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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVED PLANT GENETIC RESOURCES FOR PASTURES AND RANGELANDS IN THE TEMPERATE SEMIARID REGIONS OF THE WESTERN U.S. Title: New Genomic Resources for Orchardgrass

Authors
item Robins, Joseph
item Bushman, Shaun
item Jensen, Kevin

Submitted to: Eucarpia Cucurbitaceae Symposium Proceedings
Publication Type: Proceedings
Publication Acceptance Date: August 20, 2007
Publication Date: August 1, 2008
Citation: Robins, J.G., Bushman, B.S., Jensen, K.B. 2008. New Genomic Resources for Orchardgrass. XXVIIth Eucarpia Symposium Proceedings on Improvement of Fodder Crops and Amenity Grasses. pp. 202-203. Copenhagen, Denmark.

Interpretive Summary: One of the initial requirements of utilizing genomic approaches in plant improvement is the availability of DNA sequence information. Toward the goal of generating sequence information for forage and pasture grasses, we are developing an EST library from orchardgrass, or cocksfoot (Dactylis glomerata). Tissues collected from orchardgrass included water and salt stressed shoot and roots, etiolated seedlings, and low temperature acclimated crowns. Library construction, sequencing, and bioinformatics are carried out through cooperation with the University of Illinois W.M. Keck Center for Comparative and Functional Genomics. The resulting EST library will be normalized, tagged for identification by tissue, and sequenced from both the 5' and 3' ends in order to include the 3' untranslated regions (UTR). SSRs identified from this library containing contigs/singletons will be aligned to rice chromosomes to determine predicted locations of the SSR markers. PCR primers designed from 3' UTR regions from other species contained high degrees of polymorphism, and the same is expected from this orchardgrass library. Additionally, the sequence data from the library will be used to identify SNPs. The USDA ARS Forage and Range Research Laboratory has an extensive orchardgrass improvement program, and our objective is to identify phenotypic associations and apply the markers to a marker-assisted selection program for increased salt tolerance and winter hardiness. Sequence information and resulting primers will be presented.

Technical Abstract: One of the initial requirements of utilizing genomic approaches in plant improvement is the availability of DNA sequence information. Toward the goal of generating sequence information for forage and pasture grasses, we are developing an EST library from orchardgrass, or cocksfoot (Dactylis glomerata). Tissues collected from orchardgrass included water and salt stressed shoot and roots, etiolated seedlings, and low temperature acclimated crowns. Library construction, sequencing, and bioinformatics are carried out through cooperation with the University of Illinois W.M. Keck Center for Comparative and Functional Genomics. The resulting EST library will be normalized, tagged for identification by tissue, and sequenced from both the 5' and 3' ends in order to include the 3' untranslated regions (UTR). SSRs identified from this library containing contigs/singletons will be aligned to rice chromosomes to determine predicted locations of the SSR markers. PCR primers designed from 3' UTR regions from other species contained high degrees of polymorphism, and the same is expected from this orchardgrass library. Additionally, the sequence data from the library will be used to identify SNPs. The USDA ARS Forage and Range Research Laboratory has an extensive orchardgrass improvement program, and our objective is to identify phenotypic associations and apply the markers to a marker-assisted selection program for increased salt tolerance and winter hardiness. Sequence information and resulting primers will be presented.

Last Modified: 10/26/2014
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