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

Eckes, Annemarie H.; Gubała, Tomasz; Nowakowski, Piotr; Szymczyszyn, Tomasz; Wells, Rachel; Irwin, Judith A.; Horro, Carlos; Hancock, John M.; King, Graham J.; Dyer, Sarah; Jurkowski, Wiktor

doi:10.12688/f1000research.11301.1

Cited by 15 publications

(8 citation statements)

References 21 publications

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“…Considering that 65% of annotated genes in plant genomes are multi-copied due to repeated whole-genome duplication and gene duplication 44 , 45 , it is necessary to obtain all the homologous sequences of each reference and target gene of interest in a plant genome. The homologous sequences of each gene can be downloaded from public whole-genome sequence databases, including NCBI Genomes ( https://www.ncbi.nlm.nih.gov/genome/ ), Phytozome 46 , PlantGDB 47 , Ensembl Plants 48 , Sol Genomics Network 49 , and Brassica Information Portal 50 . In case that the whole-genome sequences of a plant species have not been publically available, the cDNA sequences of all the homologous sequences of each gene can be obtained from the plant genome of interest by using transcriptomics data or rapid amplification of cDNA ends (RACE).…”

Section: Discussionmentioning

confidence: 99%

“…However, optimization of these factors has often been overlooked in publications 22 , 52 , 53 . A number of skilled commercial providers claimed that the optimization of qPCR conditions could be skipped when using their particular master mixes 50 . Here, we proposed an optimized method by combining the efficiency calibrated 16 , 17 and standard curve methods 16 , 18 , 19 with the 2 −ΔΔCt method 15 to sequentially optimize qPCR parameters for each reference and target gene using T. ravennae as a model (Fig.…”

Section: Discussionmentioning

confidence: 99%

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An optimized protocol for stepwise optimization of real-time RT-PCR analysis

et al. 2021

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Computational tool-assisted primer design for real-time reverse transcription (RT) PCR (qPCR) analysis largely ignores the sequence similarities between sequences of homologous genes in a plant genome. It can lead to false confidence in the quality of the designed primers, which sometimes results in skipping the optimization steps for qPCR. However, the optimization of qPCR parameters plays an essential role in the efficiency, specificity, and sensitivity of each gene’s primers. Here, we proposed an optimized approach to sequentially optimizing primer sequences, annealing temperatures, primer concentrations, and cDNA concentration range for each reference (and target) gene. Our approach started with a sequence-specific primer design that should be based on the single-nucleotide polymorphisms (SNPs) present in all the homologous sequences for each of the reference (and target) genes under study. By combining the efficiency calibrated and standard curve methods with the 2−ΔΔCt method, the standard cDNA concentration curve with a logarithmic scale was obtained for each primer pair for each gene. As a result, an R2 ≥ 0.9999 and the efficiency (E) = 100 ± 5% should be achieved for the best primer pair of each gene, which serve as the prerequisite for using the 2−ΔΔCt method for data analysis. We applied our newly developed approach to identify the best reference genes in different tissues and at various inflorescence developmental stages of Tripidium ravennae, an ornamental and biomass grass, and validated their utility under varying abiotic stress conditions. We also applied this approach to test the expression stability of six reference genes in soybean under biotic stress treatment with Xanthomonas axonopodis pv. glycines (Xag). Thus, these case studies demonstrated the effectiveness of our optimized protocol for qPCR analysis.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

An optimized protocol for stepwise optimization of real-time RT-PCR analysis

et al. 2021

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“…for 60 nutritional components, alongside a comparative study of five legume species that incorporates 97 components and 155 studies. In addition, we will apply the CNDO terms to existing and new datasets associated with the BIP (Eckes et al, 2017) that include various seed fatty acid (Barker, Larson, Graham, Lynn, & King, 2007), leaf Ca + and Mg + (Broadley et al, 2008), and Zn (Broadley et al, 2010). Based on these initial use cases, we expect wider adoption within communities of practice such as Divseek and the Multinational Brassica Genome Project (www.brassica.info), and dissemination via networks such as the Global Action Plant for Agricultural Diversification and the Food Security Information Network.…”

