Abstract
Large genome size and complexity hamper considerably the genomics research in relevant species. Rye (Secale cereale L.) has one of the largest genomes among cereal crops and repetitive sequences account for over 90% of its length. Diversity Arrays Technology is a high-throughput genotyping method, in which a preferential sampling of gene-rich regions is achieved through the use of methylation sensitive restriction enzymes. We obtained sequences of 6,177 rye DArT markers and following a redundancy analysis assembled them into 3,737 non-redundant sequences, which were then used in homology searches against five Pooideae sequence sets. In total 515 DArT sequences could be incorporated into publicly available rye genome zippers providing a starting point for the integration of DArT- and transcript-based genomics resources in rye. Using Blast2Go pipeline we attributed putative gene functions to 1101 (29.4%) of the non-redundant DArT marker sequences, including 132 sequences with putative disease resistance-related functions, which were found to be preferentially located in the 4RL and 6RL chromosomes. Comparative analysis based on the DArT sequences revealed obvious inconsistencies between two recently published high density consensus maps of rye. Furthermore we demonstrated that DArT marker sequences can be a source of SSR polymorphisms. Obtained data demonstrate that DArT markers effectively target gene space in the large, complex, and repetitive rye genome. Through the annotation of putative gene functions and the alignment of DArT sequences relative to reference genomes we obtained information, that will complement the results of the studies, where DArT genotyping was deployed, by simplifying the gene ontology and microcolinearity based identification of candidate genes.
Highlights
Rye (Secale cereale L., 2n = 2x = 14, 1 C = 7917 Mbp; Dolezel et al, 1998) is a member of the Poaceae family, which comprises 12 subfamilies with 11,000 species in total, including other cereal crops and the model plant Brachypodium (Kellogg, 2015)
Mapped (Milczarski et al, 2011), they differentiated diverse rye accessions (Bolibok-Bragoszewskaet al., 2014), they were located in the vicinity of QTLs for powdery mildew or leaf rust (Ciszkowicz et al, in preparation), or they were addressed to BAC clones following DArT based BAC library screening (Bolibok-Bragoszewskaet al., 2015)
DArT markers sequences from the Diversity Arrays Technology web site and 109 unpublished rye DArT marker sequences, consisted of 6,177 DArT marker sequences
Summary
Rye is a close relative of wheat and barley These three species are members of the Triticeae tribe and shared a common ancestor ca. DArT Sequences in Rye Genomics established for rye in 2009 with the development of a 1520clone DArT genotyping panel (Bolibok-Bragoszewskaet al., 2009) Since it was successfully applied for high density genetic map construction, both in rye and triticale (BolibokBragoszewskaet al., 2009; Milczarski et al, 2011; Tyrka et al., 2011, 2015), genome-wide germplasm characterization (BolibokBragoszewskaet al., 2014), QTL/gene mapping (Stojałowski et al., 2011; Miedaner et al, 2012; Myśków et al, 2012; Milczarski et al., 2016), and genomic selection (Wang et al, 2014, 2015; Schulthess et al, 2015). Low coverage chromosomal survey sequencing of flow sorted rye chromosomes was performed, and the resulting reads together with transcriptome assemblies were incorporated into rye genome zippers, which present a virtual linear gene order for seven rye chromosomes (Martis et al, 2013)
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