Identification of Marker Trait Associations in a Barley Four Way Cross

Until recently, genetic mapping in cereals has been exclusively applied to populations derived from simple crosses. Genetic studies are now targeting broader population structures to take advantage of association mapping and whole genome analysis techniques. This paper presents a study of a Doubled Haploid (DH) population derived from the complex cross, Chieftan/Barque//Manley/VB9104, which is a significant departure from conventional mapping population structures. The population has been extensively phenotyped for malt quality and adaptation characteristics, through evaluation as a mainstream breeding population within the SA Barley Improvement Program (SABIP). Of the 841 (DH) lines, 837 lines were evaluated in double row trials, with 350 individuals promoted to stage one, 70 individuals to stage two and 10 individuals to stage three. One line (WI3408) has subsequently progressed to pilot scale malting and brewing trials, with potential for commercial release. Using high throughput technology the stage one DH lines (350) were extensively screened with fluorescently labelled simple sequence repeats (SSRs) based on their association with the traits of interest for this population. There was a 60% rate of polymorphism between one or more parents. In total, 200 SSRs were assayed and analysed using both Gene Flow and Gene Mapper data bases.