Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes

Abstract

Switchgrass (Panicum virgatum L.) is a native perennial warm season (C 4 ) grass that has been identified as a promising species for bioenergy research and production. Consequently, biomass yield and feedstock quality improvements are high priorities for switchgrass research. The objective of this study was to develop a switchgrass genetic linkage map using a full-sib pseudo-testcross mapping population derived from a cross between two heterozygous genotypes selected from the lowland cultivar 'Alamo' (AP13) and the upland cultivar 'Summer' (VS16). The female parent (AP13) map consists of 515 loci in 18 linkage groups (LGs) and spans 1,733 cM. The male parent (VS16) map arranges 363 loci in 17LGs and spans 1,508 cM. No obvious cause for the lack of one LG in VS16 could be identified. Comparative analyses between the AP13 and VS16 maps showed that the two major ecotypic classes of switchgrass have highly colinear maps with similar recombination rates, suggesting that chromosomal exchange between the two ecotypes should be able to occur freely. The AP13 and VS16 maps are also highly similar with respect to marker orders and recombination levels to previously published switchgrass maps. The genetic maps will be used to identify quantitative trait loci associated with biomass and quality traits. The AP13 Desalegn Serba, Limin Wu, and Guillaume Daverdin contributed equally to the work. Bioenerg. Res. (2013) 6:953-965 DOI 10.1007 genotype was used for the whole genome-sequencing project and the map will thus also provide a tool for the anchoring of the switchgrass genome assembly. Electronic supplementary material

Senescence, dormancy and tillering in perennial C4 grasses

“…Parallel work on the genetics and genomics of switchgrass has resulted in a deeper understanding of genome organization, linkage groups, single nucleotide polymorphisms (SNPs) and molecular markers associated with specific linkage groups, for example: [118][119][120]. These studies along with conventional breeding efforts [34,111,121] portend rapid development of switchgrass germplasm for specific end uses.…”

Biofuels Get in the Fast Lane: Developments in Plant Feedstock Production and Processing

“…Notably, crosses between tetraploid upland and lowland switchgrass resulted in hybrid vigor and progeny displayed increase of biomass yields in the range of 30-60% pointing to exploiting heterosis for generating elite cultivars [211]. Recently a genetic linkage map was developed by crossing upland and lowland switchgrass ecotypes which will provide a complete switch grass map and enable the identification of quantitative trait loci associated with biomass quantity and quality characters as well as cold tolerance and abiotic stress traits [212]. At the level of specific gene targeting, efforts to reduce lignin content focused on the down regulation of the 4CL1, COMT and CAD genes that are involved in lignin biosynthesis [213][214][215] and the over expression of the R2R3-MYB transcription factor [216,217].…”

Comparative Relationships and Chromosome Evolution in Switchgrass (Panicum virgatum) and Its Genomic Model, Foxtail Millet (Setaria italica)

“…To enhance the breeding process, genetic maps have been developed for switchgrass [4][5][6][7][8], and its genome has been sequenced (www.phytozome.net). However, genetic analyses have been hampered by the complexity of the switchgrass genome.…”

“…It is also largely an obligate outcrossing species, and consequently, switchgrass genotypes are heterozygous at most loci. Most genetic maps published to date have been developed in pseudo-F1 populations resulting from crossing two heterozygous switchgrass genotypes [4][5][6]8]. The exception is the genetic map generated by Liu et al [7] who used an F2 population obtained by selfing a heterozygous self-compatible accession.…”

“…However, marker densities on the individual classically constructed switchgrass genetic maps are relatively low (average of 0.32 markers/cM) [5,6]. Recently, the Joint Genome Institute (JGI) has sequenced the progeny of the AP13×VS16 mapping population [6] and used this data combined with information from the assembly of the genome sequence of Panicum hallii, a close relative of P. virgatum, to order the switchgrass sequence contigs (assembly v1.1; www.phytozome.net). A consensus map integrating three published genetics maps could be used as an independent tool to validate the sequence-based map.…”