High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing

Fiedler, Jason D.; Lanzatella, Christina; Okada, Miki; Jenkins, Jerry; Schmutz, Jeremy; Tobias, Christian M.

doi:10.3835/plantgenome2014.10.0065

High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing

Journal Article · Wed Jul 01 00:00:00 EDT 2015 · The Plant Genome

DOI:https://doi.org/10.3835/plantgenome2014.10.0065· OSTI ID:1616040

Fiedler, Jason D. ^[1]; Lanzatella, Christina ^[1]; Okada, Miki ^[2]; Jenkins, Jerry ^[3]; Schmutz, Jeremy ^[3]; Tobias, Christian M. ^[1]

USDA-ARS, Albany, CA (United States)
Univ. of California, Davis, CA (United States)
HudsonAlpha Genome Sequencing Center, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Switchgrass (Panicum virgatum L.) is a warm-season perennial grass with promising potential as a 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 progeny of a cross between two parents of lowland ecotype from the cultivars Kanlow and Alamo. Over 350 million reads were generated and aligned, which enabled identification and ordering of 4611 high-quality SNPs. The total lengths of the resulting framework maps were 1770 cM for the Kanlow parent and 2059 cM for the Alamo parent. These maps show collinearity with maps generated with polymerase chain reaction (PCR)-based simple-sequence repeat (SSR) markers, and new SNP markers were identified in previously unpopulated regions of the genome. Transmission segregation distortion affected all linkage groups (LGs) to differing degrees, and ordering of distorted markers highlighted 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 of these linkage maps with a draft version of the switchgrass genome assembly demonstrated high levels of collinearity and provides greater confidence in the validity of both resources. This methodology has proven to be a rapid and cost-effective way to generate high-quality linkage maps of an outcrossing species.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDA-ARS

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1616040

Journal Information:: The Plant Genome, Journal Name: The Plant Genome Journal Issue: 2 Vol. 8; ISSN 1940-3372

Publisher:: Alliance of Crop, Soil, and Environmental Science SocietiesCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 1 of Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum Luo, Ying; Zhang, Xiujie; Xu, Jiahong figshare https://doi.org/10.6084/m9.figshare.12799267.v1	dataset	January 2020
Genotypic and phenotypic evaluation of off-type grasses in hybrid Bermudagrass [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] putting greens using genotyping-by-sequencing and morphological characterization Reasor, Eric H.; Brosnan, James T.; Staton, Margaret E. Hereditas, Vol. 155, Issue 1 https://doi.org/10.1186/s41065-017-0043-3	journal	August 2017
Genotypic and Phenotypic Evaluation of Off-Type Grasses in Hybrid Bermudagrass [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] Putting Greens using Genotyping-by-Sequencing and Morphological Characterization Reasor, Eric; Brosnan, Jim; Staton, Margaret figshare https://doi.org/10.6084/m9.figshare.5339656	text	January 2017
Genotypic and Phenotypic Evaluation of Off-Type Grasses in Hybrid Bermudagrass [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] Putting Greens using Genotyping-by-Sequencing and Morphological Characterization Reasor, Eric; Brosnan, Jim; Staton, Margaret figshare https://doi.org/10.6084/m9.figshare.5339656.v1	text	January 2017