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Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1.
Theor Appl Genet. 2008 Oct; 117(6):915-26.TA

Abstract

We developed 74 microsatellite marker primer pairs yielding 76 polymorphic loci, specific for the short arm of rye chromosome 1R (1RS) in wheat background. Four libraries enriched for microsatellite motifs AG, AAG, AC and AAC were constructed from DNA of flow-sorted 1RS chromosomes and 1,290 clones were sequenced. Additionally, 2,778 BAC-end-sequences from a 1RS specific BAC library were used for microsatellite screening and marker development. From 724 designed primer pairs, 119 produced 1RS specific bands and 74 of them showed polymorphism in a set of ten rye genotypes. We show that this high attrition rate was due to the highly repetitive nature of the rye genome consisting of a large number of transposable elements. We mapped the 76 polymorphic loci physically into three regions (bins) on 1RS; 29, 30 and 17 loci were assigned to the distal, intercalary and proximal regions of the 1RS arm, respectively. The average polymorphism information content increases with distance from the centromere, which could be due to an increased recombination rate along the chromosome arm toward's the telomere. Additionally, we demonstrate, using the data of the whole rice genome, that the intra-genomic length variation of microsatellites correlates (r = 0.87) with microsatellite polymorphism. Based on these results we suggest that an analysis of the microsatellite length variation is conducted for each species prior to microsatellite development, provided that sufficient sequence information is available. This will allow to selectively design microsatellite markers for motifs likely to yield a high level of polymorphism.

Authors+Show Affiliations

Department for Agrobiotechnology, Institute for Plant Production Biotechnology, University of Natural Resources and Applied Life Sciences, Konrad Lorenz Str. 20, 3430 Tulln, Austria. tamas.lelley@boku.ac.atNo 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)

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

Language

eng

PubMed ID

18626624

Citation

Kofler, Robert, et al. "Development of Microsatellite Markers Specific for the Short Arm of Rye (Secale Cereale L.) Chromosome 1." TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, vol. 117, no. 6, 2008, pp. 915-26.
Kofler R, Bartos J, Gong L, et al. Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1. Theor Appl Genet. 2008;117(6):915-26.
Kofler, R., Bartos, J., Gong, L., Stift, G., Suchánková, P., Simková, H., Berenyi, M., Burg, K., Dolezel, J., & Lelley, T. (2008). Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 117(6), 915-26. https://doi.org/10.1007/s00122-008-0831-2
Kofler R, et al. Development of Microsatellite Markers Specific for the Short Arm of Rye (Secale Cereale L.) Chromosome 1. Theor Appl Genet. 2008;117(6):915-26. PubMed PMID: 18626624.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1. AU - Kofler,Robert, AU - Bartos,Jan, AU - Gong,Li, AU - Stift,Gertraud, AU - Suchánková,Pavla, AU - Simková,Hana, AU - Berenyi,Maria, AU - Burg,Kornel, AU - Dolezel,Jaroslav, AU - Lelley,Tamas, Y1 - 2008/07/15/ PY - 2007/11/12/received PY - 2008/06/11/accepted PY - 2008/7/16/pubmed PY - 2009/2/21/medline PY - 2008/7/16/entrez SP - 915 EP - 26 JF - TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik JO - Theor Appl Genet VL - 117 IS - 6 N2 - We developed 74 microsatellite marker primer pairs yielding 76 polymorphic loci, specific for the short arm of rye chromosome 1R (1RS) in wheat background. Four libraries enriched for microsatellite motifs AG, AAG, AC and AAC were constructed from DNA of flow-sorted 1RS chromosomes and 1,290 clones were sequenced. Additionally, 2,778 BAC-end-sequences from a 1RS specific BAC library were used for microsatellite screening and marker development. From 724 designed primer pairs, 119 produced 1RS specific bands and 74 of them showed polymorphism in a set of ten rye genotypes. We show that this high attrition rate was due to the highly repetitive nature of the rye genome consisting of a large number of transposable elements. We mapped the 76 polymorphic loci physically into three regions (bins) on 1RS; 29, 30 and 17 loci were assigned to the distal, intercalary and proximal regions of the 1RS arm, respectively. The average polymorphism information content increases with distance from the centromere, which could be due to an increased recombination rate along the chromosome arm toward's the telomere. Additionally, we demonstrate, using the data of the whole rice genome, that the intra-genomic length variation of microsatellites correlates (r = 0.87) with microsatellite polymorphism. Based on these results we suggest that an analysis of the microsatellite length variation is conducted for each species prior to microsatellite development, provided that sufficient sequence information is available. This will allow to selectively design microsatellite markers for motifs likely to yield a high level of polymorphism. SN - 0040-5752 UR - https://www.unboundmedicine.com/medline/citation/18626624/Development_of_microsatellite_markers_specific_for_the_short_arm_of_rye__Secale_cereale_L___chromosome_1_ L2 - https://dx.doi.org/10.1007/s00122-008-0831-2 DB - PRIME DP - Unbound Medicine ER -