Legume Federation

• PI: David Fernandez-Baca (ISU)
• Co-PIs: Steven Cannon (USDA-ARS) Chris Town (JCVI) Andrew Farmer (NCGR) Amanda Cooksey (Cyverse)

Legumes play a central role in food security and nearly every cropping system worldwide. Among cultivated plants, legumes such as beans, peas and lentils are unique in their ability to fix atmospheric nitrogen which is converted into a soluble organic form that can be taken up by plants through symbiosis with a soil bacterium. Approximately 33% of all nutritional nitrogen comes from legumes which are the most important source of protein in most developing countries. Genomic resources have been or are being developed for many legume crops, but the fragmented nature of these data resources limits the ability of researchers to leverage information generated in one species to infer function or identify candidate genes in another species. The overarching goal of this project is to address this deficiency by developing software and methods for a "Legume Federation" (LF) of diverse, independently funded and geographically separated genomic data portals (GDPs). The LF will facilitate utilization of genomic, genetic and phenotypic information across a wide range of legume species that will allow researchers and breeders to take full advantage of the data that are currently available at the GDPs. The project will provide research training opportunities for students from diverse backgrounds at different educational levels. In the context of outreach, the project will pro-actively engage the community of legume data providers through presentations and workshops at national and international meetings as well as through a central web portal that will provide information describing project goals, methods of implementation and progress reports to the community.

The pace of data collection across crop and model plants has increased dramatically. Most crop species have both a data management problem and great opportunities to access genetic "big data". The objectives of this project are to develop a federation model for legume databases, to facilitate data exchange across a wide range of legume species to enable cross-species translational genomics, and to adapt an existing set of open-source tools for biological information management that will provide a framework for project-oriented data management enabling both long-term integration and widespread use. The specific goals are to:

1). Adopt and port the data currently managed in each of the custom frameworks into a set of well-integrated, open source model organism database tools;

2). Define data formats, metadata standards, data exchange and Web service protocols to facilitate communications between species-centric databases at various levels;

3). Utilize orthology, synteny, and mappings of other significant features to integrate genetic, genomic, and phenotypic data across legume species, to enable identification of common molecular bases for important traits and enable traversal across database projects;

4). Improve the capacity of organism database projects to collect and manage complex phenotype data using ontologies, controlled vocabularies and well-defined protocols and schemas; and,

5). Facilitate productive data exchange by implementing a common, open, virtualized Data Repository for data exchange across sites and for stable, long-term archiving of data sets, standardized metadata, and robust methods for archiving, searching, and accessing data sets from federated GDPs.

