Development of a set of SNP markers for population genetics of the sea peach (Halocynthia papillosa)

A set of single nucleotide polymorphism (SNP) markers was developed from the transcriptome of the solitary ascidian Halocynthia papillosa. 1399 putative SNPs with coverage larger than 100 reads were identified, and a selected set of 320 SNPs was tested using a MassARRAY System on 95 samples from the NW Mediterranean. A total of 175 SNPs were successfully genotyped, polymorphic and in Hardy-Weinberg equilibrium over all samples. The newly developed loci will be a valuable tool for population genetics studies of this endemic ascidian species of the Mediterranean Sea

Development of nuclear SNP markers for the timber tracking of the African tree species Sapelli, Entandrophragma cylindricum

We describe the development of new nuclear SNP markers for the genetic timber tracking of the geographical origin of Sapelli, Entandrophragma cylindricum (Meliaceae). Restriction associated DNA sequencing (RADseq) of two reference individuals yielded 1131 putative SNPs. Among those, 131 were selected to design four MassARRAY multiplexes and screened at 178 individuals. Seventy-two loci were selected for further use in genetic tracking

Sequenome_SNP_matrix_2ndscreen

SEQUENCE output file of the second SNP screening. The file is separated into four sheets detailing i) assay summary ii) sample summary iii) genotypes and iv) genotype are

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. 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. 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. 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). 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. 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

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

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

SNP_extract_stringent_approach

Custom bash script for SNP detection using stringent approach after PyRAD/RADami analysis

Development of highly validated SNP markers for genetic analyses of chestnut species

To better study and manage chestnut trees and species, we identified nuclear single nucleotide polymorphism (SNP) markers using restriction-associated DNA sequencing. Out of 343 loci tested, 68 SNP markers were selected that withhold stringent quality criteria such as quasi-systematic amplification across species and Mendelian segregation in both purebred and hybrid individuals. They provide sufficient power for species, hybrids and backcross characterization as well as for clonal identification, as shown by a comparison with single sequenced repeat (SSR) loci.Plateforme d'Innovation " Forêt-Bois-Fibre-Biomasse du Futur

Sequenome_SNP_matrix_1stscreen

SEQUENCE output file of the first SNP screening. The file is separated into four sheets detailing i) assay summary ii) sample summary iii) genotypes and iv) genotype are

Sequenome_SNP_matrix_potentialparents

SEQUENCE output file for genotyping potential parent individuals. The file is separated into three sheets detailing i) assay summary ii) sample summary and iii) genotype