Use of Association Mapping On the Barley CAP at North Dakota State University.

The barley (Hordeum vulgare L.) breeding program at North Dakota State University (NDSU) is one of nine US barley breeding programs participating in the USDA-CSREES Barley Coordinated Agricultural Project (Barley CAP).  As part of our participation, we submit six-rowed and two-rowed barley breeding lines to the program for phenotyping by collaborating breeders and genotyping by the USDA-ARS Cereal Genotyping Lab in Fargo, ND.  These phenotype and genotype data are used for identification of QTL controlling agronomic performance, malt quality, disease resistance, and abiotic stresses using whole-genome scan association mapping.  NDSU researchers are mapping QTL controlling seed dormancy and common root rot resistance using the spring Barley CAP lines and heading date and plant height using the Midwest Barley CAP lines.  Our presentation will report on the findings of our mapping research, and discuss the different user decisions that must be considered in association mapping analyses and the consequences of those decisions.  User decisions include the choice of STRUCTURE vs. principal component analysis for determining population structure, use of all lines vs. a sub-set of lines for removing over-represented lines when estimating population structure, and use of a general linear model or mixed linear model for association mapping analyses.