KnowPulse: A Web-Resource Focused on Diversity Data for Pulse Crop Improvement

Sanderson, Lacey-Anne; Caron, Carolyn T.; Tan, Reynold; Shen, Yichao; Liu, Ruobin; Bett, Kirstin E.

doi:10.3389/fpls.2019.00965

Cited by 40 publications

(24 citation statements)

References 25 publications

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“…Identification of outlier markers can be facilitated using high throughput sequencing methods for genetic mapping and identification of candidate genes. Alleles adapted to specific abiotic stresses may be associated with such environments, a means of prioritizing CWR accessions for genetic analysis and introgression into elite crop cultivars (Baute et al, 2015; Sanderson et al, 2019).…”

Section: How To Effectively Use the Diversity Of Cwrs?mentioning

confidence: 99%

“…Tolerant segregants are being advanced for trait fixation. Sanderson, Caron, Shen, Liu, and Bett (2019), with a focus on drought tolerance and disease resistance, studied RILs of crosses of lentil cultivars with L. orientalis , L. odemensis , and L ervoides in the ICARDA lentil prebreeding project. This aims to develop genetic maps and markers for lentil and CWR for the transfer of key drought traits into breeding programs for drought tolerance.…”

Section: Lentilmentioning

confidence: 99%

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Potential and limits of exploitation of crop wild relatives for pea, lentil, and chickpea improvement

Coyne¹,

Kumar²,

Wettberg

et al. 2020

Legume Science

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Legumes represent the second most important family of crop plants after grasses, accounting for approximately 27% of the world's crop production. Past domestication processes resulted in a high degree of relatedness between modern varieties of crops, leading to a narrower genetic base of cultivated germplasm prone to pests and diseases. Crop wild relatives (CWRs) harbor genetic diversity tested by natural selection in a range of environments. To fully understand and exploit local adaptation in CWR, studies in geographical centers of origin combining ecology, physiology, and genetics are needed. With the advent of modern genomics and computation, combined with systematic phenotyping, it is feasible to revisit wild accessions and landraces and prioritize their use for breeding, providing sources of disease resistances; tolerances of drought, heat, frost, and salinity abiotic stresses; nutrient densities across major and minor elements; and food quality traits. Establishment of hybrid populations with CWRs gives breeders a considerable benefit of a prebreeding tool for identifying and harnessing wild alleles and provides extremely valuable long-term resources. There is a need of further collecting and both ex situ and in situ conservation of CWR diversity of these taxa in the face of habitat loss and degradation and climate change. In this review, we focus on three legume crops domesticated in the Fertile Crescent, pea, chickpea, and lentil, and summarize the current state and potential of their respective CWR taxa for crop improvement.

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Section: How To Effectively Use the Diversity Of Cwrs?mentioning

confidence: 99%

Section: Lentilmentioning

confidence: 99%

Potential and limits of exploitation of crop wild relatives for pea, lentil, and chickpea improvement

Coyne¹,

Kumar²,

Wettberg

et al. 2020

Legume Science

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“…Dendrome (now TreeGenes) initially begun in 1993 to house forest tree genetic maps and markers (4); the Rat Genome Database (RGD) (5, 6) in 1999 for rat research; The Arabidopsis Information Portal (TAIR), also in 1999, for genomic and genetic data for Arabidopsis thaliana , a model plant species (7). Later examples include the Saccharomyces Genome Database (SGD) in 2002 for the model species Saccharomyces cerevisiae (8); the Genome Database for Rosaceae (GDR) in 2003 for Rosaceae species including agriculturally important tree fruit and berry species (9); Knowpulse began in 2010 for pulse crop breeding (10); and many others.…”

Section: Introductionmentioning

confidence: 99%

“…For example, sites such as the GDR (9), TreeGenes (4), Hardwood Genomics Project (https://hardwoodgenomics.org/) and the Citrus Genome Database (26) house genomic, genetic and breeding data for their respective tree crop communities using Tripal. Similarly, Knowpulse (10), Cool Season Food Legume (27), PeanutBase (28) and the Legume Information System (29) house legume data using Tripal.…”

Section: Introductionmentioning

confidence: 99%

Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases

et al. 2019

Self Cite

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Community biological databases provide an important online resource for both public and private data, analysis tools and community engagement. These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades. Due to the complexity and increasing quantities of these data, construction of online resources is increasingly difficult especially with limited funding and access to technical expertise. Furthermore, online repositories are expected to promote FAIR data principles (findable, accessible, interoperable and reusable) that presents additional challenges. The open-source Tripal database toolkit seeks to mitigate these challenges by creating both the software and an interactive community of developers for construction of online community databases. Additionally, through coordinated, distributed co-development, Tripal sites encourage community-wide sustainability. Here, we report the release of Tripal version 3 that improves data accessibility and data sharing through systematic use of controlled vocabularies (CVs). Tripal uses the community-developed Chado database as a default data store, but now provides tools to support other data stores, while ensuring that CVs remain the central organizational structure for the data. A new site developer can use Tripal to develop a basic site with little to no programming, with the ability to integrate other data types using extension modules and the Tripal application programming interface. A thorough online User’s Guide and Developer’s Handbook are available at http://tripal.info, providing download, installation and step-by-step setup instructions.

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“…These so-called community databases also provide analytical tools to their users. Some Tripal-based sites include the Genome Database for Rosaceae (8), KnowPulse (9), the Legume Information System (10), i5K Workspace (11), the Banana Genome Hub (12), CottonGen (13), GeneNetEngine (14) and others. With the advent of next-generation sequencing technologies and the increased quantities of data, integration of Tripal with Galaxy provides an important link for these research communities.…”

Section: Introductionmentioning

confidence: 99%

blend4php: a PHP API for galaxy

Wytko

Pando

Ficklin³

2017

Database

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Galaxy is a popular framework for execution of complex analytical pipelines typically for large data sets, and is a commonly used for (but not limited to) genomic, genetic and related biological analysis. It provides a web front-end and integrates with high performance computing resources. Here we report the development of the blend4php library that wraps Galaxy’s RESTful API into a PHP-based library. PHP-based web applications can use blend4php to automate execution, monitoring and management of a remote Galaxy server, including its users, workflows, jobs and more. The blend4php library was specifically developed for the integration of Galaxy with Tripal, the open-source toolkit for the creation of online genomic and genetic web sites. However, it was designed as an independent library for use by any application, and is freely available under version 3 of the GNU Lesser General Public License (LPGL v3.0) at https://github.com/galaxyproject/blend4php.Database URL: https://github.com/galaxyproject/blend4php

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KnowPulse: A Web-Resource Focused on Diversity Data for Pulse Crop Improvement

Cited by 40 publications

References 25 publications

Potential and limits of exploitation of crop wild relatives for pea, lentil, and chickpea improvement

Potential and limits of exploitation of crop wild relatives for pea, lentil, and chickpea improvement

Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases

blend4php: a PHP API for galaxy

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