Chagné, D., Lalanne, C., Madur, D., Kumar, S., & Frigério, J. Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): A genomic and population genetics approach. Cavender-Bares, J., González-Rodríguez.Diversity, distribution and ecosystem services of the North American Oaks. Stacks: An analysis tool set for population genomics. A., Bassham, S., Amores, A., & Cresko, W. Stacks: Building and genotyping loci de novo from short-read sequences. M., Amores, A., Hohenlohe, P., Cresko, W., & Postlethwait, J. Detection of hybrids in nature: Application to oaks ( Quercus suber and Q. ilex). Burgarella, C., Lorenzo, Z., Jabbour-Zahab, R., Lumaret, R., Guichoux, E., Petit, R.Methods in Molecular Biology (Methods and Protocols) (pp. Rockman (Eds.), Molecular methods for evolutionary genetics, vol. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. Barchi, L., Lanteri, S., Portis, E., Acquadro, A., Valè, G., Toppino, L., & Rotino, G.Rapid SNP discovery and genetic mapping using sequenced RAD markers. Deciduous trees and the application of universal DNA barcodes: A case study on the circumpolar fraxinus. D., Cruaud, C., Tillier, A., Bousquet, J., & Frascaria-Lacoste, N. New technologies for ultra-high throughput genotyping in plants. Appleby, N., Edwards, D., & Batley, J.Journal of Molecular Biology, 215, 403– 410. Imprints of natural selection along environmental gradients in phenology-related genes of Quercus petraea. Together, RAD-seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera. Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa, and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. As a proof-of-concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range ( Q. michauxii, Q. montana, Q muehlenbergii/ Q. prinoides, and Q. stellata) into a horticultural collection surrounded by natural forests of locally native trees ( Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. In this study, we utilized restrictionsite-associated DNA sequencing (RAD-seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus.
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