Overcoming polyploidy pitfalls: a user guide for effective SNP conversion into KASP markers in wheat

Conversion of SNP chip assays into locus-specific KASP markers requires adapted strategies in polyploid species with high genome homeology. Procedures are exemplified by QTL-associated SNPs in hexaploid wheat. Kompetitive allele-specific PCR (KASP) markers are commonly used in marker-assisted commercial plant breeding due to their cost-effectiveness and throughput for high sample volumes. However, conversion of trait-linked SNP markers from array-based SNP detection technologies into KASP markers is particularly challenging in polyploid crop species, due to the presence of highly similar homeologous and paralogous genome sequences. We evaluated strategies and identified key requirements for successful conversion of Illumina Infinium assays from the wheat 90 K SNP array into robust locus-specific KASP markers. Numerous examples showed that commonly used software for semiautomated KASP primer design frequently fails to achieve locus-specificity of KASP assays in wheat. Instead, alignment of SNP probes with multiple reference genomes and Sanger sequencing of relevant genotypes, followed by visual KASP primer placement, was critical for locus-specificity. To identify KASP assays resulting in false calling of heterozygous individuals, validation of KASP assays using extended reference genotype sets including heterozygous genotypes is strongly advised for polyploid crop species. Applying this strategy, we developed highly reproducible, stable KASP assays that are predictive for root biomass QTL haplotypes from highly homoeologous wheat chromosome regions. Due to their locus-specificity, these assays predicted root biomass considerably better than the original trait-associated markers from the Illumina array.

Characterization of retinal expression of vascular cell adhesion molecule (VCAM-1) during experimental autoimmune uveitis

Leukocyte adhesion to the blood retinal barrier is a critical step in the pathogenesis of non-infectious uveitis and is mediated in part through the induction of adhesion molecules on retinal cells. Here, we have investigated the retinal expression of Vascular Cell Adhesion Molecule 1 (VCAM-1) in mouse experimental models of non-infectious uveitis. For each eyes, a histological score was given, and the expression of VCAM-1 analyzed by immunohistology. Co-labellings for GFAP, endoglin, aquaporin 4 and recoverin were also performed in order to determine which cell type expressed VCAM-1. In low grade uveitis, obtained after adoptive transfer of semi-purified autoreactive lymphocytes, VCAM-1 was only punctually expressed in the internal limiting membrane and epithelial cells of the ciliary body. Using the same adoptive transfer protocol, we found that, in correlation with disease severity, the staining extended to all internal limiting membranes, vasculitis lesions, Müller cell extensions, outer limiting membranes and RPE cells. VCAM-1 expression in the inner limiting membrane and Müller cell extensions co-stained with GFAP expression. In vasculitis lesions, VCAM-1 co-localized with either GFAP and endoglin expression. The labeling in the outer limiting membrane, did not exactly co-stained with AQ4 (Müller cells marker) or recoverin (photoreceptor marker) and the nature of this expression remained unexplained. Finally, VCAM-1 expression was also analyzed in classical experimental autoimmune uveitis eyes, and a similar pattern of expression was found. In conclusion VCAM-1 is expressed on all blood retinal barrier cells during experimental non-infectious uveitis and might thus play an important role in inflammatory cell recruitment during disease development.