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

Abstract

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 reducedrepresentation sequencing approach by genotyping 231 F 1 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.

QTL and Drought Effects on Leaf Physiology in Lowland Panicum virgatum

“…The QTL on LG 1b co-localizes with QTL for base tiller width, internode width, and fourth leaf length and area that we detected in parallel experiments using ALB [49]. It was a result of segregating variation in Kanlow-K5, in a region of the genome that is covered by maps for both parents [42,47]. By contrast, the QTL we detected for LMA at 146 cM on LG 5b is novel, and segregation from Alamo-A4 was implicit in its location: in the original male and female maps for ALB that our map is derived from, no information was available for the Kanlow-K5 (female) parent beyond 84 cM of LG 5b [47].…”

“…By contrast, the QTL we detected for LMA at 146 cM on LG 5b is novel, and segregation from Alamo-A4 was implicit in its location: in the original male and female maps for ALB that our map is derived from, no information was available for the Kanlow-K5 (female) parent beyond 84 cM of LG 5b [47]. Interestingly, the tip of LG 5b is also not covered in the NF × GA map [56], more recent genotyping-by-sequencing maps for ALB [42] or a novel four-way cross that incorporates the Alamo-AP13 genotype as a male parent [45]. These results suggest that there may be a low level of polymorphism in the genome of cv.…”

“…Switchgrass breeding for bioenergy purposes is being facilitated by existing genetic resources and cutting-edge technologies for genomics and transgenics [12,41], including the development of genetic maps [42][43][44][45][46][47]. Quantitative trait loci (QTL) mapping is an important component of switchgrass improvement programs both because it identifies the native genetic variability available to breeders and because information from QTL studies can be utilized directly in markerassisted selection approaches.…”

The genetic and phenotypic variability of interspecific hybrid bermudagrasses (Cynodon dactylon (L.) Pers. × C. transvaalensis Burtt-Davy) used on golf course putting greens

“…Single nucleotide polymorphisms (SNPs) are mutations that occur between the genomes of related organisms, and are commonly used as molecular markers for genetic research (Fiedler et al 2015; Mammadov et al 2012; Vignal et al 2002; Wang et al 1998; Yang et al 2010). Genotyping-by-sequencing described by Elshire et al (2011) can produce thousands of SNPs, which may be more capable of elucidating differences among bermudagrass cultivars within the Tifgreen mutation family (Elshire et al 2011; Poland et al 2012; Poland and Rife 2012).…”

“…Genotyping-by-sequencing described by Elshire et al (2011) can produce thousands of SNPs, which may be more capable of elucidating differences among bermudagrass cultivars within the Tifgreen mutation family (Elshire et al 2011; Poland et al 2012; Poland and Rife 2012). Fiedler et al (2015) and Poland and Rife (2012) suggested that GBS offers the potential to identify sets of closely linked loci that contribute to phenotypic variation. The ability to connect phenotype to genotype is of great value to researchers to gain a better understanding of the development and progression of bermudagrass cultivars used on golf course putting greens.…”