<abstract xmlns="http://www.w3.org/1999/xhtml"><p>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 <italic>Quercus rubra</italic> L. natural range with 4,030X-6,297X coverage and assembled the genome sequences using the publicly available chloroplast genome of <italic>Quercus rubra</italic> 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 <italic>Q. rubra</italic>. 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 <italic>Q. rubra</italic> 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, <italic>Quercus ellipsoidalis</italic> E. J. Hill.</p></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.

Development of novel <italic>Quercus rubra</italic> chloroplast genome CAPS markers for haplotype identification

Faculty of Forest Sciences and Forest Ecology, Department of Forest Genetics and Forest Tree Breeding

Laboratory of Forest Genomics, Genome Research and Education Center

N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences

Department of Ecosystem Science and Management

Silvae Genetica

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Development of novel  chloroplast genome CAPS markers for haplotype identification

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...

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

Published Online: Aug 20, 2020

Page range: 78 - 85

DOI: https://doi.org/10.2478/sg-2020-0011

Keywords
Quercus rubra, oak, chloroplast genome, sequencing, SNP, indel, CAPS, SSR

© 2020 Tim Pettenkofer et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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

Published Online: Aug 20, 2020

Page range: 78 - 85

DOI: https://doi.org/10.2478/sg-2020-0011

KeywordsQuercus rubra, oak, chloroplast genome, sequencing, SNP, indel, CAPS, SSR

© 2020 Tim Pettenkofer et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Keywords
Quercus rubra, oak, chloroplast genome, sequencing, SNP, indel, CAPS, SSR