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

Bauchet, Guillaume J.; Bett, Kirstin E.; Cameron, Connor T.; Campbell, Jacqueline D.; Cannon, Ethalinda K. S.; Cannon, Steven B.; Carlson, Joseph W.; Chan, Agnes; Cleary, Alan; Close, Timothy J.; Cook, Douglas R.; Cooksey, Amanda M.; Coyne, Clarice; Dash, Sudhansu; Dickstein, Rebecca; Farmer, Andrew D.; Fernández‐Baca, David; Hokin, Samuel; Jones, Elizabeth S.; Kang, Yun; Monteros, Maria J.; Muñoz‐Amatriaín, María; Mysore, Kirankumar S.; Pislariu, Catalina I.; Richards, Chris; Shi, Ainong; Town, Christopher D.; Udvardi, Michael; von Wettberg, Eric Bishop; Young, Nevin D.; Zhao, Patrick X.

doi:10.1002/leg3.16

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

Journal Article · 23 November 2019 · Legume Science

DOI: https://doi.org/10.1002/leg3.16 · OSTI ID:1575321

Bauchet, Guillaume J. ^[1]; Bett, Kirstin E. ^[2]; Cameron, Connor T. ^[3]; Campbell, Jacqueline D. ^[4]; Cannon, Ethalinda K. S. ^[4];

^[5]; Carlson, Joseph W. ^[6]; Chan, Agnes ^[7]; Cleary, Alan ^[3]; Close, Timothy J. ^[8]; Cook, Douglas R. ^[9]; Cooksey, Amanda M. ^[10]; Coyne, Clarice ^[11]; Dash, Sudhansu ^[3]; Dickstein, Rebecca ^[12]; Farmer, Andrew D. ^[3]; Fernández‐Baca, David ^[4]; Hokin, Samuel ^[3]; Jones, Elizabeth S. ^[13]; Kang, Yun ^[14] more »

Boyce Thompson Institute Ithaca New York USA
Department of Plant Sciences University of Saskatchewan Saskatoon Saskatchewan Canada
National Center for Genome Resources Santa Fe New Mexico
Department of Computer Science Iowa State University Ames Iowa USA
USDA‐Agricultural Research Service, Corn Insects and Crop Genetics Research Unit Ames Iowa USA
Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley California USA
J. Craig Venter Institute Rockville Maryland
Department of Botany and Plant Sciences University of California Riverside California USA
Department of Plant Pathology University of California Davis Davis California USA
CyVerse, University of Arizona Tucson Arizona
USDA‐ARS Plant Germplasm Introduction and Testing Washington State University Pullman Washington USA
Department of Biological Sciences University of North Texas Denton Texas
Institute of Biotechnology, Cornell University Ithaca New York USA
Noble Research Institute LLC Ardmore Oklahoma
Department of Soil and Crop Sciences Colorado State University Fort Collins Colorado
Department of Biology Texas Woman's University Denton Texas
USDA‐ARS National Center for Genetic Resources Preservation Fort Collins Colorado
Department of Horticulture University of Arkansas Fayetteville Arkansas
Department of Plant and Soil Science University of Vermont Burlington Vermont
Department of Plant Pathology University of Minnesota St. Paul Minnesota

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 datasets, 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.

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

OSTI ID:: 1575321

Journal Information:: Legume Science, Journal Name: Legume Science Journal Issue: 1 Vol. 1; ISSN 2639-6181

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: Country unknown/Code not available

Language:: English

References (88)

