Development of a set of SNP markers for population genetics studies of Ipe (Handroanthus sp.), a valuable tree genus from Latin America
A combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing was used for the development of single nucleotide polymorphisms (SNP) and INDEL (insertion/deletions) genetic markers for Ipe (Handroanthus sp.). Of the 402 putative loci identified, 389 SNPs and INDELs (315 nuclear SPNs, six chloroplast INDELs, 15 chloroplast SNPs, 12 mitochondrial INDELs and 41 mitochondrial SNPs) were successfully genotyped at 93 individuals from Brazil, Bolivia and French Guiana using a MassARRAY® iPLEX™ platform. This set of markers will be invaluable for population genetics, phylogeography and DNA fingerprinting studies.
KeywordsHandroanthus sp. Single nucleotide polymorphism MassARRAY
This research was supported by the German Federal Ministry of Food and Agriculture in the frame of the “Large scale project on genetic timber verification”. Genotyping was performed at the Genomic and Sequencing Facility of Bordeaux (grants from the Conseil Regional d’Aquitaine Nos 20030304002FA and 20040305003FA, the European Union, FEDER No 2003227 and Investissements d’avenir, Nos ANR-10-EQPX-16-01 and CEBA: ANR-10-LABX-25-01 to the UMR EcoFoG). We would like to thank the Conselho Nacional de Ciencia e Tecnologia (CAPES) (Mater scholarship at the UNESP/FEIS to B.R.V.M-S), the Chico Mendes Biodiversity Institute (authorizations Nos 47960 and 49369 for sample transportation), FLONA do Jamari, AMATA Company, FLONA Amapá, FLONA de Tapajós, FLONA do Carajás, RESEX Chico Mendes, RESEX Tapajós - Arapins in Brazil, the Museo de Historia Natural Noel Kempff Mercado in Bolivia, as well as the Office National des Forêts in French Guiana for their support in the field.