Tagging the dwarfing gene Ddw1 in a rye population derived from doubled haploid parents

To prevent lodging and sprouting damage in rye, a dominant dwarfing gene, Ddw1, has been incorporated into breeding lines to reduce plant height in Finland. However, the inability to identify heterozygous plants makes it difficult to purify breeding lines. Doubled haploidy (EM-1 x Voima) and bulked segregant analysis were used to search for an efficient PCR-based tool to identify homozygous short plants. In addition, SNP (single nucleotide polymorphism) markers were created from the endosperm-specific beta-amylase gene and the microsatellite locus REMS1218 expressed in rye and known to be located near Ddw1. The best marker was a combination of the microsatellite REMS1218 and the SNP created from it, located 13 cM from the QTL corresponding to Ddw1. However, for a rye breeder, the SNP alone is an adequate tool to identify plants homozygous for the EM-1 allele and it can be used in selection for the desirable growth habit in rye.