Identification of genomic regions carrying QTL for agronomic and quality traits in rye (Secale cereale) introgression libraries

Introgression libraries can be used to localize genomic regions carrying quantitative trait loci (QTL). We used this approach to detect QTL regions affecting the per se performance of agronomic and quality traits with two rye (Secale cereale L.) introgression libraries. Our objectives were to detect candidate introgression lines (pre‐ILs) that have a different per se performance than the recurrent parent and to identify the underlying QTL regions. The introgression libraries containing 40 BC₂S₃ lines each were established with marker‐assisted backcrossing from crosses of the heterozygous Iranian primitive rye accession Altevogt 14160 and the elite inbred line L2053‐N. To assess the phenotypic effect of the donor chromosome segments (DCS) the pre‐ILs were evaluated for grain yield, plant height, thousand‐kernel weight, test weight, falling number and protein content in replicated field trials at five locations in Germany over 2 years. In total, 58 significant (P < 0.05) differences between pre‐ILs and L2053‐N were observed in each introgression library. The DCS in pre‐ILs differing from the recurrent parent possess most likely the responsible QTL. Genomic regions carrying favourable QTL alleles were detected for test weight, thousand‐kernel weight and protein content. We conclude that Altevogt 14160 can not only be used to enrich the genetic variation of the restricted hybrid rye gene pools but will also allow the breeder to efficiently detect favourable QTL for marker‐assisted selection.