Development of new SNP and INDEL loci for the valuable African timber species Lophira alata
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METHODS AND RESOURCES ARTICLE
Development of new SNP and INDEL loci for the valuable African timber species Lophira alata Celine Blanc‑Jolivet1 · Malte Mader1 · Henri‑Noël Bouda1 · Marie Massot2 · Kasso Daïnou3,4 · Germain Yene5 · Emmanuel Opuni‑Frimpong6,7 · Bernd Degen1 Received: 3 April 2020 / Accepted: 17 September 2020 © The Author(s) 2020
Abstract The timber of the species Lophira alata (azobe) is very popular for outdoor constructions, which favours its overexploitation and illegal logging. We sampled individuals from Liberia, Ivory Coast, Ghana, Nigeria, Cameroon, Gabon, Congo Brazzaville and Republic Democratic of Congo to discover new nuclear and plastidial SNP and INDEL loci through restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. From an initial set of 397 loci, a final set of 126 loci was selected for timber tracking purposes. Keywords Lophira alata · Azobe · Single nucleotide polymorphism · MassARRAY Lophira alata is a tropical pioneer timber species typical from secondary humid forests. Its distribution ranges from Sierra Leone in Western Africa to Congo in Central Africa. The timber is highly valuable because of its resistance against insects and moulding, which enables it’s use in outdoor constructions. Despite a minimum cutting diameter of at least 60 cm in all producer countries, this species is Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-020-01173-5) contains supplementary material, which is available to authorized users. * Celine Blanc‑Jolivet celine.blanc‑[email protected] 1
Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
2
INRAE, Univ. Bordeaux, BIOGECO, 33610 Cestas, France
3
Nature+ asbl/TERRA Forest Is Life, Gembloux Agro‑Bio Tech, Université de Liège, Passage des déportés 2, 5030 Gembloux, Belgium
4
Service Evolution Biologique Et Ecologie, Faculté Des Sciences, Université Libre de Bruxelles, CP160/12, 50 av. F. Roosevelt, 1050 Brussels, Belgium
5
Biteng‑Maetur, Behind Pi and Ju International College, Yaoundé, Cameroon
6
University of Energy and Natural Resources, Sunyani, Ghana
7
CSIR-Forestry Research Institute of Ghana (FORIG), Kumasi, Ghana
heavily exploited and classified as vulnerable in the IUCN red list. The genus Lophira has been poorly studied until now and only consist of two species: L. alata typical from humid forest habitats while the species L. lanceolata is mostly found in savannahs. However, when both species are growing in sympatry, species identification is difficult (Biwole et al. 2012). Genetic studies are limited to the development and use of SSRs markers (Ewédjè et al. 2020; Pineiro et al. 2015), which aimed at studying the genetic structure and hybridisation between L. alata and L. lanceolata. With 10 SSRs, the presence of a cryptic species in L. alata was suggested in West Gabon (Ewédjè et al 2020). Thus, little information is available on the diversity and differentiation within both species
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