1. bookVolume 69 (2020): Issue 1 (January 2020)
Journal Details
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Format
Journal
eISSN
2509-8934
First Published
22 Feb 2016
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1 time per year
Languages
English
Open Access

Development of novel Quercus rubra chloroplast genome CAPS markers for haplotype identification

Published Online: 20 Aug 2020
Volume & Issue: Volume 69 (2020) - Issue 1 (January 2020)
Page range: 78 - 85
Journal Details
License
Format
Journal
eISSN
2509-8934
First Published
22 Feb 2016
Publication timeframe
1 time per year
Languages
English
Abstract

Our main objective was to generate cost-effective chloroplast (cp) DNA markers that are easy to apply and to score. In combination with already published cpSSR markers they should increase haplotype resolution in populations. To discover new cpDNA markers, we sequenced 87-97 % of the entire chloroplast genome (except the second inverted repeat) of 8 trees representing different regions of the Quercus rubra L. natural range with 4,030X-6,297X coverage and assembled the genome sequences using the publicly available chloroplast genome of Quercus rubra L. as a reference. In total, 118 single nucleotide polymorphisms (SNPs) and 107 insertions or deletions (indels) were detected, and 15 cleaved amplified polymorphic sequence (CAPS) markers were developed for Q. rubra. Using these new markers together with five chloroplast microsatellite or simple sequence repeat (cpSSR) markers, we identified 10 haplotypes in our diversity panel of 19 Q. rubra populations. Specifically, two haplotypes based only on the cpSSR markers could now be separated in five haplotypes. These markers are useful to assess haplotype diversity with high resolution and are also transferable to a closely related species, Quercus ellipsoidalis E. J. Hill.

Keywords

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