The legume information system and associated online genomic resources

Authors: BERENDZEN, J - NATIONAL CENTER FOR GENOME RESOURCES; BROWN, ANNE; CAMERON, C - NATIONAL CENTER FOR GENOME RESOURCES; CAMPBELL, JACQUELINE - IOWA STATE UNIVERSITY; CLEARY, A - NATIONAL CENTER FOR GENOME RESOURCES; DASH, S - NATIONAL CENTER FOR GENOME RESOURCES; HOKIN, S - NATIONAL CENTER FOR GENOME RESOURCES; HUANG, WEI; Kalberer, Scott; Nelson, Rex; REDSUN, S - NATIONAL CENTER FOR GENOME RESOURCES; Weeks, Nathan; WILKEY, A - OAK RIDGE INSTITUTE FOR SCIENCE AND EDUCATION (ORISE); FARMER, A - NATIONAL CENTER FOR GENOME RESOURCES; Cannon, Steven

Submitted to: Legume Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/19/2021
Publication Date: 2/4/2021
Citation: Berendzen, J., Brown, A.V., Cameron, C.T., Campbell, J.D., Cleary, A.M., Dash, S., Hokin, S., Huang, W., Kalberer, S.R., Nelson, R., Redsun, S., Weeks, N.T., Wilkey, A., Farmer, A.D., Cannon, S.B. 2021. The legume information system and associated online genomic resources. Legume Science. Article e74. https://doi.org/10.1002/leg3.74.
DOI: https://doi.org/10.1002/leg3.74

Interpretive Summary: Modern plant breeding methods are highly data-intensive, often using many thousands or even millions of genetic markers, evaluated across breeding populations to help efficiently identify the varieties that are most likely to perform well. Online databases maintained by the USDA-ARS provide genetic and genomic data to help facilitate this kind of work by plant researchers and breeders. This manuscript describes resources and online research tools in the Legume Information System (LIS; https://legumeinfo.org) and SoyBase (https://soybase.org), illustrating their use with the example of the genetic control of the determinacy trait in soybean and cowpea. LIS maintains genetic information for legume crops such as bean, chickpea, alfalfa, and peanut; and SoyBase maintains such information for soybean. In many crops, determinate varieties have been selected during domestication, as these plants have a fixed lifespan and produce a crop of seeds at a predictable time, in contrast to indeterminate varieties, which produce flowers and seeds over a longer time frame, and often continue to grow and become viny and difficult to harvest. In the example described in this paper, tools at LIS and SoyBase are used to show that determinacy in soybean and cowpea have the same underlying genetic basis, despite the fact that these species separated from one another roughly 20 million years ago. The genetic data and tools described here will help researchers and breeders to produce crops with improved characteristics for farmers and consumers.

Technical Abstract: The Legume Information System (LIS; https://legumeinfo.org) houses genetic and genomic data, integrated in various online tools to allow comparative genomic analyses. The website and database maintain data for approximately two dozen species, particularly focusing on crop and model species, but also holding data for other diverse species of taxonomic interest. Major analysis features include: genome browsers, sequence-search tools, legume-focused gene families and a phylogenetic tree viewer, a gene annotation service (which places a submitted gene into a gene family and phylogenetic tree), an interactive microsynteny and pan-genome viewer, a novel viewer of genetic variant data, genetic maps and viewers, a Data Store for data sets such as assemblies and annotations, InterMine instances for querying genetic and genomic data, a tool for viewing geographic distributions of accessions for legume species maintained in the USDA Germplasm Resources Information Network (GRIN); and search interfaces for genetic features such as QTLs, markers, and genes. LIS also integrates with several other legume data resources and tools, including PeanutBase (https://peanutbase.org), SoyBase (https://soybase.org), and the Legume Federation (https://legumefederation.org).