title: A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae).
abstract: OBJECTIVE
  Recently released Pinus plastome sequences support characterization of 15 plastid simple sequence repeat (cpSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. •
  
  
  METHODS
  Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compared interspecific variation between cpSSRs and nucleotide sequences of ycf1 and tested intraspecific variation for cpSSRs using 911 samples in the P. ponderosa species complex. •
  
  
  RESULTS
  The cpSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions, and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. •
  
  
  CONCLUSIONS
  The protocol allows efficient genotyping of many samples. The cpSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for cpSSR loci in a plastome alignment for the target group.
authors.affiliation: Department of Biology, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032 USA.
authors.forename: Austin M
authors.initials: AM
authors.lastname: Wofford
authors.affiliation: Department of Biology, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032 USA.
authors.forename: Kristen
authors.initials: K
authors.lastname: Finch
authors.affiliation: Department of Biology, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032 USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Bigott
authors.affiliation: Department of Biology, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032 USA.
authors.forename: Ann
authors.initials: A
authors.lastname: Willyard
keywords: Pinus; discriminant analysis of principal components; intraspecific taxonomy; microsatellites; plastid