Detecting footprint of selection in rye (Secale cereale L.) - unraveling the past for future crop improvement

• Applicant: Dr. Grit Haseneyer
• Subject Area: Plant Breeding and Plant Pathology
• Term: from 2010 to 2014
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 188323228

Much is known about the breeding history of cereals but the effects of anthropogenic/artificial selection on cereal genomes have rarely been examined. Main emphasis of the proposed project is the identification of genes subject to selection in rye (Secale cereale L.). The effect of selection during rye breeding will be investigated by working on three hypotheses: 1) Increasing crop improvement is correlated with a reduction of nucleotide diversity. 2) The DNA sequence linked to an advantageous allele increases to high frequency and experiences a loss of pre-existing polymorphism (=‘selective sweep‘). 3) Signatures of selective sweeps are observed in the chromosomal region affected by the beneficial mutation. Applying genome capture technology and high-throughput next generation sequencing, more than 500 genes will be sequenced in a collection comprising rye populations that represent the breeding history of rye from founder landraces to elite inbred lines. Sequence analysis encompasses exon-intron assignment, SNP detection, nucleotide diversity analysis, and the determination of linkage disequilibrium patterns within and between genes as well as within and between populations. With this large-scale selection screen we aim to establish a first-generation map of selection for rye. The identified genes provide candidate genes for agronomic important traits and are relevant to association studies.

• DFG Programme: Research Grants