Discovery and genotyping of SNP markers and grouping of advanced bread wheat lines by ddRAD-Seq

The aim of this study was todiscover, genotyping and determining the genotype, the number, distribution and density of SNP markers and grouping of an advanced breeding population using the ddRAD-Seqmethod. DNA was extracted from 14-old-day seedlings and the NextSeq TM 500 Illumina ®   platform was used for sequencing. The average quality score for all individual was Phred’s 30. The correct reads were 150108678 out of 178811846 and the average of 2207480 reads produced by individual. The highest and the lowest alignment rate were related to B and D genomes, respectively. Based on the filter conditions, (DP≥5), quality score=≥999, MAF>5% and Het<10%, the total number of SNP calling for 50% missing data were 3342 which identified 1322, 1253, and 767 on B, A and D genomes, respectively. The highest SNP markers were identified on 2B and 3B and the lowest on 4D chromosomes. A significant linear regression was observed between marker density (SNP/Mbp) and chromosome size in three genomes. The principal components analysis and the heatmap dendrogram together with the use of SNP marker information were able to identify and segregate sub-populations from a main population.