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Bushman BS, Larson SR, Mott IW, Cliften PF, Wang RRC, Chatterton NJ, Hernandez AG, Ali S, Kim RW, Thimmapuram J, Gong G, Liu L, Mikel MA. Development and annotation of perennial Triticeae ESTs and SSR markers. Genome 2008; 51:779-88. [DOI: 10.1139/g08-062] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Triticeae contains hundreds of species of both annual and perennial types. Although substantial genomic tools are available for annual Triticeae cereals such as wheat and barley, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three expressed sequence tag (EST) libraries were developed and annotated for Pseudoroegneria spicata , a mixture of both Elymus wawawaiensis and E. lanceolatus , and a Leymus cinereus × L. triticoides interspecific hybrid. The ESTs were combined into unigene sets of 8 780 unigenes for P. spicata, 11 281 unigenes for Leymus, and 7 212 unigenes for Elymus. Unigenes were annotated based on putative orthology to genes from rice, wheat, barley, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Simple sequence repeat (SSR) markers were developed, tested for amplification and polymorphism, and aligned to the rice genome. Leymus EST markers homologous to rice chromosome 2 genes were syntenous on Leymus homeologous groups 6a and 6b (previously 1b), demonstrating promise for in silico comparative mapping. All ESTs and SSR markers are available on an EST information management and annotation database ( http://titan.biotec.uiuc.edu/triticeae/ ).
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Affiliation(s)
- B. Shaun Bushman
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Steve R. Larson
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ivan W. Mott
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paul F. Cliften
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Richard R.-C. Wang
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - N. Jerry Chatterton
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alvaro G. Hernandez
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shahjahan Ali
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ryan W. Kim
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jyothi Thimmapuram
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - George Gong
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lei Liu
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mark A. Mikel
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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