Abstract
BackgroundThe improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology.ResultsMore than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool.ConclusionsThe established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye.
Highlights
The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research
Establishment and description of the rye expressed sequence tag (EST) resource Assembly The five independent sequencing runs produced between 364,343 and 681,787 reads corresponding to ~87 and ~166 Mb of raw data per inbred line (Table 1)
2,573,590 high quality reads with a median length of 216 nucleotides were obtained, totalling 548 Mb
Summary
The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology. Understanding the functional genetic basis of stress tolerance in rye will facilitate the improvement of stress tolerance in wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). Genetic and genomic resources are limited compared to other Triticeae. Available genomic resources for rye are restricted to one BAC library [10], a limited number of genetic markers http://wheat. Available genomic resources for rye are restricted to one BAC library [10], a limited number of genetic markers http://wheat. pw.usda.gov/GG2/index.shtml, and genetic maps with low marker density [11,12,13,14,15]
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