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Analysis of the genomic structure of a wheat NIL population segregating for resistance to glume blotch with a 90k ILLUMINA SNP chip

Analysis of the genomic structure of a wheat NIL population segregating for resistance to glume blotch with a 90k ILLUMINA SNP chip content piece image
Single nucleotide polymorphism (SNP) markers have recently become highly relevant for genetic analysis in wheat because of new SNP genotyping technologies like the Illumina Golden-Gate Assay. There, SNP markers allow high-throughput and cost-effective genotyping, even in the polyploid wheat genome.
We used the wheat Illumina Golden-Gate Infinium array 90K [1] to unravel the genetic structure of a population of 89 near-isogenic lines (28 BC3F8 and 61 BC3F7) derived from the introgression of a specific genomic region coming from Arina (resistant) into Forno (susceptible) involved in quantitative resistance to Stagonospora nodorum glume blotch (SNG), a necrotophic fungal disease affecting bread wheat spikes [2]. We wanted to know the extent and size of genomic fragments derived from the donor line in the NILs.
From a dataset of 81.587 SNPs, 14.158 SNP markers (17.35%) failed in all samples, leaving a total of 67.418 (82.63%) functional SNPs. The reproducibility of the SNP chip was confirmed given the tiny % of non-conclusive SNPs (13, 0.016%) comparing replicates coming from the same DNA sample for both parents.
Among the functional SNPs, 8.407 (12.46%) were polymorphic between Arina and Forno. This is surprisingly high if compared with the percentage of polymorphism observed between winter wheat Arina and the spring wheat cultivar Chinese Spring (11.000 polymorphic SNPs), two wheat varieties with an obviously very different origin. Thus, the SNP chip reveals a large number of genetic differences, even between elite winter wheat varieties derived from the same breeding program.
Most of the SNPs polymorphic between Arina and Forno (8.363, 12.40%) were polymorphic also across the NIL population. Examining the allelic composition of the polymorphic SNPs within the population, 66.63% of SNPs shared less than 6.25% and approximately 27% of SNPs share > 25% of allelic composition with Arina. We will also present data on over- and underrepresentation of genomic regions in the NILs which might be indicative of some selection during population development. Furthermore, we will present the analysis of genetic size and frequency of specific introgressions in the NILs to determine the molecular nature of such a population in wheat.