Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

Not Guilty Of Association: Finding Genes In A SNP Haystack

Alfonso Cuesta-Marcos¹ , Péter Szûcs¹ , Tanya Filichkina¹ , Prasanna R. Bhat² , Timothy J. Close ² , Gary J. Muehlbauer³ , Patrick M. Hayes¹

¹  Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA

²  Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA

³  Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA

We compared the power of the association mapping using SNP data from a large set of genes versus haplotype information from candidate genes determining the growth habit and inflorescence type of barley. Our model was the Barley CAP Core, a set of 102 cultivated barley accessions representing key cultivars and accessions of interest to the U.S. Barley CAP breeding programs and international participants. The CAP core was genotyped for 4,596 EST-based Pilot-OPA markers. Markers were filtered using quality and polymorphism criteria until a set of 1802 markers was obtained whose position could be determined according to the HarvEST:Barley (http://harvest-web.org) consensus map. We found that allele type at the POPA2 marker corresponding to VRN-H1 – one of the primary determinants of growth habit – showed no relationship with growth habit in this germplasm set. Possible explanations for this lack of association of the VRN-H1 SNP include rapid LD decay within the gene, the complexity of the functional allelic differences, and the power of current association analysis tools to detect multi-locus epistatic interactions, such as the one determining winter vs. spring/facultative growth habit. We re-sequenced/genotyped the full germplasm set for candidate genes at the principal genes controlling growth habit (VRN-H1, VRN-H2, VRN-H3, PPD-H1, PPD-H2), and inflorescence type (VRS1) and found many nucleotide polymorphisms, ample haplotype diversity, as well as novel VRN-H3 and VRS1 alleles. Working with an array of diverse germplasm, we ascertained the importance of using complete haplotype information and markers determining functional polymorphisms when conducting association mapping.