ArticleBMC plant biology2011
From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.).
Article in BMC plant biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
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- Whole-Genome-Based Web Genomic Resource for Water Buffalo (Frontiers in genetics · 2022Article
- Rapid Genome-Wide Location-Specific Polymorphic SSR Marker Discovery in Black Pepper by GBS Approach.Frontiers in plant science · 2022Article
- A ddRADseq Survey of the Genetic Diversity of Rye (Plants (Basel, Switzerland) · 2021Article
- LegumeSSRdb: A Comprehensive Microsatellite Marker Database of Legumes for Germplasm Characterization and Crop Improvement.International journal of molecular sciences · 2021Article
- Genomic Scan of Male Fertility Restoration Genes in a 'Gülzow' Type Hybrid Breeding System of Rye (International journal of molecular sciences · 2021Article
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- Salt-responsive transcriptome analysis of triticale reveals candidate genes involved in the key metabolic pathway in response to salt stress.Scientific reports · 2020Article
- The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific markers, and relationship with α-amylase activity.BMC genomics · 2020Article
- De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea).Scientific reports · 2020Article
- Article
- Gene Networks Underlying Cannabinoid and Terpenoid Accumulation in Cannabis.Plant physiology · 2019Article
- Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping-by-sequencing.Evolutionary applications · 2019Article
- Gene Expression Profiling and Fine Mapping Identifies a Gibberellin 2-Oxidase Gene Co-segregating With the Dominant Dwarfing GeneFrontiers in plant science · 2019Article
- VigSatDB: genome-wide microsatellite DNA marker database of three species of Vigna for germplasm characterization and improvement.Database : the journal of biological databases and curation · 2019Article
- Development of Genome-Wide SNP Markers for Barley via Reference- Based RNA-Seq Analysis.Frontiers in plant science · 2019Article
- Exploring new alleles for frost tolerance in winter rye.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
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11 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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