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ARS Home » Pacific West Area » Logan, Utah » Forage and Range Research » Research » Publications at this Location » Publication #316096

Research Project: Develop Improved Plant Genetic Resources to Enhance Pasture and Rangeland Productivity in the Semiarid Regions of the Western U.S.

Location: Forage and Range Research

Title: Genotype by sequencing in autotetraploid cocksfoot (Dactylis glomerata) without a reference genome

Author
item Bushman, Shaun
item Robbins, Matthew
item Larson, Steven
item Staub, Jack

Submitted to: Eucarpia Fodder Crops and Amenity Grasses Section Symposium
Publication Type: Proceedings
Publication Acceptance Date: 5/20/2015
Publication Date: 9/13/2015
Citation: Bushman, B.S., Robbins, M.D., Larson, S.R., Staub, J.E. 2015. Genotype by sequencing in autotetraploid cocksfoot (Dactylis glomerata) without a reference genome. Eucarpia Fodder Crops and Amenity Grasses Section Symposium. Ghent, Belgium, Sept 13-17, 2015.

Interpretive Summary:

Technical Abstract: Quantitative trait locus mapping is often useful for understanding the number of effects and the direction of effects for traits in germplasm of interest. New genotype-by-sequencing (GBS) methods are available, but their application toward autopolyploid plants is limited. In this paper we discuss adapting semi-conductor sequencing to GBS of autotetraploid cocksfoot. We identified that no more than 48 plants should be included on an Ion Torrent P1 sequencing chip, and that the longer length of semi-conductor sequences can be mined for additional markers above those detected following Illumina-based bioinformatic pipelines. With a subset of plant from an F1 cocksfoot mapping population, most linkage groups were detectetd with high LOD probability. These data indicate successful implementation of existing GBS pipelines when using semi-conductor sequencing and on complex autotetraploid plants.