Breeding Research and Education Needs Assessment for Organic Vegetable Growers in the Northeast

This work was supported by U.S. Department of Agriculture (USDA) Agriculture and Food Research Initiative (AFRI) Competitive Grant 2014-67013-22409

Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.)

Linkage map. This file contains the details of the linkage map. (XLSX 38 kb

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

[EN] The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a `SyntenyViewer¿ to view genome synteny between different cucurbit species and an `RNA-Seq¿ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.USDA National Institute of Food and Agriculture Specialty Crop Research Initiative [2015-51181-24285]; US-Israel Binational Agricultural Research and Development Fund [IS-3333-02, IS-3877-06CR and IS-4223-09C]; USDA Agricultural Research Service, and by SNC Laboratoire ASL, de 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 and Cie S.A. and Zeraim Gedera Ltd, all of them as part of the support to the International Cucurbit Genomics Initiative (ICuGI). Funding for open access charge: USDA National Institute of Food and Agriculture.Zheng, Y.; Wu, S.; Bai, Y.; Sun, H.; Jiao, C.; Guo, S.; Zhao, K.... (2018). Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research. 47(D1):D1128-D1136. https://doi.org/10.1093/nar/gky944SD1128D113647D

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism

Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment

As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms

A genome-wide genetic map of NB-LRR disease resistance loci in potato

Like all plants, potato has evolved a surveillance system consisting of a large array of genes encoding for immune receptors that confer resistance to pathogens and pests. The majority of these so-called resistance or R proteins belong to the super-family that harbour a nucleotide binding and a leucine-rich-repeat domain (NB-LRR). Here, sequence information of the conserved NB domain was used to investigate the genome-wide genetic distribution of the NB-LRR resistance gene loci in potato. We analysed the sequences of 288 unique BAC clones selected using filter hybridisation screening of a BAC library of the diploid potato clone RH89-039-16 (S. tuberosum ssp. tuberosum) and a physical map of this BAC library. This resulted in the identification of 738 partial and full-length NB-LRR sequences. Based on homology of these sequences with known resistance genes, 280 and 448 sequences were classified as TIR-NB-LRR (TNL) and CC-NB-LRR (CNL) sequences, respectively. Genetic mapping revealed the presence of 15 TNL and 32 CNL loci. Thirty-six are novel, while three TNL loci and eight CNL loci are syntenic with previously identified functional resistance genes. The genetic map was complemented with 68 universal CAPS markers and 82 disease resistance trait loci described in literature, providing an excellent template for genetic studies and applied research in potato

A Sustainable Agricultural Future Relies on the Transition to Organic Agroecological Pest Management

The need to improve agricultural sustainability to secure yields, minimize environmental impacts and buffer environmental change is widely recognized. Investment in conventional agriculture has supported its present yield advantage. However, organic agriculture with agroecological management has nascent capacity for sustainable production and for increasing yields in the future. Conventional systems have leveraged reductionist approaches to address pests, primarily through pesticides that seek to eliminate biological factors that reduce yield, but come at a cost to human and ecosystem health, and leave production systems vulnerable to the development of pest resistance to these chemicals or traits. Alternatives are needed, and are found in organic production approaches. Although both organic and agroecology approaches encompass more than pest management, this aspect is a pivotal element of our agricultural future. Through increased investment and application of emerging analytical approaches to improve plant breeding for and management of these systems, yields and resilience will surpass approaches that address components alone

Evaluation of Selection Methods for Resistance to a Specialist Insect Pest of Squash (Cucurbita pepo)

Plant varieties resistant to insect pests are a critical component of integrated pest management, but challenges associated with plant breeding for insect resistance, such as a long breeding cycle duration and low trait heritability, slow progress in the field. In this study, we tested two novel selection schemes to improve genetic gain for resistance to the major pest, the striped cucumber beetle (Acalymma vittatum), in squash (Cucurbita pepo, e.g., zucchini). First, we tested an indirect selection scheme using a proxy insect with correlated resistance phenotypes, Trichoplusia ni, in place of the seasonally available A. vittatum. We found that while resistance to herbivory by T. ni was heritable, there was no reciprocal benefit for resistance to A. vittatum. Second, we tested genomic selection, a method that allows for selection without phenotyping every generation, for both resistance to A. vittatum directly and resistance to the proxy T. ni. Although there was moderate genomic predictive ability, we did not observe realized gains from selection in field trials. Overall, strategies that minimize investment in direct phenotyping, leverage efficiencies from phenotyping correlated traits, and shorten breeding cycle duration are needed to develop insect resistant varieties, and this study provides examples and empirical data of two such approaches deployed in an applied breeding program

Second-site, intragenic alterations in the gene encoding subunit II of cytochrome c oxidase from yeast can suppress two different missense mutations

Cytochrome c oxidase, a multi-subunit enzyme complex, accepts electrons from cytochrome c and transfers them to molecular oxygen to form water. Subunit II (Cox2p) of the enzyme complex provides the initial entry site for the electrons from cytochrome c. We report here the characterization of a yeast strain bearing a mutation in the gene encoding Cox2p which abolishes the activity of the enzyme complex. The alteration, at residue 163 in the yeast polypeptide, substitutes isoleucine for threonine and leads to loss of Cox2p and loss of the ability to carry out cellular respiration. We have also characterized 55 independent revertants of the mutant which have recovered the ability to respire. Of these revertants, 37 recover the ability to respire due to a compensatory alteration at residue 163, which produces either a wild-type threonine codon or one for valine or serine. The other 18 revertants recover function due to secondary changes at four different codons within the gene encoding Cox2p. Some of these second-site, intragenic revertants occur at sites significantly distant from the position of the original mutation. In addition, alterations at two of these sites have previously been shown to suppress a completely different missense mutation in the gene