Adaptation in plant genomes: Bigger is different Mei, Wenbin; Stetter, Markus G.; Gates, Daniel J. American Journal of Botany, Vol. 105, Issue 1 https://doi.org/10.1002/ajb2.1002	journal	January 2018
De novo assembly of a Chinese soybean genome Shen, Yanting; Liu, Jing; Geng, Haiying Science China Life Sciences, Vol. 61, Issue 8 https://doi.org/10.1007/s11427-018-9360-0	journal	July 2018
The Mycorrhizal Fungus, Sebacina vermifera, Enhances Seed Germination and Biomass Production in Switchgrass (Panicum virgatum L) Ghimire, Sita R.; Charlton, Nikki D.; Craven, Kelly D. BioEnergy Research, Vol. 2, Issue 1-2 https://doi.org/10.1007/s12155-009-9033-2	journal	April 2009
Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing Denyer, Tom; Ma, Xiaoli; Klesen, Simon Developmental Cell, Vol. 48, Issue 6 https://doi.org/10.1016/j.devcel.2019.02.022	journal	March 2019
Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement Chen, Xiaoping; Lu, Qing; Liu, Hao Molecular Plant, Vol. 12, Issue 7 https://doi.org/10.1016/j.molp.2019.03.005	journal	July 2019
Copy Number Variation in Domestication Lye, Zoe N.; Purugganan, Michael D. Trends in Plant Science, Vol. 24, Issue 4 https://doi.org/10.1016/j.tplants.2019.01.003	journal	April 2019
Genome sequence of the palaeopolyploid soybean Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica Nature, Vol. 463, Issue 7278 https://doi.org/10.1038/nature08670	journal	January 2010
The Medicago genome provides insight into the evolution of rhizobial symbioses Young, Nevin D.; Debellé, Frédéric; Oldroyd, Giles E. D. Nature, Vol. 480, Issue 7378 https://doi.org/10.1038/nature10625	journal	November 2011
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers Varshney, Rajeev K.; Chen, Wenbin; Li, Yupeng Nature Biotechnology, Vol. 30, Issue 1 https://doi.org/10.1038/nbt.2022	journal	November 2011
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement Varshney, Rajeev K.; Song, Chi; Saxena, Rachit K. Nature Biotechnology, Vol. 31, Issue 3 https://doi.org/10.1038/nbt.2491	journal	January 2013
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits Li, Ying-hui; Zhou, Guangyu; Ma, Jianxin Nature Biotechnology, Vol. 32, Issue 10 https://doi.org/10.1038/nbt.2979	journal	September 2014
Genome sequence of mungbean and insights into evolution within Vigna species Kang, Yang Jae; Kim, Sue K.; Kim, Moon Young Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6443	journal	November 2014
A reference genome for common bean and genome-wide analysis of dual domestications Schmutz, Jeremy; McClean, Phillip E.; Mamidi, Sujan Nature Genetics, Vol. 46, Issue 7 https://doi.org/10.1038/ng.3008	journal	June 2014
The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut Bertioli, David John; Cannon, Steven B.; Froenicke, Lutz Nature Genetics, Vol. 48, Issue 4 https://doi.org/10.1038/ng.3517	journal	February 2016
Graphtyper enables population-scale genotyping using pangenome graphs Eggertsson, Hannes P.; Jonsson, Hakon; Kristmundsdottir, Snaedis Nature Genetics, Vol. 49, Issue 11 https://doi.org/10.1038/ng.3964	journal	September 2017
Minimum information about a microarray experiment (MIAME)—toward standards for microarray data Brazma, Alvis; Hingamp, Pascal; Quackenbush, John Nature Genetics, Vol. 29, Issue 4 https://doi.org/10.1038/ng1201-365	journal	December 2001
An imputation platform to enhance integration of rice genetic resources Wang, Diane R.; Agosto-Pérez, Francisco J.; Chebotarov, Dmytro Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05538-1	journal	August 2018
A reference-grade wild soybean genome Xie, Min; Chung, Claire Yik-Lok; Li, Man-Wah Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09142-9	journal	March 2019
Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor Zhao, Jiantao; Sauvage, Christopher; Zhao, Jinghua Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09462-w	journal	April 2019