Section: Discussionmentioning

confidence: 99%

“…However, these are seldom integrated with each other, although there is increasing effort to standardize and harmonize approaches within research communities such as Divseek (Meyer, 2015). For example, the Brassica Information Portal (BIP) (Eckes et al, 2017) is an open-source repository for managing phenotypic trait data in brassica crops such as canola (Brassica napus L.) and is based on the generic CropStoreDB (http://www.cropstoredb.org/) relational schema (Love et al, 2012). To enhance interoperability and accessibility, BIP makes use of the Breeding Application Programming Interface (BrAPI) (https://brapi.org/) for data download.…”

Section: Navigating Crop Genetic Diversit Ymentioning

confidence: 99%

Knowledge representation and data sharing to unlock crop variation for nutritional food security

et al. 2020

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Meeting the challenge of food and nutritional security requires ongoing innovation, particularly in managing dietary nutritional information for pre-breeding analysis, selection, and cultivation of specific food crops and cultivars. At present, the ability to compare the relative nutritional value of crops is limited, with data management systems for most crops often inconsistent and poorly integrated. Here, we review generic efforts to standardize the description and management of crop trait data and discuss several issues currently constraining their exchange and comparison, with a focus on knowledge representation related to dietary nutrition. These issues include lack of consistency within or between crop specific databases, as well as limited data standardization and interoperability. At present, the use of common descriptors or controlled vocabularies between crops is fragmentary, with only partial implementation or uptake of formal ontologies, particularly for dietary nutritional composition. Although development of the existing Crop Ontology (CO) system has improved data sharing and reuse, it represents only a limited set of trait classes and crops. We identify the need for more robust and generic ontologies, particularly those that may address crop contributions to human dietary nutrition. We propose development of a Crop Dietary Nutrition Ontology (CDNO) as a robust structured controlled vocabulary for dietary nutritional composition and function, and provide examples of specific use cases and different end users who would benefit from using CDNO terms in their database searches. This development is likely to transform the way in which crops may be compared in terms of optimal dietary nutritional values.

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“…Due to their wide adaptation and ability to thrive under varying agroclimatic conditions, Brassica crops are grown throughout the world for food, animal forage and fodder and also for industrial applications [5]; they also have an allelopathic use for sustainable agriculture [6] and are grown as phytoremediators against heavy metals such as cadmium [7]. As far as food is concerned, nowadays, consumers are demanding products that are rich in nutrients for optimal health benefits.…”

Section: Introductionmentioning

confidence: 99%

Development of Transgenic Brassica Crops against Biotic Stresses Caused by Pathogens and Arthropod Pests

Poveda

Francisco

Cartea

et al. 2020

Plants

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The Brassica genus includes one of the 10 most agronomically and economically important plant groups in the world. Within this group, we can find examples such as broccoli, cabbage, cauliflower, kale, Brussels sprouts, turnip or rapeseed. Their cultivation and postharvest are continually threatened by significant stresses of biotic origin, such as pathogens and pests. In recent years, numerous research groups around the world have developed transgenic lines within the Brassica genus that are capable of defending themselves effectively against these enemies. The present work compiles all the existing studies to date on this matter, focusing in a special way on those of greater relevance in recent years, the choice of the gene of interest and the mechanisms involved in improving plant defenses. Some of the main transgenic lines developed include coding genes for chitinases, glucanases or cry proteins, which show effective results against pathogens such as Alternaria brassicae, Leptosphaeria maculans or Sclerotinia sclerotiorum, or pests such as Lipaphis erysimi or Plutella xylostella.

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

Cited by 15 publications

References 21 publications

An optimized protocol for stepwise optimization of real-time RT-PCR analysis

An optimized protocol for stepwise optimization of real-time RT-PCR analysis

Knowledge representation and data sharing to unlock crop variation for nutritional food security

Development of Transgenic Brassica Crops against Biotic Stresses Caused by Pathogens and Arthropod Pests

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