Development of E-chromosome Specific Molecular Markers for Thinopyrum elongatum in a Wheat Background.

Chen, S., Gao, Y., Zhu, X., Zhang, C., Cao, W., Fedak, G., He, Z., Chen, X., and Chen, J.M. (2015). "Development of E-chromosome Specific Molecular Markers for Thinopyrum elongatum in a Wheat Background.", Crop Science, 55(6), pp. 2777-2785. doi : 10.2135/cropsci2014.08.0539  Access to full text


Eleven primers were synthesized according to the reverse transcriptase and long terminal repeat (LTR) conserved regions of retrotransposons BARE-1 from barley (Hordeum vulgare L.) and RIRE-1 from rice (Oryza sativa L.). Fifty-two pairs of primer combinations based on these 11 primers were used for DNA amplification of Chinese Spring-Thinopyrum elongatum addition lines, substitution lines plus the two parents. It showed that 145 specific fragments of inter-simple sequence repeat (ISSR), inter-retrotransposon amplified polymorphism (IRAP), and retrotransposon microsatellite amplified polymorphism (REMAP) were obtained which distributed over all the seven E-genome chromosomes of Th. elongatum. Sixty specific fragments of ISSR, IRAP, and REMAP were randomly selected for cloning and sequencing. Thirty-four sequences were found not to be homologous with wheat (Triticum aestivum L.) sequences in GenBank, which were considered to be the specific sequences of Th. elongatum. Thirty-four pairs of primers based on these 34 specific sequences were synthesized, and 13 chromosome-specific markers of Th. elongatum were identified and converted into SCAR markers. The results indicated that ISSR, IRAP, and REMAP techniques can be used to develop chromosome-specific sequence-characterized amplified regions (SCAR) markers with good stability and repeatability. These specific SCAR markers can now be used to detect Th. elongatum chromosomes and possibly even some introgressed segments in a wheat background.

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