InterStoreDB: a generic integration resource for genetic and genomic data

Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies

Crop phenotypic data underpin many pre-breeding efforts to characterize variation within germplasm collections. Although there has been an increase in the global capacity for accumulating and comparing such data, a lack of consistency in the systematic description of metadata often limits integration and sharing. We therefore aimed to understand some of the challenges facing findable, accesible, interoperable and reusable (FAIR) curation and annotation of phenotypic data from minor and underutilized crops. We used bambara groundnut (Vigna subterranea) as an exemplar underutilized crop to assess the ability of the Crop Ontology system to facilitate curation of trait datasets, so that they are accessible for comparative analysis. This involved generating a controlled vocabulary Trait Dictionary of 134 terms. Systematic quantification of syntactic and semantic cohesiveness of the full set of 28 crop-specific COs identified inconsistencies between trait descriptor names, a relative lack of cross-referencing to other ontologies and a flat ontological structure for classifying traits. We also evaluated the Minimal Information About a Phenotyping Experiment and FAIR compliance of bambara trait datasets curated within the CropStoreDB schema. We discuss specifications for a more systematic and generic approach to trait controlled vocabularies, which would benefit from representation of terms that adhere to Open Biological and Biomedical Ontologies principles. In particular, we focus on the benefits of reuse of existing definitions within pre- and post-composed axioms from other domains in order to facilitate the curation and comparison of datasets from a wider range of crops. Database URL: https://www.cropstoredb.org/cs_bambara.html.

Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data

The Brassica Information Portal (BIP) is a centralised repository for brassica phenotypic data. The site hosts trait data associated with brassica research and breeding experiments conducted on brassica crops, that are used as oilseeds, vegetables, livestock forage and fodder and for biofuels. A key feature is the explicit management of meta-data describing the provenance and relationships between experimental plant materials, as well as trial design and trait descriptors. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for researchers, breeders and other end-users. BIP opens up the opportunity to apply integrative, cross-project analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository.

Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data

The Brassica Information Portal (BIP) is a centralised repository for Brassica phenotypic data. Trait data associated with Brassica research and breeding experiments conducted on Brassica crops, used as vegetables, for livestock fodder and biofuels, is hosted on the site, together with information on the experimental plant materials used, as well as trial design. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for scientists and breeders. BIP opens up the opportunity to apply big data analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository.

SeedUSoon: A New Software Program to Improve Seed Stock Management and Plant Line Exchanges between Research Laboratories

Plant research is supported by an ever-growing collection of mutant or transgenic lines. In the past, a typical basic research laboratory would focus on only a few plant lines that were carefully isolated from collections of lines containing random mutations. The subsequent technological breakthrough in high-throughput sequencing, combined with novel and highly efficient mutagenesis techniques (including site-directed mutagenesis), has led to a recent exponential growth in plant line collections used by individual researchers. Tracking the generation and genetic properties of these genetic resources is thus becoming increasingly challenging for researchers. Another difficulty for researchers is controlling the use of seeds protected by a Material Transfer Agreement, as often only the original recipient of the seeds is aware of the existence of such documents. This situation can thus lead to difficult legal situations. Simultaneously, various institutions and the general public now demand more information about the use of genetically modified organisms (GMOs). In response, researchers are seeking new database solutions to address the triple challenge of research competition, legal constraints, and institutional/public demands. To help plant biology laboratories organize, describe, store, trace, and distribute their seeds, we have developed the new program SeedUSoon, with simplicity in mind. This software contains data management functions that allow the separate tracking of distinct mutations, even in successive crossings or mutagenesis. SeedUSoon reflects the biotechnological diversity of mutations and transgenes contained in any specific line, and the history of their inheritance. It can facilitate GMO certification procedures by distinguishing mutations on the basis of the presence/absence of a transgene, and by recording the technology used for their generation. Its interface can be customized to match the context and rules of any laboratory. In addition, SeedUSoon includes functions to help the laboratory protect intellectual property, export data, and facilitate seed exchange between laboratories. The SeedUSoon program, which is customizable to match individual practices and preferences, provides a powerful toolkit to plant laboratories searching for innovative approaches in laboratory management.

A Belated Green Revolution for Cannabis: Virtual Genetic Resources to Fast-Track Cultivar Development

Cannabis is a predominantly diecious phenotypically diverse domesticated genus with few if any extant natural populations. International narcotics conventions and associated legislation have constrained the establishment, characterization, and use of Cannabis genetic resource collections. This has resulted in the underutilization of genepool variability in cultivar development and has limited the inclusion of secondary genepools associated with genetic improvement strategies of the Green Revolution. The structured screening of ex situ germplasm and the exploitation of locally-adapted intraspecific traits is expected to facilitate the genetic improvement of Cannabis. However, limited attempts have been made to establish the full extent of genetic resources available for pre-breeding. We present a thorough critical review of Cannabis ex situ genetic resources, and discuss recommendations for conservation, pre-breeding characterization, and genetic analysis that will underpin future cultivar development. We consider East Asian germplasm to be a priority for conservation based on the prolonged historical cultivation of Cannabis in this region over a range of latitudes, along with the apparent high levels of genetic diversity and relatively low representation in published genetic resource collections. Seed cryopreservation could improve conservation by reducing hybridization and genetic drift that may occur during Cannabis germplasm regeneration. Given the unique legal status of Cannabis, we propose the establishment of a global virtual core collection based on the collation of consistent and comprehensive provenance meta-data and the adoption of high-throughput DNA sequencing technologies. This would enable representative core collections to be used for systematic phenotyping, and so underpin breeding strategies for the genetic improvement of Cannabis.

