Technology and Code ARTICLE
KnowPulse: a web-resource focused on diversity data for pulse crop improvement
- 1University of Saskatchewan, Canada
KnowPulse (https://knowpulse.usask.ca) is a breeder-focused web portal for pulse breeders and geneticists. With a focus on diversity data, KnowPulse provides information on genetic markers, sequence variants, phenotypic traits and germplasm for chickpea, common bean, field pea, faba bean and lentil. Genotypic data is accessible through the genotype matrix tool, displayed as a marker-by-germplasm table of genotype calls specific to germplasm chosen by the researcher. It is also summarized on genetic marker and sequence variant pages. Phenotypic data is visualized in trait distribution plots: violin plots for quantitative data and histograms for qualitative data. These plots are accessible through trait, germplasm and experiment pages, as well as through a single page search tool. KnowPulse is built using the open-source Tripal toolkit and utilizes open-source tools including, but not limited to, species-specific JBrowse instances, a BLAST interface, and whole-genome CViTjs visualizations. KnowPulse is constantly evolving with data and tools added as they become available. Full integration of genetic maps and quantitative trait loci is imminent, and development of tools exploring structural variation is being explored.
Keywords: legumes, pulses, web resource, diversity, Genotypic data, Phenotypic data
Received: 03 Apr 2019;
Accepted: 10 Jul 2019.
Edited by:Matthew N. Nelson, Agriculture & Food, Commonwealth Scientific and Industrial Research Organisation, Australia
Reviewed by:Elisa Bellucci, Marche Polytechnic University, Italy
Ethalinda K. Cannon, Iowa State University, United States
Copyright: © 2019 Sanderson, Caron, Tan, Shen, Liu and Bett. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Prof. Kirstin E. Bett, University of Saskatchewan, Saskatoon, Canada, firstname.lastname@example.org