The Development of a Customised Single Nucleotide Polymorphism (SNPs) Panel for Molecular Marker Assisted Selection within an Applied Breeding Program.

The Field Crop Development Centre (FCDC), based in Lacombe, Alberta (Canada) conducts breeding programs for feed, forage and food barley (2-row, 6-row and hulless), 2-row malting barley, spring and winter triticale, and winter wheat.  These breeding programs are focused on developing improved cultivars for production in western Canada.  New varieties must be high yielding, lodging resistant, adapted to unique regional growing conditions, resistant to major diseases and meet the quality demands of the malt, feed or food industry.  At present, cereal lines are primarily selected using phenotypic data (field testing, wet chemistry and NIRS), although a limited amount of marker assisted selection (MAS) has been applied.  If genotyping data is to be used routinely as a selection method within our current breeding program, our genotyping assays must be done quickly, economically and accurately. As a new approach we are developing a low density SNPs panel that will be customised for trait selection within FCDC breeding lines.  We are working with FCDC breeders to identify genes, QTLs and molecular markers available for usage in their breeding germplasm.   We are focused on identifying SNPs linked to disease resistance (scald, net blotch, fusarium head blight, and stripe rust), malt quality enzymes, and in vitro fiber digestibility.  We plan to add the selected SNP markers to the commercially available 400+ SNP panel from Eureka Genomics (California).  With this panel, we plan to speed up and reduce the cost of genotyping across breeding programs, by simultaneously genotyping multiple genes/ QTLs on one array.