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A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R.
BMC Plant Biol. 2008 Sep 19; 8:95.BP

Abstract

BACKGROUND

Rye (Secale cereale L.) belongs to tribe Triticeae and is an important temperate cereal. It is one of the parents of man-made species Triticale and has been used as a source of agronomically important genes for wheat improvement. The short arm of rye chromosome 1 (1RS), in particular is rich in useful genes, and as it may increase yield, protein content and resistance to biotic and abiotic stress, it has been introgressed into wheat as the 1BL.1RS translocation. A better knowledge of the rye genome could facilitate rye improvement and increase the efficiency of utilizing rye genes in wheat breeding.

RESULTS

Here, we report on BAC end sequencing of 1,536 clones from two 1RS-specific BAC libraries. We obtained 2,778 (90.4%) useful sequences with a cumulative length of 2,032,538 bp and an average read length of 732 bp. These sequences represent 0.5% of 1RS arm. The GC content of the sequenced fraction of 1RS is 45.9%, and at least 84% of the 1RS arm consists of repetitive DNA. We identified transposable element junctions in BESs and developed insertion site based polymorphism markers (ISBP). Out of the 64 primer pairs tested, 17 (26.6%) were specific for 1RS. We also identified BESs carrying microsatellites suitable for development of 1RS-specific SSR markers.

CONCLUSION

This work demonstrates the utility of chromosome arm-specific BAC libraries for targeted analysis of large Triticeae genomes and provides new sequence data from the rye genome and molecular markers for the short arm of rye chromosome 1.

Authors+Show Affiliations

Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Olomouc, Czech Republic. bartos@ueb.cas.czNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

18803819

Citation

Bartos, Jan, et al. "A First Survey of the Rye (Secale Cereale) Genome Composition Through BAC End Sequencing of the Short Arm of Chromosome 1R." BMC Plant Biology, vol. 8, 2008, p. 95.
Bartos J, Paux E, Kofler R, et al. A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R. BMC Plant Biol. 2008;8:95.
Bartos, J., Paux, E., Kofler, R., Havránková, M., Kopecký, D., Suchánková, P., Safár, J., Simková, H., Town, C. D., Lelley, T., Feuillet, C., & Dolezel, J. (2008). A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R. BMC Plant Biology, 8, 95. https://doi.org/10.1186/1471-2229-8-95
Bartos J, et al. A First Survey of the Rye (Secale Cereale) Genome Composition Through BAC End Sequencing of the Short Arm of Chromosome 1R. BMC Plant Biol. 2008 Sep 19;8:95. PubMed PMID: 18803819.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R. AU - Bartos,Jan, AU - Paux,Etienne, AU - Kofler,Robert, AU - Havránková,Miroslava, AU - Kopecký,David, AU - Suchánková,Pavla, AU - Safár,Jan, AU - Simková,Hana, AU - Town,Christopher D, AU - Lelley,Tamas, AU - Feuillet,Catherine, AU - Dolezel,Jaroslav, Y1 - 2008/09/19/ PY - 2008/05/15/received PY - 2008/09/19/accepted PY - 2008/9/23/pubmed PY - 2008/11/6/medline PY - 2008/9/23/entrez SP - 95 EP - 95 JF - BMC plant biology JO - BMC Plant Biol VL - 8 N2 - BACKGROUND: Rye (Secale cereale L.) belongs to tribe Triticeae and is an important temperate cereal. It is one of the parents of man-made species Triticale and has been used as a source of agronomically important genes for wheat improvement. The short arm of rye chromosome 1 (1RS), in particular is rich in useful genes, and as it may increase yield, protein content and resistance to biotic and abiotic stress, it has been introgressed into wheat as the 1BL.1RS translocation. A better knowledge of the rye genome could facilitate rye improvement and increase the efficiency of utilizing rye genes in wheat breeding. RESULTS: Here, we report on BAC end sequencing of 1,536 clones from two 1RS-specific BAC libraries. We obtained 2,778 (90.4%) useful sequences with a cumulative length of 2,032,538 bp and an average read length of 732 bp. These sequences represent 0.5% of 1RS arm. The GC content of the sequenced fraction of 1RS is 45.9%, and at least 84% of the 1RS arm consists of repetitive DNA. We identified transposable element junctions in BESs and developed insertion site based polymorphism markers (ISBP). Out of the 64 primer pairs tested, 17 (26.6%) were specific for 1RS. We also identified BESs carrying microsatellites suitable for development of 1RS-specific SSR markers. CONCLUSION: This work demonstrates the utility of chromosome arm-specific BAC libraries for targeted analysis of large Triticeae genomes and provides new sequence data from the rye genome and molecular markers for the short arm of rye chromosome 1. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/18803819/A_first_survey_of_the_rye__Secale_cereale__genome_composition_through_BAC_end_sequencing_of_the_short_arm_of_chromosome_1R_ DB - PRIME DP - Unbound Medicine ER -