Whole-genome landscape of Medicago truncatula symbiotic genes Pecrix, Yann; Staton, S. Evan; Sallet, Erika Nature Plants, Vol. 4, Issue 12 https://doi.org/10.1038/s41477-018-0286-7	journal	November 2018
Genebank genomics highlights the diversity of a global barley collection Milner, Sara G.; Jost, Matthias; Taketa, Shin Nature Genetics, Vol. 51, Issue 2 https://doi.org/10.1038/s41588-018-0266-x	journal	November 2018
The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication Zhuang, Weijian; Chen, Hua; Yang, Meng Nature Genetics, Vol. 51, Issue 5 https://doi.org/10.1038/s41588-019-0402-2	journal	May 2019
The genome sequence of segmental allotetraploid peanut Arachis hypogaea Bertioli, David J.; Jenkins, Jerry; Clevenger, Josh Nature Genetics, Vol. 51, Issue 5 https://doi.org/10.1038/s41588-019-0405-z	journal	May 2019
The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor Gao, Lei; Gonda, Itay; Sun, Honghe Nature Genetics, Vol. 51, Issue 6 https://doi.org/10.1038/s41588-019-0410-2	journal	May 2019
A reference genome for pea provides insight into legume genome evolution Kreplak, Jonathan; Madoui, Mohammed-Amin; Cápal, Petr Nature Genetics, Vol. 51, Issue 9 https://doi.org/10.1038/s41588-019-0480-1	journal	September 2019
A draft genome for Spatholobus suberectus Qin, Shuangshuang; Wu, Lingqing; Wei, Kunhua Scientific Data, Vol. 6, Issue 1 https://doi.org/10.1038/s41597-019-0110-x	journal	July 2019
The FAIR Guiding Principles for scientific data management and stewardship Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan Scientific Data, Vol. 3, Issue 1 https://doi.org/10.1038/sdata.2016.18	journal	March 2016
Draft genome sequence of adzuki bean, Vigna angularis Kang, Yang Jae; Satyawan, Dani; Shim, Sangrea Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep08069	journal	January 2015
An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.) Parween, Sabiha; Nawaz, Kashif; Roy, Riti Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep12806	journal	August 2015
The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome Sakai, Hiroaki; Naito, Ken; Ogiso-Tanaka, Eri Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep16780	journal	November 2015
Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement De Vega, Jose J.; Ayling, Sarah; Hegarty, Matthew Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep17394	journal	November 2015
Draft genome sequence of subterranean clover, a reference for genus Trifolium Hirakawa, Hideki; Kaur, Parwinder; Shirasawa, Kenta Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep30358	journal	August 2016
Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome Kim, M. Y.; Lee, S.; Van, K. Proceedings of the National Academy of Sciences, Vol. 107, Issue 51 https://doi.org/10.1073/pnas.1009526107	journal	December 2010
Genome sequencing of adzuki bean ( Vigna angularis ) provides insight into high starch and low fat accumulation and domestication Yang, Kai; Tian, Zhixi; Chen, Chunhai Proceedings of the National Academy of Sciences, Vol. 112, Issue 43 https://doi.org/10.1073/pnas.1420949112	journal	October 2015
Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria Greenlon, Alex; Chang, Peter L.; Damtew, Zehara Mohammed Proceedings of the National Academy of Sciences, Vol. 116, Issue 30 https://doi.org/10.1073/pnas.1900056116	journal	July 2019
Legume Crops Phylogeny and Genetic Diversity for Science and Breeding Smýkal, Petr; Coyne, Clarice J.; Ambrose, Mike J. Critical Reviews in Plant Sciences, Vol. 34, Issue 1-3 https://doi.org/10.1080/07352689.2014.897904	journal	October 2014
Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA) Leebens-Mack, Jim; Vision, Todd; Brenner, Eric OMICS: A Journal of Integrative Biology, Vol. 10, Issue 2 https://doi.org/10.1089/omi.2006.10.231	journal	June 2006
Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature Shrestha, Rosemary; Arnaud, Elizabeth; Mauleon, Ramil AoB PLANTS, Vol. 2010 https://doi.org/10.1093/aobpla/plq008	journal	May 2010
Flapjack--graphical genotype visualization Milne, I.; Shaw, P.; Stephen, G. Bioinformatics, Vol. 26, Issue 24 https://doi.org/10.1093/bioinformatics/btq580	journal	October 2010
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data Smith, Richard N.; Aleksic, Jelena; Butano, Daniela Bioinformatics, Vol. 28, Issue 23 https://doi.org/10.1093/bioinformatics/bts577	journal	September 2012
Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny Cleary, Alan; Farmer, Andrew Bioinformatics, Vol. 34, Issue 9 https://doi.org/10.1093/bioinformatics/btx757	journal	November 2017
BrAPI—an application programming interface for plant breeding applications Selby, Peter; Abbeloos, Rafael; Backlund, Jan Erik Bioinformatics, Vol. 35, Issue 20 https://doi.org/10.1093/bioinformatics/btz190	journal	March 2019
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture Harper, Lisa; Campbell, Jacqueline; Cannon, Ethalinda K. S. Database, Vol. 2018 https://doi.org/10.1093/database/bay088	journal	January 2018
Genome Structure of the Legume, Lotus japonicus Sato, S.; Nakamura, Y.; Kaneko, T. DNA Research, Vol. 15, Issue 4 https://doi.org/10.1093/dnares/dsn008	journal	May 2008
The draft genomes of five agriculturally important African orphan crops Chang, Yue; Liu, Huan; Liu, Min GigaScience, Vol. 8, Issue 3 https://doi.org/10.1093/gigascience/giy152	journal	December 2018
OptiMAS: A Decision Support Tool for Marker-Assisted Assembly of Diverse Alleles Valente, Fabio; Gauthier, Franck; Bardol, Nicolas Journal of Heredity, Vol. 104, Issue 4 https://doi.org/10.1093/jhered/est020	journal	January 2013
Towards recommendations for metadata and data handling in plant phenotyping Krajewski, Paweł; Chen, Dijun; Ćwiek, Hanna Journal of Experimental Botany, Vol. 66, Issue 18 https://doi.org/10.1093/jxb/erv271	journal	June 2015
Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes Cannon, Steven B.; McKain, Michael R.; Harkess, Alex Molecular Biology and Evolution, Vol. 32, Issue 1 https://doi.org/10.1093/molbev/msu296	journal	October 2014
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics Waterhouse, Robert M.; Seppey, Mathieu; Simão, Felipe A. Molecular Biology and Evolution, Vol. 35, Issue 3 https://doi.org/10.1093/molbev/msx319	journal	December 2017
The Sol Genomics Network (SGN)—from genotype to phenotype to breeding Fernandez-Pozo, Noe; Menda, Naama; Edwards, Jeremy D. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1195	journal	November 2014
InterMine: extensive web services for modern biology Kalderimis, Alex; Lyne, Rachel; Butano, Daniela Nucleic Acids Research, Vol. 42, Issue W1 https://doi.org/10.1093/nar/gku301	journal	April 2014
AraPheno: a public database for Arabidopsis thaliana phenotypes Seren, Ümit; Grimm, Dominik; Fitz, Joffrey Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw986	journal	October 2016
The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog Togninalli, Matteo; Seren, Ümit; Meng, Dazhe Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx954	journal	October 2017
Legumes as a Model Plant Family. Genomics for Food and Feed Report of the Cross-Legume Advances through Genomics Conference Gepts, Paul; Beavis, William D.; Brummer, E. Charles Plant Physiology, Vol. 137, Issue 4 https://doi.org/10.1104/pp.105.060871	journal	April 2005
Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform Van Bel, Michiel; Proost, Sebastian; Wischnitzki, Elisabeth Plant Physiology, Vol. 158, Issue 2 https://doi.org/10.1104/pp.111.189514	journal	December 2011
Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform Wang, Jinpeng; Sun, Pengchuan; Li, Yuxian Plant Physiology, Vol. 174, Issue 1 https://doi.org/10.1104/pp.16.01981	journal	March 2017
