Abstract
We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia.
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References
Blanc-Jolivet C, Kersten B, Daïnou K, Hardy O, Guichoux E, Delcamp A, Degen B (2017) Development of nuclear SNP markers for genetic tracking of Iroko, Milicia excelsa and Milicia regia. Conserv Genet Resour 9:531–533
Chaves CL, Degen B, Pakull B, Mader M, Honorio E, Ruas P, Tysklind N, Sebbenn AM (2018) Assessing the ability of chloroplast and nuclear DNA gene markers to verify the geographic origin of Jatoba (Hymenaea courbaril L.) timber. J Hered 109:543–552
Dumolin S, Demesure B, Pettit R (1995) Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. Theor Appl Genet 91:1253–1256
Gregorius HR (1987) The relationship between the concepts of genetic diversity and differentiation. Theor Appl Genet 74:397–401
IUCN (2018) The IUCN red list of threatened species version 2018-2. http://www.iucnredlist.org. Accessed 15 Nov 2018
Jardine DI, Blanc-Jolivet C, Dixon RRM, Dormontt EE, Dunker B, Gerlach J 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 Genet Resour 8:129–139
Meyer-Sand BRV, Blanc-Jolivet C, Mader M, Paredes-Villanueva K, Tysklind N, Sebbenn AM, Guichoux E, Degen B (2018) Development of a set of SNP markers for population genetics studies of Ipe (Handroanthus sp.), a valuable tree genus from Latin America. Conserv Genet Resour 10:779–781
Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248
Pakull B, Mader M, Kersten B, Ekue MRM, Dipelet UGB, Paulini M et al (2016) Development of nuclear, chloroplast and mitochondrial SNP markers for Khaya sp. Conserv Genet Resour 8:283–297
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Putzel L, Peters CM, Romo M (2011) Post-logging regeneration and recruitment of shihuahuaco (Dipteryx spp.) in Peruvian Amazonia: implications for management. For Ecol Manag 261:1099–1105
Soares TN, Melo DB, Resende LV, Vianello RP, Chaves LJ, Collevatti RG, Telles MPDC (2012) Development of microsatellite markers for the neotropical tree species Dipteryx alata (Fabaceae). Am J Bot 99:e72–e73
Straub SC, Parks M, Weitemier K, Fishbein M, Cronn RC, Liston A (2012) Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics. Am J Bot 99:349–364
Vinson CC, Ribeiro DO, Harris SA, Sampaio I, Ciampi AY (2009) Isolation of polymorphic microsatellite markers for the tetraploid Dipteryx odorata, an intensely exploited Amazonian tree species. Mol Ecol Resour 9:1542–1544
Acknowledgements
This research was supported by the German Federal Ministry of Food and Agriculture (BMEL) and the Programa Nacional de Innovación para la Competitividad y Productividad (Innóvate Perú—contract 381-PNICP-PIAP-2014). 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, No. ANR-10-EQPX-16-01 and CEBA: ANR-10-LABX-25-01 to the UMR EcoFoG). Permits ICMBIO Nos. 4760, 49369, registration CGen No. A16E4DA (Brazil), MAYA/VMABCCGDF/DGBAP/MEG No. 0280/2016 (Bolivia), R.D. No. 001-2016-SERNANP-DGANP, R.D. No. 001A-2015-SERFOR-DGGSPFFS-DGSPF, and Contrato No. 001-2016-SERFOR-DGGSPFFS-DGSPF (Peru) were granted for the collection, transport and genetic analyses of samples. We are also grateful to colleagues from IIAP, INRA French Guiana, Cirad Paracou Station, Office National des Forêts, and Thünen Institute for their assistance during field work and laboratory work.
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Honorio Coronado, E.N., Blanc-Jolivet, C., Mader, M. et al. Development of nuclear and plastid SNP markers for genetic studies of Dipteryx tree species in Amazonia. Conservation Genet Resour 11, 333–336 (2019). https://doi.org/10.1007/s12686-019-01081-3
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DOI: https://doi.org/10.1007/s12686-019-01081-3