From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

BMC Plant Biology

Research Article

Thomas Schmutzer¹  Uwe Scholz¹  Martin Mascher¹  Stefan Taudien²  Ruonan Zhou³  Nils Stein³  Klaus FX Mayer⁴  Michael Seidel⁴  Grit Haseneyer⁵  Eva Bauer⁵  Chris-Carolin Schön⁵ 

[1] Bioinformatics and Information Technology, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany;Genome Analysis, Leibniz Institute for Age Research, Fritz-Lipmann-Institute (FLI), 07745, Jena, Germany;Genome Diversity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany;MIPS/IBIS, Institute for Bioinformatics and Systems Biology, Helmholtz Centre Munich, German Research Centre for Environmental Health (GmbH), 85764, Neuherberg, Germany;Plant Breeding, Technische Universität München, Centre of Life and Food Sciences Weihenstephan, 85354, Freising, Germany;

关键词: EST resource;    next generation sequencing;    Secale cereale;    Rye5K SNP array;    single nucleotide polymorphisms;   

DOI  :  10.1186/1471-2229-11-131

 received in 2011-02-16, accepted in 2011-09-28,  发布年份 2011

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Haseneyer et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.