You are here: Home
/ Publication Information
Title: Length polymorphism scanning is an efficient approach for revealing chloroplast DNA variation.
Author: Horning, Matthew E.; Cronn, Richard C.;
Source: Genome. 49: 134-142
Publication Series: Miscellaneous Publication
Description: Phylogeographic and population genetic screens of chloroplast DNA (cpDNA) provide insights into seedbased gene flow in angiosperms, yet studies are frequently hampered by the low mutation rate of this genome. Detection methods for intraspecific variation can be either direct (DNA sequencing) or indirect (PCR-RFLP), although no single method incorporates the best features of both approaches. We show that screening universal chloroplast amplicons for length polymorphism provides an accurate and efficient method for identifying cpDNA variation. By sequencing 4500 bp of cpDNA from 17 accessions of Purshia tridentata (bitterbrush), we detected 9 haplotypes, 8 of which were identifiable by unique multilocus length combinations resolvable by automated fragment analysis. In silico estimates of PCR-RFLP for these loci show that 5 haplotypes would be resolved by agarose electrophoresis. A survey of 4 intraspecific data sets from diverse angiosperms revealed that length variation in cpDNA amplicons is nearly ubiquitous, and 61 of 67 haplotypes identified by direct sequencing could be identified by screening length variation. Combined with automated fluorescent detection, length polymorphism screening of universal cpDNA regions offers a simple screen for intraspecific variation that can be used across angiosperms with minimal optimization, providing detection limits that rival direct sequencing at a fraction of the cost.
Keywords: cpDNA, intraspecific polymorphism, population genetics, phylogeography, indels
- We recommend that you also print this page and attach it to the printout of the article, to retain the full citation information.
- This article was written and prepared by U.S. Government employees on official time, and is therefore in the public domain.
- You may send email to email@example.com to request a hard copy of this publication. (Please specify exactly
which publication you are requesting and your mailing address.)
XML: View XML
Horning, Matthew E.; Cronn, Richard C. 2006. Length polymorphism scanning is an efficient approach for revealing chloroplast DNA variation. Genome. 49: 134-142
Get the latest version of the Adobe Acrobat reader or Acrobat Reader for Windows with Search and Accessibility