Genome-Wide Identification of Medicago Peptides Involved in Macronutrient Responses and Nodulation de Bang, Thomas C.; Lundquist, Peter K.; Dai, Xinbin Plant Physiology, Vol. 175, Issue 4 https://doi.org/10.1104/pp.17.01096	journal	October 2017
Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells Ryu, Kook Hui; Huang, Ling; Kang, Hyun Min Plant Physiology, Vol. 179, Issue 4 https://doi.org/10.1104/pp.18.01482	journal	February 2019
Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences Veeckman, Elisabeth; Ruttink, Tom; Vandepoele, Klaas The Plant Cell, Vol. 28, Issue 8 https://doi.org/10.1105/tpc.16.00349	journal	August 2016
easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies Grimm, Dominik G.; Roqueiro, Damian; Salomé, Patrice A. The Plant Cell, Vol. 29, Issue 1 https://doi.org/10.1105/tpc.16.00551	journal	December 2016
Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover Griffiths, Andrew G.; Moraga, Roger; Tausen, Marni The Plant Cell, Vol. 31, Issue 7 https://doi.org/10.1105/tpc.18.00606	journal	April 2019
Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana Jean-Baptiste, Ken; McFaline-Figueroa, José L.; Alexandre, Cristina M. The Plant Cell, Vol. 31, Issue 5 https://doi.org/10.1105/tpc.18.00785	journal	March 2019
Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants Silverstein, Kevin A. T.; Moskal, William A.; Wu, Hank C. The Plant Journal, Vol. 51, Issue 2 https://doi.org/10.1111/j.1365-313X.2007.03136.x	journal	June 2007
Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops: Tansley review Meyer, Rachel S.; DuVal, Ashley E.; Jensen, Helen R. New Phytologist, Vol. 196, Issue 1 https://doi.org/10.1111/j.1469-8137.2012.04253.x	journal	August 2012
Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species Ren, Longhui; Huang, Wei; Cannon, Steven B. New Phytologist, Vol. 223, Issue 4 https://doi.org/10.1111/nph.15770	journal	March 2019
A comprehensive draft genome sequence for lupin ( Lupinus angustifolius ), an emerging health food: insights into plant-microbe interactions and legume evolution Hane, James K.; Ming, Yao; Kamphuis, Lars G. Plant Biotechnology Journal, Vol. 15, Issue 3 https://doi.org/10.1111/pbi.12615	journal	September 2016
Rapid generation cycling of an F ₂ population derived from a cross between Lens culinaris Medik. and Lens ervoides (Brign.) Grande after aphanomyces root rot selection Lulsdorf, Monika M.; Banniza, Sabine Plant Breeding, Vol. 137, Issue 4 https://doi.org/10.1111/pbr.12612	journal	June 2018
Assembly and annotation of a draft genome sequence for Glycine latifolia , a perennial wild relative of soybean Liu, Qiong; Chang, Sungyul; Hartman, Glen L. The Plant Journal, Vol. 95, Issue 1 https://doi.org/10.1111/tpj.13931	journal	May 2018
The genome of cowpea ( Vigna unguiculata [L.] Walp.) Lonardi, Stefano; Muñoz‐Amatriaín, María; Liang, Qihua The Plant Journal, Vol. 98, Issue 5 https://doi.org/10.1111/tpj.14349	journal	March 2019
Construction and comparison of three reference‐quality genome assemblies for soybean Valliyodan, Babu; Cannon, Steven B.; Bayer, Philipp E. The Plant Journal, Vol. 100, Issue 5 https://doi.org/10.1111/tpj.14500	journal	October 2019
Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean Cook, D. E.; Lee, T. G.; Guo, X. Science, Vol. 338, Issue 6111 https://doi.org/10.1126/science.1228746	journal	October 2012
Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis Griesmann, Maximilian; Chang, Yue; Liu, Xin Science https://doi.org/10.1126/science.aat1743	journal	May 2018
The Glycine max cv. Enrei Genome for Improvement of Japanese Soybean Cultivars Shimomura, Michihiko; Kanamori, Hiroyuki; Komatsu, Setsuko International Journal of Genomics, Vol. 2015 https://doi.org/10.1155/2015/358127	journal	January 2015
Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application) Zhou, Peng; Silverstein, Kevin AT; Gao, Liangliang BMC Bioinformatics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2105-14-335	journal	January 2013
An improved genome release (version Mt4.0) for the model legume Medicago truncatula Tang, Haibao; Krishnakumar, Vivek; Bidwell, Shelby BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-312	journal	January 2014
solGS: a web-based tool for genomic selection Tecle, Isaak Y.; Edwards, Jeremy D.; Menda, Naama BMC Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1186/s12859-014-0398-7	journal	December 2014
Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes Zhou, Peng; Silverstein, Kevin A. T.; Ramaraj, Thiruvarangan BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-3654-1	journal	March 2017
Measures for interoperability of phenotypic data: minimum information requirements and formatting Ćwiek-Kupczyńska, Hanna; Altmann, Thomas; Arend, Daniel Plant Methods, Vol. 12, Issue 1 https://doi.org/10.1186/s13007-016-0144-4	journal	November 2016
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes Vlasova, Anna; Capella-Gutiérrez, Salvador; Rendón-Anaya, Martha Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-0883-6	journal	February 2016
Next-generation genome annotation: we still struggle to get it right Salzberg, Steven L. Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1715-2	journal	May 2019
Gigwa—Genotype investigator for genome-wide analyses Sempéré, Guilhem; Philippe, Florian; Dereeper, Alexis GigaScience, Vol. 5, Issue 1 https://doi.org/10.1186/s13742-016-0131-8	journal	June 2016
A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny – The Legume Phylogeny Working Group (LPWG) Azani, Nasim; Babineau, Marielle; Bailey, C. Donovan Taxon, Vol. 66, Issue 1 https://doi.org/10.12705/661.3	journal	February 2017
Research priorities for harnessing plant microbiomes in sustainable agriculture Busby, Posy E.; Soman, Chinmay; Wagner, Maggie R. PLOS Biology, Vol. 15, Issue 3 https://doi.org/10.1371/journal.pbio.2001793	journal	March 2017
Fingerprinting Soybean Germplasm and Its Utility in Genomic Research Song, Qijian; Hyten, David L.; Jia, Gaofeng G3: Genes\|Genomes\|Genetics, Vol. 5, Issue 10 https://doi.org/10.1534/g3.115.019000	journal	July 2015
Field Book: An Open-Source Application for Field Data Collection on Android Rife, Trevor W.; Poland, Jesse A. Crop Science, Vol. 54, Issue 4 https://doi.org/10.2135/cropsci2013.08.0579	journal	January 2014
Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family Stai, Jacob S.; Yadav, Akshay; Sinou, Carole Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00345	journal	April 2019
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species Walls, Ramona L.; Cooper, Laurel; Elser, Justin Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00631	journal	June 2019
The Impact of Genetic Changes during Crop Domestication on Healthy Food Development Smýkal, Petr; Nelson, Matthew; Berger, Jens Agronomy, Vol. 8, Issue 3 https://doi.org/10.3390/agronomy8030026	journal	March 2018

Similar Records

LungMAP Portal Ecosystem: Systems-level Exploration of the Lung

Journal Article · 2022 · American Journal of Respiratory Cell and Molecular Biology · OSTI ID:2439995

Gaddis, Nathan; Fortriede, Joshua; Guo, Minzhe; +32 more

Reviews and syntheses: The promise of big diverse soil data, moving current practices towards future potential

Journal Article · 2022 · Biogeosciences (Online) · OSTI ID:1878417

Todd-Brown, Katherine E. O.; Abramoff, Rose Z.; Beem-Miller, Jeffrey; +21 more

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies

Journal Article · 2022 · Database · OSTI ID:1994344

Matentzoglu, Nicolas; Goutte-Gattat, Damien; Tan, Shawn Kai; +24 more

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

Citation Formats

References (88)

Similar Records

Related Subjects