A 12K BeadChip Array Design for Populus nigra using Genome–Wide Re-Sequencing Data

Recent advances in high throughput SNP arrays allow accurate genotyping of several thousand loci for thousand individuals at relatively low cost. Such progress opens perspectives for genetic studies that cover more genomic variations useful for population genomics, hybrid controls and monitoring of genetic diversity in natural and breeding populations. Hence, we have designed an Illumina Infinium® II 12K BeadChip array (10 332 SNP), taking the advantage of Next Generation Sequencing data to identify SNP. In the aim of carrying out association studies, the SNPs were selected in candidate gene and in QTL regions. Black Poplar Infinium® assay yielded 9127 SNPs of which 77% were polymorphic while only 0.87% were monomorphic. Remaining 22% are currently under the process of thorough visual inspection, correction and validation. Preliminary analysis revealed 557 genotypes with good quality scores (call rate ≥0.95), while 19 genotypes had call rate between 0.8-0.9 and were eliminated from further analysis. Heritability-based SNP validation was estimated to assess SNP assay quality. Heritability is defined as the number of offspring genotypes that agree with the expected inheritance over the total number of possible genotype calls. In 7 families, there were 806 Mendelian transmission inconsistencies out of the 331,128 allelic transmissions assayed i.e. a genotyping miscall rate of 0.24%. We observed 0.68% of SNPs with segregating errors. SNP validation and further down stream analysis are currently in progress.