Genetic strategies for dissecting complex traits in biomass willows (Salix spp.)

Willows are highly diverse catkin-bearing trees and shrubs of the genus Salix. They occur in many growth forms, from tall trees to creeping alpines, and successfully occupy a wide variety of ecological niches. Shrubby willows (sub-genus Vetrix) have many characteristics that render them suited to cultivation in much faster growth cycles than conventional forestry. They respond well to coppicing, can be propagated vegetatively as cuttings and achieve rapid growth with low fertilizer inputs. As a result, willows grown as short rotation coppice are now among the leading commercially grown biomass crops in temperate regions. However, although willows have a long history of cultivation for traditional uses, their industrial use is relatively recent and, compared with major arable crops, they are largely undomesticated. Breeding programmes initiated to improve willow as a biomass crop achieved a doubling of yields within a period of <15 years. These advances were made by selecting for stem characteristics (height and diameter) and coppicing response (shoot number and shoot vigour), as well as resistance to pests, diseases and environmental stress, with little or no knowledge of the genetic basis of these traits. Genetics and genomics, combined with extensive phenotyping, have substantially improved our understanding of the basis of biomass traits in willow for more targeted breeding via marker-assisted selection. Here, we present the strategy we have adopted in which a genetic-based approach was used to dissect complex traits into more defined components for molecular breeding and gene discovery.

Phenolic composition analysis and gene expression in developing seeds of yellow- and black-seeded Brassica napus

Breeders have focused on yellow-seeded Brassica napus (rapeseed) for its better quality compared with the black-seeded variety. Moreover, flavonoids have been associated with this kind of rapeseed. In this study, we applied lipid chromatography-electrospray ionization mass spectrometry (LC-ESI-MS(n)) to compare flavonoids in developing seeds of natural black-seeded B. napus and yellow-seeded introgression lines selected from progenies of B. napus-Sinapis alba somatic hybrids. Aside from the most abundant phenolic compounds (sinapine and sinapic acid) and 1, 2-disinapoylglucose, 16 different flavonoids were identified and quantified, including (-)-epicatechin, five monocharged oligomers of (-)-epicatechin ([DP 2](-), [DP 3](-), [DP 4] [DP 2](-) B2 and [DP 2](-) B5), quercetin, kaempferol, isorhamnetin-dihexoside, kaempferol-sinapoyl-trihexoside, isorhamnetin-sinapoyl-trihexoside, isorhamnetin-hexoside-sulfate, and isorhamnetin-3-O-glucoside. Most of the flavonoids accumulated with seed development, whereas some rapidly decreased during maturation. The content of these flavonoids were lower in the yellow-seeded materials than in the black seeds. In addition, variations of insoluble procyanidin oligomers and soluble phenolic acids were observed among both rapeseed varieties. Transcriptome changes of genes participating in the flavonoid pathway were discovered by quantitative reverse transcription polymerase chain reaction analysis. Consistent with flavonoid changes identified by high performance liquid chromatography analysis, the expression of most genes in the flavonoid biosynthetic pathway was also downregulated.

The EBI enzyme portal

The availability of comprehensive information about enzymes plays an important role in answering questions relevant to interdisciplinary fields such as biochemistry, enzymology, biofuels, bioengineering and drug discovery. At the EMBL European Bioinformatics Institute, we have developed an enzyme portal (http://www.ebi.ac.uk/enzymeportal) to provide this wealth of information on enzymes from multiple in-house resources addressing particular data classes: protein sequence and structure, reactions, pathways and small molecules. The fact that these data reside in separate databases makes information discovery cumbersome. The main goal of the portal is to simplify this process for end users.

60 years of development of the journal of integrative plant biology

In celebration of JIPB's 60(th) anniversary, this paper summarizes and reviews the development process of the journal. To start, we offer our heartfelt thanks to JIPB's pioneer Editors-in-Chief who helped get the journal off the ground and make it successful. Academic achievement is the soul of academic journals, and this paper summarizes JIPB's course of academic development by analyzing it in four stages: the first two stages are mostly qualitative analyses, and the latter two stages are dedicated to quantitative analyses. Most-cited papers were statistically analyzed. Improvements in editing, publication, distribution and online accessibility--which are detailed in this paper--contribute to JIPB's sustainable development. In addition, JIPB's evaluation index and awards are provided with accompanying pictures. At the end of the paper, JIPB's milestones are listed chronologically. We believe that JIPB's development, from a national journal to an international one, parallels the development of the Chinese plant sciences.