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

Joseph Crawford, Patrick J. Brown, Thomas Voigt, D. K. Lee

Research output: Contribution to journalArticlepeer-review


Prairie cordgrass (Spartina pectinata Link) is a polyploid Chloridoid grass with tetraploid (2n = 40), hexaploid (2n = 60), and octoploid (2n = 80) cytotypes and is a potential dedicated energy crop with promising yields in marginal environments. Efforts to breed prairie cordgrass are currently hampered by the lack of a linkage map, the lack of a Chloridoid reference genome, and the lack of information on inheritance patterns (disomic versus polysomic). Genotyping-by-sequencing (GBS) was applied to a population of 85 progenies 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 3034 single-dose, high-coverage SNPs was used for pseudo-testcross mapping with 63 progenies, resulting in two parental maps of 20 linkage groups containing 1522 and 1016 SNPs and a nearly 1:1 ratio of coupling to repulsion phase linkages, again suggesting disomic inheritance. Genomic contigs from tef, another Chloridoid grass, were used as a bridge to associate genetic markers in prairie cordgrass with unique positions in the sorghum genome, providing a glimpse into synteny between Chloridoids and other grasses. GBS enabled rapid generation of a linkage map that will aid in future breeding and genomics efforts in prairie cordgrass.

Original languageEnglish (US)
Article number62
JournalMolecular Breeding
Issue number5
StatePublished - May 1 2016


  • Allopolyploidy
  • Autopolyploidy
  • Disomic inheritance
  • Genotyping-by-sequencing (GBS)
  • Linkage mapping
  • Polyploidy
  • Polysomic inheritance
  • Prairie cordgrass (Spartina pectinata)

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Agronomy and Crop Science
  • Genetics
  • Plant Science


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