Development of nuclear, chloroplast and mitochondrial SNP markers for Khaya sp.
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TECHNICAL NOTE
Development of nuclear, chloroplast and mitochondrial SNP markers for Khaya sp. Birte Pakull1 • Malte Mader1 • Birgit Kersten1 • Marius R. M. Ekue´2 Ulrich G. Bouka Dipelet3,4 • Maike Paulini1 • Z. Henri-Noe¨l Bouda1 • Bernd Degen1
•
Received: 20 May 2016 / Accepted: 25 May 2016 Ó Springer Science+Business Media Dordrecht 2016
Abstract 100 SNP and one Indel markers were developed for Khaya using a combination of restriction associated DNA sequencing and low coverage MiSeq genome sequencing. The marker set was successfully used to genotype a set of 1919 individuals, representing 5 Khaya species from 18 African countries, using MassARRAYÒiPLEXTM genotyping. Keywords Khaya SNP Tropical tree MassARRAYÒiPLEXTM Genetic differentiation
Introduction The genus Khaya currently comprises five species (K. ivorensis, K. anthotheca, K. grandifoliola, K. senegalensis and K. madagascariensis), which are native to tropical Africa, Madagascar and the Comoros. It belongs to the family Meliaceae and seems most closely related to the genera Carapa and Swietenia (Louppe et al. 2008) (Sexton et al. 2015).
Timber from K. ivorensis, K. anthotheca and K. grandifoliola is traded as high-value timber under the name ‘‘African mahagony’’. All three species are listed as vulnerable by the IUCN. Natural regeneration after logging is seriously hindered by the low density of adult trees and low regeneration rates (Louppe et al. 2008; IUCN 2015). Up to now marker development and application in Khaya was focused on development (Sexton et al. 2010; Karan et al. 2012) and cross species amplification (White and Powell 1997; Lemes et al. 2011) of microsatellite markers and cpDNA sequence analysis (Ho¨ltken et al. 2012; Sexton et al. 2015). Here we present a set of 101 SNP/Indel markers which were analyzed using MassARRAYÒiPLEXTM genotyping (Agena Bioscience, Hamburg, Germany). This marker set can be used for effective analysis of molecular population structures within the genus.
Materials and methods Samples
& Birte Pakull [email protected] & Bernd Degen [email protected] 1
Thu¨nen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
2
Bioversity International, s/c IITA, BP 2008, Yaounde´, Cameroon
3
4
CIRAD, B&SEF Unit, Campus international de Baillarguet, 34398 Montpellier Cedex 5, France Laboratoire de Botanique et Ecologie, Faculte´ des Sciences, Universite´ Marien Ngouabi, BP 69, Brazzaville, Congo
Leaf, cambium, bark or wood samples were obtained from various countries and locations within Africa and from the greenhouses of the Thu¨nen Institute. African samples were harvested, dried with Silica Gel and sent to the Thu¨nen Institute. DNA isolation DNA isolation from wood was carried out according to Lowe et al. (2015). DNA isolation from all other materials was carried out according to Dumolin et al. (1995).
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Alleles
C/A
C/T
T/A
C/A
G/A
G/A
A/G
G/A
T/A
T/A
G/T
C/T
Marker name
Kha0000147
123
Kha0000164
Kha0000582
Kha0000768
Kha0000945
Kha0001500
K
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