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Towards a whole-genome sequence for rye (Secale cereale L.)
Technical University of Munich, Germany.
Leibniz Institute Plant Genet and Crop Plant Research IPK Gat, Germany.
University of Hohenheim, Germany.
Leibniz Institute Plant Genet and Crop Plant Research IPK Gat, Germany.
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2017 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 89, no 5, p. 853-869Article in journal (Refereed) Published
Abstract [en]

We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.

Place, publisher, year, edition, pages
WILEY , 2017. Vol. 89, no 5, p. 853-869
Keywords [en]
Secale cereale L.; rye; whole-genome shotgun sequencing; de novo genome assembly; single nucleotide variants; Rye600k genotyping array; high-density genetic map; rye genome zipper; diversity; selection signals
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:liu:diva-136664DOI: 10.1111/tpj.13436ISI: 000395810800001PubMedID: 27888547OAI: oai:DiVA.org:liu-136664DiVA, id: diva2:1089754
Note

Funding Agencies|German Federal Ministry of Education and Research (BMBF) within project RYE-SELECT [0315946A-E]

Available from: 2017-04-20 Created: 2017-04-20 Last updated: 2017-05-08

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Martis, Mihaela-Maria
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