Doing genetic and genomic biology using the Legume Information System and associated resources

Authors: REDSUN, SVEN - National Center For Genome Resources; HOKIN, SAM - National Center For Genome Resources; CAMERON, CONNNER - National Center For Genome Resources; CLEARY, ALAN - National Center For Genome Resources; BERENDZEN, JOEL - National Center For Genome Resources; DASH, SUDHANSU - National Center For Genome Resources; Brown, Anne; WILKEY, ANDREW - Oak Ridge Institute For Science And Education (ORISE); Campbell, Jacqueline; Huang, Wei; Kalberer, Scott; Weeks, Nathan; Cannon, Steven; FARMER, ANDREW - National Center For Genome Resources

Submitted to: Methods in Molecular Biology
Publication Type: Book / Chapter
Publication Acceptance Date: 11/10/2021
Publication Date: 1/15/2022
Citation: Redsun, S., Hokin, S., Cameron, C.T., Cleary, A.M., Berendzen, J., Dash, S., Brown, A.V., Wilkey, A., Campbell, J.D., Huang, W., Kalberer, S.R., Weeks, N.T., Cannon, S.B., Farmer, A.D. 2022. Doing genetic and genomic biology using the Legume Information System and associated resources. Methods in Molecular Biology. 2443. https://doi.org/10.1007/978-1-0716-2067-0_4.
DOI: https://doi.org/10.1007/978-1-0716-2067-0_4

Interpretive Summary: Producing improved crop varieties requires repeatedly selecting for traits that farmers and consumers care about - for example, greater tolerance to plant diseases, better nutritional quality, or improved growth characteristics in the field. These kinds of improvements can be made more efficiently through the use of information about the genetic basis of these traits. The USDA-ARS maintains online databases of such data. This chapter describes the Legume Information System (LIS, at https://legumeinfo.org) and is featured in a book focusing on bioinformatic methods. The chapter illustrates several online tools while walking through an example, investigating whether flowering time has a similar genetic basis in two legume crops: soybean and common bean. This is an important trait in crops, helping determine whether a variety can be grown at a particular latitude. The answer is yes: flowering time is controlled by an evolutionarily conserved genetic mechanism, despite the fact that these two species diverged nearly 20 million years ago, with soybean originating in Asia and common bean in Central- and South America. The data and methods described in this chapter are applicable to many legume crops held in LIS associated databases, such as chickpea, common bean, soybean, peanut, alfalfa, lentil, and pea. These resources will help plant researchers and breeders to efficiently improve crops for farmers and ultimately for consumers.

Technical Abstract: In this chapter, we introduce the main components of the Legume Information System (https://legumeinfo.org) and several associated resources. Additionally, we provide an example of their use by exploring a biological question: is there a common molecular basis, across legume species, that underlies the photoperiod-mediated transition from vegetative to reproductive development - i.e., days to flowering? The Legume Information System (LIS) holds genetic and genomic data for a large number of crop and model legumes, and provides a set of online bioinformatic tools designed to help biologists address questions and tasks related to legume biology. Such tasks include identifying the molecular basis of agronomic traits; identifying orthologs for known genes; determining gene expression patterns; accessing genomic data sets; identifying markers for breeding work; and identifying genetic similarities and differences among selected accessions. LIS integrates with other legume-focused informatics resources such as SoyBase (https://soybase.org), PeanutBase (https://peanutbase.org), legume InterMine instances (https://mines.legumeinfo.org), and projects of the Legume Federation (https://legumefederation.org).