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Published December 23, 2015 | Version v1
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Data from: New resources for genetic studies in Populus nigra: genome wide SNP discovery and development of a 12k Infinium array

Authors/Creators

  • 1. University of Udine
  • 2. Institut National des Sciences Appliquées Centre Val de Loire
  • 3. Centre National de Génotypage
  • 4. University of Southampton
  • 5. Istituto di Genomica Applicata

Description

Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1,878,727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions; 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10,000 SNPs were selected for the construction of a 12k Infinium BeadChip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5 to 7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.

Notes

List of SNPs extracted from HT-sequencing data
The SNPs are denoted by SNP_IGA followed by the chromosome or scaffold number (V2.0) and the base position within the scaffold.
List of SNPs from HTsequencing data.xlsx
P. nigra Genotype data
Genotype calling of P. nigra individuals originating from 12 western european river basins and full sib progenies. The individuals are listed in Tables S1
Input files for ADMIXTURE and PCA
Input files for ADMIXTURE and PCA analysis see Material and methods section
P. nigra reference sequence
This .zip file contains the fasta-formatted and compressed complete sequence of Populus nigra genotype 71077-308.
Consensus_71077-308_version0915-MER.fa.zip

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Additional details

Related works

Is cited by
10.1111/1755-0998.12513 (DOI)