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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #311106
Title: High-density SNP linkage map of lowland Panicum virgatum L. (switchgrass) using genotyping by sequencing

Author
item Fiedler, Jason
item Lanzatella-Craig, Christina
item OKADA, MIKI - University Of California
item JENKINS, JERRY - Hudsonalpha Institute For Biotechnology
item SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology
item Tobias, Christian

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/15/2015
Publication Date: 3/16/2015
Citation: Fiedler, J.D., Lanzatella-Craig, C., Okada, M., Jenkins, J., Schmutz, J., Tobias, C.M. 2015. High-density SNP linkage map of lowland Panicum virgatum L. (switchgrass) using genotyping by sequencing. The Plant Genome. doi: 10.3835/plantgenome2014.10.0065.

Interpretive Summary: Switchgrass is a warm-season perennial grass with great potential to be a dedicated bioenergy crop in the United States. However, the lack of genomic resources has slowed the development of varieties with optimal characteristics for sustainable feedstock production. Here we present a high-density genetic linkage map from a population derived by crossing two different lowland switchgrass stocks. The map integrates novel Genotype-By-Sequencing (GBS) markers with traditional Polymerase Chain Reaction markers and can be aligned to the partially assembled physical map derived by sequencing the switchgrass genome. The GBS maps are more informative than previously published maps due to the increase in marker density, the inclusion of markers that are not transmitted efficiently to progeny, and the discovery of markers in regions not previously mapped. These maps and the protocols developed here will be utilized for further analysis of the genetic architecture underlying complex traits of switchgrass.

Technical Abstract: Switchgrass is a C4 warm-season perennial grass with great potential as a dedicated bioenergy crop in the United States. However, the lack of genomic resources has slowed the development of plant lines with optimal characteristics for sustainable feedstock production. We generated high-density single nucleotide polymorphism (SNP) linkage maps using a reduced representation sequencing approach by genotyping 231 F1 individuals of a Kanlow K5 x Alamo A4 cross, which are both high-yielding lowland cultivars. We generated a total of 350M reads and from these identified and mapped 4,100 SNPs with quality scores greater than 20. The total lengths of the resulting framework maps were 1770 cM for Kanlow K5 and 2059 cM for Alamo A4. These maps show collinearity with maps generated with traditional short sequence repeat markers and new markers were identified in previously unpopulated regions of the genome. Markers exhibiting transmission segregation distortion were present in all distorted linkage groups and ordering of distorted marker highlight several regions of unequal inheritance. Framework maps were adversely affected by the addition of distorted markers with varying severity, but distorted maps were of higher marker density and provided additional information for analysis. Alignment K5xA4 linkage maps with the early release draft genome assembly results in collinearity and provides an independent metric of map and assembly quality. This methodology has proven to be a rapid and cost effective way to generate high quality linkage maps of this outcrossing species.