Data to: Development and application of a molecular marker resource for improving drought stress tolerance in rye (Secale cereale L.)

Rye (Secale cereale L.) is an important cereal crop in Northern Europe and known for its outstanding tolerance to biotic and abiotic stress including drought. Although the application of next generation sequencing increased the genomic resources for rye significantly, only limited knowledge is yet available on transcripts involved in drought stress tolerance. To identify and map respective genes, transcription profiling combined with in silico mapping of drought-regulated transcripts was performed. Two elite inbred lines of a German hybrid breeding program were exposed to drought under controlled conditions. RNA-seq was performed on cDNA libraries from leaves and from a bulk comprising flag leaves, ears and shoots, respectively. Each of these libraries was derived from both, a stressed and a well-watered variant, resulting in four libraries per genotype, i.e. eight libraries in total. The resulting sequence information supplemented the expressed sequence tag (EST) resource available for rye with 128,010 contigs (S1.fasta). Gene expression was quantified by DeepSuperSAGE tag-based transcription profiling and the response to stress of 47,842 transcripts was determined with respect to drought treatment, genotype and tissue (S3.tsv). In addition, 19,826 single nucleotide polymorphisms (SNP) between the two genotypes (S2.tsv) were detected in 4,437 of the differentially expressed genes (S4.fasta). The chromosomal location of 2,869 transcripts was predicted by comparative mapping using the genome zipper linear gene order model of cereals (S5.tsv). The gene expression data and polymorphisms established here provide a deeper insight in the molecular basis of drought stress response in rye (S6.tsv) and will help to further promote breeding for abiotic stress tolerance in rye and in closely related important cereals. To evaluate the data a bi-parental population was genotyped with the marker resource and phenotyped. Subsequently a genetic map was built (S7.tsv), and a QTL mapping conducted to prove the value of the newly developed resource.