PRJNA421405
Identification and in silico mapping of drought stress induced transcripts 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 an in silico mapping approach of drought regulated transcripts was performed. Two elite inbred lines of a German hybrid breeding program, which are known to respond differently to drought stress in the field, were exposed to drought under controlled environmental conditions and transcript profiling was conducted on cDNA libraries. These libraries were created from leaves and 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 and therefore eight libraries in total. Using massively parallel sequencing of cDNA, the expressed sequence tag (EST) resource available for rye was supplemented by 128,010 contigs. The expression level of 47,842 transcripts was determined using the deepSuperSAGE technology and the change in transcription rate with respect to drought treatment, genotype and tissue was determined. In addition, single nucleotide polymorphisms between the two genotypes were detected in 4,437 of the differentially expressed genes. Based on a comparative mapping approach using the genome zipper based linear gene order model of rye the chromosomal location of 2,869 transcripts was predicted. The established sequence resources provide a first comprehensive survey on the molecular basis of drought stress tolerance in rye and will further advance genetic and genomic research in this species.