A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae).

ABSTRACT: 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. • 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. • 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 ar

SUBMITTER: Wofford AM 

PROVIDER: S-EPMC4103111 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature