1
|
Redsun S, Hokin S, Cameron CT, Cleary AM, Berendzen J, Dash S, Brown AV, Wilkey A, Campbell JD, Huang W, Kalberer SR, Weeks NT, Cannon SB, Farmer AD. Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources. Methods Mol Biol 2022; 2443:81-100. [PMID: 35037201 DOI: 10.1007/978-1-0716-2067-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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, that is, 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/syntelogs for known genes; determining gene expression patterns; accessing genomic datasets; 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 ), and projects of the Legume Federation ( https://legumefederation.org ).
Collapse
Affiliation(s)
- Sven Redsun
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Sam Hokin
- National Center for Genome Resources, Santa Fe, NM, USA
| | | | - Alan M Cleary
- National Center for Genome Resources, Santa Fe, NM, USA
| | | | - Sudhansu Dash
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Anne V Brown
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Andrew Wilkey
- ORISE, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Jacqueline D Campbell
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
- Department of Computer Science, Iowa State University, Ames, IA, USA
| | - Wei Huang
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Scott R Kalberer
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Nathan T Weeks
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA.
| | | |
Collapse
|
2
|
Brown AV, Grant D, Nelson RT. Using Crop Databases to Explore Phenotypes: From QTL to Candidate Genes. PLANTS 2021; 10:plants10112494. [PMID: 34834856 PMCID: PMC8626016 DOI: 10.3390/plants10112494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/08/2021] [Accepted: 11/13/2021] [Indexed: 11/16/2022]
Abstract
Seeds, especially those of certain grasses and legumes, provide the majority of the protein and carbohydrates for much of the world’s population. Therefore, improvements in seed quality and yield are important drivers for the development of new crop varieties to feed a growing population. Quantitative Trait Loci (QTL) have been identified for many biologically interesting and agronomically important traits, including many seed quality traits. QTL can help explain the genetic architecture of the traits and can also be used to incorporate traits into new crop cultivars during breeding. Despite the important contributions that QTL have made to basic studies and plant breeding, knowing the exact gene(s) conditioning each QTL would greatly improve our ability to study the underlying genetics, biochemistry and regulatory networks. The data sets needed for identifying these genes are increasingly available and often housed in species- or clade-specific genetics and genomics databases. In this demonstration, we present a generalized walkthrough of how such databases can be used in these studies using SoyBase, the USDA soybean Genetics and Genomics Database, as an example.
Collapse
Affiliation(s)
- Anne V. Brown
- United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA; (A.V.B.); (D.G.)
| | - David Grant
- United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA; (A.V.B.); (D.G.)
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Rex T. Nelson
- United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA; (A.V.B.); (D.G.)
- Correspondence: ; Tel.: +1-515-294-1297
| |
Collapse
|
3
|
Valliyodan B, Brown AV, Wang J, Patil G, Liu Y, Otyama PI, Nelson RT, Vuong T, Song Q, Musket TA, Wagner R, Marri P, Reddy S, Sessions A, Wu X, Grant D, Bayer PE, Roorkiwal M, Varshney RK, Liu X, Edwards D, Xu D, Joshi T, Cannon SB, Nguyen HT. Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Sci Data 2021; 8:50. [PMID: 33558550 PMCID: PMC7870887 DOI: 10.1038/s41597-021-00834-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/06/2021] [Indexed: 12/28/2022] Open
Abstract
We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.
Collapse
Affiliation(s)
- Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, MO, 65101, USA
| | - Anne V Brown
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Juexin Wang
- Department of Electrical Engineering and Computer Science, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Gunvant Patil
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Yang Liu
- MU Institute of Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
| | - Paul I Otyama
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Rex T Nelson
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Tri Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Qijian Song
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, 20705, USA
| | - Theresa A Musket
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Ruth Wagner
- Bayer CropScience, St. Louis, MO, 63141, USA
| | - Pradeep Marri
- Corteva Agriscience, Indianapolis, IN, 46268, USA
- Pairwise Plants LLC, Durham, NC, 27709, USA
| | - Sam Reddy
- Corteva Agriscience, Indianapolis, IN, 46268, USA
| | - Allen Sessions
- Bayer CropScience, Research Triangle Park, NC, 27709, USA
| | - Xiaolei Wu
- Bayer CropScience, Research Triangle Park, NC, 27709, USA
| | - David Grant
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Philipp E Bayer
- School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Xin Liu
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
- State Key Laboratory of Agricultural Genomics, China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- MU Institute of Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
| | - Trupti Joshi
- Department of Electrical Engineering and Computer Science, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- MU Institute of Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
- Department of Health Management and Informatics, University of Missouri, Columbia, MO, 65211, USA
| | - Steven B Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|