A doubled haploid rye linkage map with a QTL affecting α-amylase activity.

A rye doubled haploid (DH) mapping population (Amilo × Voima) segregating for pre-harvest sprouting (PHS) was generated through anther culture of F(1) plants. A linkage map was constructed using DHs, to our knowledge, for the first time in rye. The map was composed of 289 loci: amplified fragment length polymorphism (AFLP), microsatellite, random amplified polymorphic DNA (RAPD), retrotransposon-microsatellite amplified polymorphism (REMAP), inter-retrotransposon amplified polymorphism (IRAP), inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers, and extended altogether 732 cM (one locus in every 2.5 cM). All of the seven rye chromosomes and four unplaced groups were formed. Distorted segregation of markers (P ≤ 0.05) was detected on all chromosomes. One major quantitative trait locus (QTL) affecting α-amylase activity was found, which explained 16.1% of phenotypic variation. The QTL was localized on the long arm of chromosome 5R. Microsatellites SCM74, RMS1115, and SCM77, nearest to the QTL, can be used for marker-assisted selection as a part of a rye breeding program to decrease sprouting damage.