter. The results of the study suggests that certain texture traits of the compression and puncture methodologies could potentially be used to test varieties and aid in breeding program

A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)

Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org webcite), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm. Conclusions Even though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection).This work was supported in part by SNC Laboratoire ASL, Ruiter Seeds B.V., Enza Zaden B.V., Gautier Semences S.A., Nunhems B.V., Rijk Zwaan B.V., Sakata Seed Inc, Semillas Fito S. A., Seminis Vegetable Seeds Inc, Syngenta Seeds B. V., Takii and Company Ltd, Vilmorin & Cie S. A., and Zeraim Gedera Ltd (all of them as part of the support to the ICuGI); the grants AGL2009-12698-C02-02 from the Spanish "Ministerio de Ciencia e Innovacion" to AJM. NK lab was supported in part by Research Grant Award No. IS-4223-09C from BARD, the United States - Israel Binational Agricultural Research and Development Fund, and in part by Israel Science Foundation Grant No. 38606, De Ruiter Seeds, Enza Zaden, Keygene, Rijk Zwaan, Sakata Seed Corporation, Semillas Fito, Syngenta Seeds and Vilmorin Clause & Cie. AD was supported by a JAE-Doc contract from "Consejo Superior de Investigaciones Cientificas" (CSIC-Spain). MF was supported by a postdoctoral contract from CRAG. The research carried out at YX's laboratory was supported by Chinese funds (Grant No. 2008-Z42(3), 5100001, 2010AA101907).Díaz Bermúdez, A.; Fergany, M.; Formisano, G.; Ziarsolo, P.; Blanca Postigo, JM.; Fei, Z.; Staub, JE.... (2011). A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon. BMC Plant Biology. 11. https://doi.org/10.1186/1471-2229-11-111S1

tropiTree:an NGS-based EST-SSR resource for 24 tropical tree species

The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data

There and back again: historical perspective and future directions for Vaccinium breeding and research studies

The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops' relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related trait

Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping

<p>Abstract</p> <p>Background</p> <p>Cucumber, <it>Cucumis sativus </it>L. (2n = 2 × = 14) and melon, <it>C. melo </it>L. (2n = 2 × = 24) are two important vegetable species in the genus <it>Cucumis </it>(family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. In this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes.</p> <p>Results</p> <p>Using two melon mapping populations, 154 and 127 cucumber SSR markers were added onto previously reported F₂- and RIL-based genetic maps, respectively. A consensus melon linkage map was developed through map integration, which contained 401 co-dominant markers in 12 linkage groups including 199 markers derived from the cucumber genome. Syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds. It was determined that cucumber Chromosome 7 was syntenic to melon Chromosome I. Cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively. Likewise, cucumber Chromosomes 1, 3, 4, and 5 each was syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII, and IX+X, respectively. However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber.</p> <p>Conclusions</p> <p>Comparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species. Except for a possible inversion, cucumber Chromosome 7 has largely remained intact in the past nine million years since its divergence from melon. Meanwhile, many structural changes may have occurred during the evolution of the remaining six cucumber chromosomes. Further characterization of the genomic nature of <it>Cucumis </it>species closely related to cucumber and melon might provide a better understanding of the evolutionary history leading to modern cucumber.</p

Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology

Background: Switchgrass (Panicum virgatum L.) is a C4 perennial grass and widely popular as an important bioenergy crop. To accelerate the pace of developing high yielding switchgrass cultivars adapted to diverse environmental niches, the generation of genomic resources for this plant is necessary. The large genome size and polyploid nature of switchgrass makes whole genome sequencing a daunting task even with current technologies. Exploring the transcriptional landscape using next generation sequencing technologies provides a viable alternative to whole genome sequencing in switchgrass. Principal Findings: Switchgrass cDNA libraries from germinating seedlings, emerging tillers, flowers, and dormant seeds were sequenced using Roche 454 GS-FLX Titanium technology, generating 980,000 reads with an average read length of 367 bp. De novo assembly generated 243,600 contigs with an average length of 535 bp. Using the foxtail millet genome as a reference greatly improved the assembly and annotation of switchgrass ESTs. Comparative analysis of the 454-derived switchgrass EST reads with other sequenced monocots including Brachypodium, sorghum, rice and maize indicated a 70– 80 % overlap. RPKM analysis demonstrated unique transcriptional signatures of the four tissues analyzed in this study. More than 24,000 ESTs were identified in the dormant seed library. In silico analysis indicated that there are more than 2000 EST-SSRs in this collection. Expression of several orphan ESTs was confirmed by RT-PCR. Significance: We estimate that about 90 % of the switchgrass gene space has been covered in this analysis. This study nearl