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

Описание

Тип публикации: статья из журнала

Год издания: 2020

Идентификатор DOI: 10.2478/sg-2020-0011

Ключевые слова: quercus rubra, oak, chloroplast genome, sequencing, snp, indel, caps, ssr

Аннотация: 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 invПоказать полностьюerted 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.

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Издание

Журнал: SILVAE GENETICA

Выпуск журнала: Vol. 69, Is. 1

Номера страниц: 78-85

ISSN журнала: 00375349

Место издания: WARSAW

Издатель: SCIENDO

Авторы

  • Pettenkofer Tim (Univ Gottingen, Fac Forest Sci & Forest Ecol, Dept Forest Genet & Forest Tree Breeding, Busgenweg 2, D-37077 Gottingen, Germany)
  • Finkeldey Reiner (Univ Kassel, Monchebergstr 19, D-34125 Kassel, Germany)
  • Mueller Markus (Univ Gottingen, Fac Forest Sci & Forest Ecol, Dept Forest Genet & Forest Tree Breeding, Busgenweg 2, D-37077 Gottingen, Germany)
  • Krutovsky Konstantin (Univ Gottingen, Fac Forest Sci & Forest Ecol, Dept Forest Genet & Forest Tree Breeding, Busgenweg 2, D-37077 Gottingen, Germany; Georg August Univ Gottingen, Ctr Integrated Breeding Res, Gottingen, Germany; Siberian Fed Univ, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia; Russian Acad Sci, NI Vavilov Inst Gen Genet, Lab Populat Genet, Moscow 119333, Russia)
  • Vornam Barbara (Univ Gottingen, Fac Forest Sci & Forest Ecol, Dept Forest Genet & Forest Tree Breeding, Busgenweg 2, D-37077 Gottingen, Germany)
  • Leinemann Ludger (Univ Gottingen, Fac Forest Sci & Forest Ecol, Dept Forest Genet & Forest Tree Breeding, Busgenweg 2, D-37077 Gottingen, Germany)
  • Gailing Oliver (Univ Gottingen, Fac Forest Sci & Forest Ecol, Dept Forest Genet & Forest Tree Breeding, Busgenweg 2, D-37077 Gottingen, Germany; Georg August Univ Gottingen, Ctr Integrated Breeding Res, Gottingen, Germany; Michigan Technol Univ, Sch Forest Resources & Environm Sci, Houghton, MI 49931 USA)

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