A high-density simple sequence repeat-based genetic linkage map of switchgrass.

Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, Oklahoma 74078.
G3-Genes Genomes Genetics (Impact Factor: 2.51). 03/2012; 2(3):357-70. DOI: 10.1534/g3.111.001503
Source: PubMed

ABSTRACT Switchgrass (Panicum virgatum) has been identified as a promising cellulosic biofuel crop in the United States. Construction of a genetic linkage map is fundamental for switchgrass molecular breeding and the elucidation of its genetic mechanisms for economically important traits. In this study, a novel population consisting of 139 selfed progeny of a northern lowland genotype, NL 94 LYE 16X13, was used to construct a linkage map. A total of 2493 simple sequence repeat markers were screened for polymorphism. Of 506 polymorphic loci, 80.8% showed a goodness-of-fit of 1:2:1 segregation ratio. Among 469 linked loci on the framework map, 241 coupling vs. 228 repulsion phase linkages were detected that conformed to a 1:1 ratio, confirming disomic inheritance. A total of 499 loci were mapped to 18 linkage groups (LG), of which the cumulative length was 2085.2 cM, with an average marker interval of 4.2 cM. Nine homeologous LG pairs were identified based on multi-allele markers and comparative genomic analysis. Two clusters of segregation-distorted loci were identified on LG 5b and 9b, respectively. Comparative analysis indicated a one-to-one relationship between nine switchgrass homeologous groups and nine foxtail millet (Setaria italica) chromosomes, suggesting strong homology between the two species. The linkage map derived from selfing a heterozygous parent, instead of two separate maps usually constructed for a cross-fertilized species, provides a new genetic framework to facilitate genomics research, quantitative trait locus (QTL) mapping, and marker-assisted breeding.


Available from: Yunwen Wang, Oct 06, 2014
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    ABSTRACT: Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America and has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation including ploidy is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes, with significant repetitive sequence content limiting the efficiency of re-sequencing approaches for determining genome diversity. To characterize genetic diversity in upland and lowland switchgrass as a first step in linking genotype to phenotype, we designed an exome capture probe set based on transcript assemblies that represent ~50 Mb of annotated switchgrass exome sequences. We then evaluated and optimized the probe set using solid phase comparative genome hybridization and liquid phase exome capture followed by next generation sequencing. Using the optimized probe set, we assessed variation in the exomes of eight switchgrass genotypes representing tetraploid lowland and octoploid upland cultivars to benchmark our exome capture probe set design. We identified ample variation in the switchgrass genome including 1,395,501 single nucleotide polymorphisms (SNPs), 8,173 putative copy number variants and 3,336 presence/absence variants. While the majority of the SNPs (84%) detected were biallelic, a substantial number were tri-allelic with limited occurrence of tetra-allelic polymorphisms consistent with the heterozygous and polyploid nature of the switchgrass genome. Collectively, these data demonstrate the efficacy of exome capture for discovery of genome variation in a polyploid species with a large, repetitive and heterozygous genome. This article is protected by copyright. All rights reserved.
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    ABSTRACT: Switchgrass has long been characterized as an outcrossing species. However, mating behavior of plants in populations grown in the field allowing open pollination has not been documented. Accordingly, the objectives of this study were to determine the fertilization mode (i.e., selfing vs. outcrossing) of two self-compatible plants and to assess the mating behavior variability of lowland switchgrass genotypes in populations under field conditions. In Experiment I, two self-compatible genotypes ‘NL94 LYE 16 × 13’ and ‘SL93 7 × 15’ along with two populations were planted with two replications on the OSU Agronomy Research Farm, Stillwater, OK. Sixty-four progeny derived from half-sib seeds of each genotype per replication per year were genotyped with 4 to 20 simple sequence repeat (SSR) markers. In both 2010 and 2011, all progeny plants of the two parents were completely outcrossed exhibiting 100 % self-incompatibility. In Experiment II, two genetically narrow-based (NL94 C2-3 and SL93 C2-3), each having five parents, and two broad-based (NL94 C3 and SL93 C3), each comprising 26 parents, switchgrass populations with three replications were field established at the OSU Cimarron Valley Research Station, Perkins, OK. The DNA samples were isolated from 1700 open-pollinated progeny of 62 seed parents in 2010 and 773 progeny of 42 parents in 2011. Among all the progeny genotyped with eight to 16 SSR markers, only one was identified as a selfed progeny, indicating very little variability in outcrossing behavior under the field conditions. The identification of specific genotypes like NL94 LYE 16 × 13 and SL93 7 × 15 which are self-incompatible in the open field but self-compatible under the controlled conditions potentially enables efficient production of F1 hybrid seed in switchgrass.
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