New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array
Résumé
Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed on Illumina platforms. A total number of 1,878,727 SNPs distributed along a P. nigra reference sequence were identified. The SNP calling accuracy was validated by comparison with Sanger sequencing data. 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 filtered for the construction of a 12k Infinium BeadChip array dedicated to association mapping. The SNPs 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 application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread out on the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and 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 in P. nigra.
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