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 cerealeL.) 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 fivePooideaesequence 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.
Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences - SGGW Warsaw, Poland.
Piotr
P
Gawroński
Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences - SGGW Warsaw, Poland.
Magdalena
M
Pawełkowicz
Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences - SGGW Warsaw, Poland.
Katarzyna
K
Tofil
Diversity Arrays Technology P/L Bruce, ACT, Australia.
Grzegorz
G
Uszyński
Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences - SGGWWarsaw, Poland; Department of Biotechnology, Genetic Resources Institute of Azerbaijan National Academy of SciencesBaku, Azerbaijan.
Saida
S
Sharifova
Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences - SGGWWarsaw, Poland; Kusuma School of Biological Sciences, Indian Institute of TechnologyNew Delhi, India.
Shivaksh
S
Ahluwalia
Department of Biotechnology and Bioinformatics, Rzeszow University of Technology Rzeszow, Poland.
Mirosław
M
Tyrka
Department of Genetics and Cytology, Pedagogical University of Cracow Cracow, Poland.
Maria
M
Wędzony
Diversity Arrays Technology P/L Bruce, ACT, Australia.
Andrzej
A
Kilian
Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences - SGGW Warsaw, Poland.
Hanna
H
Bolibok-Brągoszewska
DArT; Secale; Triticeae Pooideae; functional annotation; genomics; rye