3 research outputs found
DArT Markers Effectively Target Gene Space in the Rye Genome
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
Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential
Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.Peer reviewe