Development of nuclear SNP markers for genetic tracking of Iroko, Milicia excelsa and Milicia regia

  • C. Blanc-Jolivet
  • B. Kersten
  • K. Daïnou
  • O. Hardy
  • E. Guichoux
  • A. Delcamp
  • B. Degen
Technical Note

Abstract

Restriction associated DNA sequencing was conducted on two genetically independent individuals of Iroko, Milicia excelsa, for the discovery of nuclear SNPs. Ninety-four samples, well-distributed over the natural range and including timber DNA, were screened at 138 loci on a MassARRAY iPLEX system. Amplification success was high and 77 loci were selected to design a set of markers for genetic timber tracking purposes.

Keywords

Single nucleotide polymorphism Milicia RAD sequencing MassARRAY Timber tracking 

Supplementary material

12686_2017_716_MOESM1_ESM.docx (83 kb)
Supplementary material 1 (DOCX 83 KB)

References

  1. Blanc-Jolivet C, Liesebach M (2015) Tracing the origin and species identity of Quercus robur and Quercus petraea in Europe: a review. Silvae Genet 64:182–193Google Scholar
  2. Daïnou K, Bizoux JP, Doucet JL et al (2010) Forest refugia revisited: nSSRs and cpDNA sequences support historical isolation in a wide-spread African tree with high colonization capacity, Milicia excelsa (Moraceae). Mol Ecol 19:4462–4477CrossRefPubMedGoogle Scholar
  3. Daïnou K, Mahy G, Duminil J et al (2014) Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae). Heredity (Edinb) 113:74–85CrossRefPubMedCentralGoogle Scholar
  4. Daïnou K, Blanc-Jolivet C, Degen B et al (2016) Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences- a case study in the tree genus Milicia. BMC Evol Biol 16:259CrossRefPubMedPubMedCentralGoogle Scholar
  5. Degen B, Blanc-Jolivet C, Stierand K, Gillet E (2017) A nearest neighbour approach by genetic distance to the assignment of individual trees to geographic origin. Forensic Sci Int Genet 27:132–141CrossRefPubMedGoogle Scholar
  6. Dumolin S, Demesure B, Petit R (1995) Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. Theor Appl Genet 91:1253–1256CrossRefPubMedGoogle Scholar
  7. Gregorius H-R (1987) The relationship between the concepts of genetic diversity and differentiation. Theor Appl Genet 74(3):397–401CrossRefPubMedGoogle Scholar
  8. Jardine DI, Blanc-Jolivet C, Dixon RRM et al (2016) Development of SNP markers for Ayous (Triplochiton scleroxylon K. Schum) an economically important tree species from tropical West and Central Africa. Conserv Genetic Resour 8:129. doi:10.1007/s12686-016-0529-8 CrossRefGoogle Scholar
  9. Pakull B, Mader M, Kersten B, Ekue MRM, Dipelet UGB, Paulini M, Bouda ZHN, Degen B (2016) Development of nuclear, chloroplast and mitochondrial SNP markers for Khaya sp. Conserv Genet Resour 8:283–297CrossRefGoogle Scholar
  10. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 94(17):9197–9201CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  • C. Blanc-Jolivet
    • 1
  • B. Kersten
    • 1
  • K. Daïnou
    • 2
    • 3
  • O. Hardy
    • 4
  • E. Guichoux
    • 5
  • A. Delcamp
    • 5
  • B. Degen
    • 1
  1. 1.Thünen Institute of Forest GeneticsGrosshansdorfGermany
  2. 2.Nature+ asbl s/c BIOSE, Management of Forest Resources, GxABT, ULgGemblouxBelgium
  3. 3.Université Nationale d’Agriculture de Porto NovoPorto NovoBenin
  4. 4.Faculté des Sciences, Evolutionary Biology and EcologyUniversité Libre de BruxellesBrusselsBelgium
  5. 5.BIOGECO, INRA, University of BordeauxCestasFrance

Personalised recommendations