Publications

• Q. Liang, M. n, S. Shu, S. Lo, X. Wu, J. Carlson, P. Davidson, D. Goodstein, J. Phillips, N. Janis, E. Lee, C. Liang, P. Morrell, A. Farmer, P. Xu, T. Close and S. Lonardi.
  A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)
  Plant Genome, e20319, 2023, PMID 36946261
  Legume Information System  Legume Federation 
• D. Bertioli, J. Clevenger, I. Godoy, H. Stalker, S. Wood, J. Santos, C. Ballén-Taborda, B. Abernathy, V. Azevedo, J. Campbell, C. Chavarro, Y. Chu, A. Farmer, D. Fonceka, D. Gao, J. Grimwood, N. Halpin, W. Korani, M. Michelotto, P. Ozias-Akins, J. Vaughn, R. Youngblood, M. Moretzsohn, G. Wright, S. Jackson, S. Cannon, B. Scheffler and S. Leal-Bertioli.
  Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange
  Proc Natl Acad Sci U S A, 118(38), 2021, PMID 34518223
  Legume Information System  Legume Federation  PeanutBase 
• J. Quilbé, L. Lamy, L. Brottier, P. Leleux, J. Fardoux, R. Rivallan, T. Benichou, R. Guyonnet, M. Becana, I. Villar, O. Garsmeur, B. Hufnagel, A. Delteil, D. Gully, C. Chaintreuil, M. Pervent, F. Cartieaux, M. Bourge, N. Valentin, G. Martin, L. Fontaine, G. Droc, A. Dereeper, A. Farmer, C. Libourel, N. Nouwen, F. Gressent, P. Mournet, A. D'Hont, E. Giraud, C. Klopp and J. Arrighi.
  Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium-legume symbiosis
  Nat Commun, 12(1), 829, 2021, PMID 33547303
  Legume Information System  Legume Federation 
• A. Pasha, S. Subramaniam, A. Cleary, X. Chen, T. Berardini, A. Farmer, C. Town and N. Provart.
  Araport Lives: An Updated Framework for Arabidopsis Bioinformatics
  The Plant Cell, 2020, DOI 10.1105/tpc.20.00358, PMID 32699173, PMCID PMC7474289
  Legume Federation 
• G. Bauchet, K. Bett, C. Cameron, J. Campbell, E. Cannon, S. Cannon, J. Carlson, A. Chan, A. Cleary, T. Close, D. Cook, A. Cooksey, C. Coyne, S. Dash, R. Dickstein, A. Farmer, D. Fernández-Baca, S. Hokin, E. Jones, Y. Kang, M. Monteros, M. Muñoz-Amatriaín, K. Mysore, C. Pislariu, C. Richards, A. Shi, C. Town, M. Udvardi, E. Wettberg, N. Young and P. Zhao.
  The future of legume genetic data resources: Challenges, opportunities, and priorities
  Legume Science, n/a(n/a), e16, 2019, DOI 10.1002/leg3.16
  Legume Information System  Legume Federation  PeanutBase  Medicago HapMap Project 
• S. Lo, M. Munoz-Amatriain, S. Hokin, N. Cisse, P. Roberts, A. Farmer, S. Xu and T. Close.
  A genome-wide association and meta-analysis reveal regions associated with seed size in cowpea [Vigna unguiculata (L.) Walp]
  Theor. Appl. Genet., 2019
  Legume Information System  Legume Federation 
• D. Bertioli, J. Jenkins, J. Clevenger, O. Dudchenko, D. Gao, G. Seijo, S. Leal-Bertioli, L. Ren, A. Farmer, M. Pandey, S. Samoluk, B. Abernathy, G. Agarwal, C. Ballén-Taborda, C. Cameron, J. Campbell, C. Chavarro, A. Chitikineni, Y. Chu, S. Dash, M. Baidouri, B. Guo, W. Huang, K. Kim, W. Korani, S. Lanciano, C. Lui, M. Mirouze, M. Moretzsohn, M. Pham, J. Shin, K. Shirasawa, S. Sinharoy, A. Sreedasyam, N. Weeks, X. Zhang, Z. Zheng, Z. Sun, L. Froenicke, E. Aiden, R. Michelmore, R. Varshney, C. Holbrook, E. Cannon, B. Scheffler, J. Grimwood, P. Ozias-Akins, S. Cannon, S. Jackson and J. Schmutz.
  The genome sequence of segmental allotetraploid peanut Arachis hypogaea
  Nature Genetics, 51(5), 877--884, 2019, DOI 10.1038/s41588-019-0405-z
  Legume Information System  Legume Federation  PeanutBase 
• S. Lonardi, M. Muñoz-Amatriaín, Q. Liang, S. Shu, S. Wanamaker, S. Lo, J. Tanskanen, A. Schulman, T. Zhu, M. Luo, H. Alhakami, R. Ounit, A. Hasan, J. Verdier, P. Roberts, J. Santos, A. Ndeve, J. Doležel, J. Vrána, S. Hokin, A. Farmer, S. Cannon and T. Close.
  The genome of cowpea (Vigna unguiculata [L.] Walp.)
  The Plant Journal, 98(5), 767--782, 2019, DOI 10.1111/tpj.14349
  Legume Information System  Legume Federation 
• A. Cleary and A. Farmer.
  Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny
  Bioinformatics, 34(9), 1562--1564, 2017, DOI 10.1093/bioinformatics/btx757
  Legume Information System  Legume Federation 
• P. Zhou, K. Silverstein, T. Ramaraj, J. Guhlin, R. Denny, J. Liu, A. Farmer, K. Steele, R. Stupar, J. Miller, P. Tiffin, J. Mudge and N. Young.
  Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes
  BMC Genomics, 18(1), 2017, DOI 10.1186/s12864-017-3654-1
  Legume Federation  Medicago HapMap Project 
• M. Munoz-Amatriain, H. Mirebrahim, P. Xu, S. Wanamaker, M. Luo, H. Alhakami, M. Alpert, I. Atokple, B. Batieno, O. Boukar, S. Bozdag, N. Cisse, I. Drabo, J. Ehlers, A. Farmer, C. Fatokun, Y. Gu, Y. Guo, B. Huynh, S. Jackson, F. Kusi, C. Lawley, M. Lucas, Y. Ma, M. Timko, J. Wu, F. You, N. Barkley, P. Roberts, S. Lonardi and T. Close.
  Genome resources for climate-resilient cowpea, an essential crop for food security
  Plant J., 89(5), 1042--1054, 2017
  Legume Information System  Legume Federation 
• R. Penmetsa, N. Carrasquilla-Garcia, E. Bergmann, L. Vance, B. Castro, M. Kassa, B. Sarma, S. Datta, A. Farmer, J. Baek, C. Coyne, R. Varshney, E. Wettberg and D. Cook.
  Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor
  New Phytologist, 211(4), 1440--1451, 2016, DOI 10.1111/nph.14010
  Legume Information System  Legume Federation 
• D. Bertioli, S. Cannon, L. Froenicke, G. Huang, A. Farmer, E. Cannon, X. Liu, D. Gao, J. Clevenger, S. Dash, L. Ren, M. Moretzsohn, K. Shirasawa, W. Huang, B. Vidigal, B. Abernathy, Y. Chu, C. Niederhuth, P. Umale, A. Araújo, A. Kozik, K. Kim, M. Burow, R. Varshney, X. Wang, X. Zhang, N. Barkley, P. Guimarães, S. Isobe, B. Guo, B. Liao, H. Stalker, R. Schmitz, B. Scheffler, S. Leal-Bertioli, X. Xun, S. Jackson, R. Michelmore and P. Ozias-Akins.
  The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut
  Nature Genetics, 48(4), 438--446, 2016, DOI 10.1038/ng.3517
  Legume Information System  Legume Federation  PeanutBase