The future of legume genetic data resources: Challenges, opportunities, and priorities

Authors: BAUCHET, GUILLAUME - Boyce Thompson Institute; BETT, KIRSTIN - University Of Saskatchewan; CAMERON, CONNOR - National Center For Genome Resources; CAMPBELL, JACQUELINE - Iowa State University; CANNON, ETHALINDA - Iowa State University; Cannon, Steven; CARLSON, JOSEPH - Berkeley National Laboratory; CHAN, AGNES - J Craig Venter Institute; CLEARY, ALAN - National Center For Genome Resources; CLOSE, TIMOTHY - University Of California; COOK, DOUGLAS - University Of California; COOKSEY, AMANDA - University Of Arizona; Coyne, Clarice - Clare; DASH, SUDHANSU - National Center For Genome Resources; DICKSTEIN, REBECCA - University Of North Texas; FARMER, ANDREW - National Center For Genome Resources; FERNANDEZ-BACA, DAVID - Iowa State University; HOKIN, SAMUEL - National Center For Genome Resources; JONES, ELIZABETH - Cornell University; KANG, YUN - Noble Research Institute; MONTEROS, MARIA - Noble Research Institute; MUNOZ-AMATRIAIN, MARIA - Colorado State University; MYSORE, KIRANKUMAR - Noble Research Institute; PISLARIU, CATALINA - Texas Woman'S University; Richards, Christopher; SHI, AINONG - University Of Arkansas; TOWN, CHRISTOPHER - J Craig Venter Institute; UDVARDI, MICHAEL - Noble Research Institute; WETTBERG, ERIC - University Of Vermont; YOUNG, NEVIN - University Of Minnesota; ZHAO, PATRICK - Noble Research Institute

Submitted to: Legume Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/29/2019
Publication Date: 12/30/2019
Citation: Bauchet, G., Bett, K.E., Cameron, C.T., Campbell, J.D., Cannon, E., Cannon, S.B., Carlson, J., Chan, A., Cleary, A., Close, T., Cook, D., Cooksey, A., Coyne, C.J., Dash, S., Dickstein, R., Farmer, A., Fernandez-Baca, D., Hokin, S., Jones, E., Kang, Y., Monteros, M., Munoz-Amatriain, M., Mysore, K., Pislariu, C., Richards, C.M., Shi, A., Town, C., Udvardi, M., Wettberg, E., Young, N., Zhao, P. 2019. The future of legume genetic data resources: Challenges, opportunities, and priorities. Legume Science. 1(1):e16. https://doi.org/10.1002/leg3.16.
DOI: https://doi.org/10.1002/leg3.16

Interpretive Summary: The legume plant family includes many important crops, such as soybean, peanut, lentil, and alfalfa. New technologies have led to generation of enormous amounts of genetic data for these crops - which presents both great opportunities for breeders and researchers, and challenges in terms of data management and integration. In March, 2019, a group of researchers met to discuss needs and priorities for data management for crops in the legume family. The recommendations of that meeting are presented in the associated white paper. These recommendations will serve to guide funders and researchers in project planning and in determining research priorities and approaches. Anticipated benefits are greater coordination and efficient use of public research funds toward crop improvement.

Technical Abstract: Legumes, comprising one of the largest, most diverse, and most economically important plant families, are the subject of vibrant research and development worldwide. Continued improvement of legume crops will benefit from the recent proliferation of genetic (including genomic) resources; but the diversity, scale, and complexity of these resources presents challenges to those managing and using them. A workshop held in March of 2019 addressed questions of data resources and priorities for the legumes. The workshop identified various needs and recommendations: (a) Develop strategies to effectively store, integrate and relate genetic resources collected in different projects. (b) Leverage information collected across many legume species by standardizing data formats and ontologies, improving the state of metadata about data sets, and increasing use of the FAIR data principles. (c) Advocate for the critical role that curators exercise in integrating complex datasets into databases and adding high value metadata that enable downstream analytics and facilitate practical applications. (d) Implement standardized software and database development practices to best leverage limited developer time and expertise gained from the various legume (and other) species. (e) Develop tools and databases that can manage genetic information for the world’s plant genetic resources, enabling efficient incorporation of important traits into breeding programs. (f) Centralize information on databases, tools and training materials and establish funding streams to support training and outreach.