Linkage mapping in prairie cordgrass (Spartina pectinata Link) using genotyping-by-sequencing markers

Global climate change from anthropogenic carbon emissions can be mitigated through the development of bioenergy systems. Bioenergy feedstocks tolerant of marginal land can reduce the tension between bioenergy production and food production. Prairie cordgrass (Spartina pectinata Link) is tolerant of poorly drained soils, saline soils, and low temperature. Prairie cordgrass (Spartina pectinata) is a polyploid Chloridoid grass with tetraploid (2n=4X=40), hexaploid (2n=6X=60), and octaploid (2n=8X=80) cytotypes, and is a potential dedicated energy crop with promising yields in marginal environments. Breeding efforts in prairie cordgrass are currently hampered by the lack of a linkage map, the lack of a Chloridoid reference genome, and by lack of information on inheritance patterns (disomic versus polysomic). Genotyping-by-sequencing (GBS) was applied to a population of 85 progeny from a reciprocal cross of heterozygous tetraploid parents. A total of 26,418 SNPs were discovered, with a distribution of allele frequencies suggesting disomic inheritance. A filtered set of 3,034 single-dose, high-coverage SNPs was used for pseudo-testcross mapping, resulting in two parental maps of 20 linkage groups containing 1,522 and 1,016 SNPs and a nearly 1:1 ratio of coupling to repulsion phase linkages, again suggesting disomic inheritance. Genomic contigs from tef (Eragrostis tef (Zucc.) Trotter), another Chloridoid grass, were used as a bridge to associate short prairie cordgrass reads with unique positions in the sorghum genome, providing a first glimpse into synteny between Chloridoids and other grasses. Genotyping-by-sequencing enabled rapid generation of a linkage map that will aid in future breeding and genomics efforts in prairie cordgrass