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, i...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2016-10-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01600/full |
| _version_ | 1818837699539238912 |
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| author | Piotr Gawronski Magdalena Pawelkowicz Katarzyna Tofil Grzegorz Uszynski Saida Sharifova Saida Sharifova Shivaksh Ahluwalia Shivaksh Ahluwalia Tyrka Miroslaw Maria Wedzony Andrzej Kilian Hanna Bolibok-Bragoszewska |
| author_facet | Piotr Gawronski Magdalena Pawelkowicz Katarzyna Tofil Grzegorz Uszynski Saida Sharifova Saida Sharifova Shivaksh Ahluwalia Shivaksh Ahluwalia Tyrka Miroslaw Maria Wedzony Andrzej Kilian Hanna Bolibok-Bragoszewska |
| author_sort | Piotr Gawronski |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-19T03:26:39Z |
| format | Article |
| id | doaj.art-c8bd6c6225854497a0c30090f49642bf |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-19T03:26:39Z |
| publishDate | 2016-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-c8bd6c6225854497a0c30090f49642bf2022-12-21T20:37:36ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-10-01710.3389/fpls.2016.01600220028DArT Markers Effectively Target Gene Space in the Rye GenomePiotr Gawronski0Magdalena Pawelkowicz1Katarzyna Tofil2Grzegorz Uszynski3Saida Sharifova4Saida Sharifova5Shivaksh Ahluwalia6Shivaksh Ahluwalia7Tyrka Miroslaw8Maria Wedzony9Andrzej Kilian10Hanna Bolibok-Bragoszewska11Warsaw University of Life Sciences - SGGWWarsaw University of Life Sciences - SGGWWarsaw University of Life Sciences - SGGWDiversity Arrays Technology P/LWarsaw University of Life Sciences - SGGWGenetic Resources Institute of Azerbaijan National Academy of Sciences (ANAS)Warsaw University of Life Sciences - SGGWIndian Institute of TechnologyRzeszow University of TechnologyPedagogical University of CracowDiversity Arrays Technology P/LWarsaw University of Life Sciences - SGGWLarge 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.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01600/fullGenomicsfunctional annotationRyePooideaeTriticeaeDArT |
| spellingShingle | Piotr Gawronski Magdalena Pawelkowicz Katarzyna Tofil Grzegorz Uszynski Saida Sharifova Saida Sharifova Shivaksh Ahluwalia Shivaksh Ahluwalia Tyrka Miroslaw Maria Wedzony Andrzej Kilian Hanna Bolibok-Bragoszewska DArT Markers Effectively Target Gene Space in the Rye Genome Frontiers in Plant Science Genomics functional annotation Rye Pooideae Triticeae DArT |
| title | DArT Markers Effectively Target Gene Space in the Rye Genome |
| title_full | DArT Markers Effectively Target Gene Space in the Rye Genome |
| title_fullStr | DArT Markers Effectively Target Gene Space in the Rye Genome |
| title_full_unstemmed | DArT Markers Effectively Target Gene Space in the Rye Genome |
| title_short | DArT Markers Effectively Target Gene Space in the Rye Genome |
| title_sort | dart markers effectively target gene space in the rye genome |
| topic | Genomics functional annotation Rye Pooideae Triticeae DArT |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01600/full |
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