2. Oregon Wolfe Barley Map 187 classical loci

3. Oregon Wolfe Barley Map 187 classical + 722 DArT = 909 loci

4. Oregon Wolfe Barley Map 187 classical + 555 pilot-OPA1 + 467 pilot-OPA2 = 1209 loci

5. Oregon Wolfe Barley Map 187 classical + 555 pilot-OPA1 + 467 pilot-OPA2 + 722 DArT = 1931 loci

6. Oregon Wolfe Barley Linkage Map - (2383 loci, Haldane cM)

7. Oregon Wolfe Barley Linkage Map (2383 loci + 463RAD = 2846 loci)

8. Marker+- NEPPhenotype = phenotype Cheap Phenotype ~ phenotype Scarce RFLPIn-house ~ Abundant A phenotype Slow, hazardous Expensive DaRTMore Abundant Cheaper ~ a phenotype Proprietary transitory platform Illumina SNPVery abundant Sequence basis Cheap, in volume Proprietary transitory platform RAD/GBSVery, very abundant Sequence basis Cheap, in volume Proprietary transitory platform

9. “Development and phenotyping of biparental populations Genotyping-by-sequencing followed by rough linkage mapping and “rough” QTL mapping. Rough because GBS involves sequencing. Sequencing involves errors. Errors mess up marker order, expand map distances and muck up marker trait- association test statistics Choosing large-effect QTL that seem worthy of marker development for breeders Conversion of GBS tags into KASP assays Current marker strategy in a major service lab

10. Application of the KASP assays to the population to create dense and high-quality linkage map of the QTL region Redoing the QTL analysis. Picking markers near the peak and running them across varieties to find markers for which alleles are likely to be rare in breeding germplasm. Releasing the markers to breeders for use in selection But with a good genome assembly, linkage mapping becomes increasingly unnecessary we can skip the linkage mapping in step 2 and just plot single-marker test statistics against physical or consensus-genetic positions.”

11. Someday, something like the MinION will work and we will have whole genomes at our fingertips

12. From SNPs (e.g. 1_1292)in linkage map order (thanks to the Oregon Wolfe Barley) genotyped in near isogenic lines (the BISON) to candidate genes, via quantitative trait loci (as detected in the Baronesse x BCD47 doubled haploid mapping population). 1_1292 is a SNP in expressed sequence tag EST) #4535, which is a respiratory burst homolog. RBs are implicated in disease resistance and in this project we are looking for genes conferring quantitative resistance to barley stripe rust, a fungal disease.