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Title: Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat

item WANJUGI, HUMPHREY - University Of California
item COLEMAN-DERR, DEVIN - University Of California
item HUO, NAXIN - University Of California
item KIANIAN, SHAHRYAR - North Dakota State University
item LUO, MING-CHENG - University Of California
item WU, JIAJIE - University Of California
item Anderson, Olin
item Gu, Yong

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/6/2009
Publication Date: 5/28/2009
Citation: Wanjugi, H., Coleman-Derr, D., Huo, N., Kianian, S.F., Luo, M., Wu, J., Anderson, O.D., Gu, Y.Q. 2009. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome. 52:576-587.

Interpretive Summary: Genetic and physical mapping in bread wheat is difficulty due to the presence of three genomes in a single cell. In this article, a novel method is developed to generate hundreds of molecular markers from repeat DNA regions from a diploid wheat species for mapping in hexaploid wheat. Such a method provides unlimited number of genome-specific markers which appeared to evenly distribute along a chromosome. This mapping technology can be easily applied to other important polyploid crops.

Technical Abstract: In hexaploid wheat (Triticum aestivum L.) (AABBDD, C=17,000Mb), repeat DNA accounts for ~ 90% of the genome of which transposable elements (TEs) constitute 60-80 %. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs between the homologous wheat genomes are conserved and collinear based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Ae. tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shot gun sequences were used to search for RJM. Out of the 300 RJM primer pairs tested, 269 (90 %) amplified single bands from diploid Ae. tauschii wheat. Of these 269 primers pairs, 260 (97 %) amplified in hexaploid wheat and 3 % amplified Ae. tauschii only. Among the RJM primers that amplified hexaploid wheat, 88 % were successfully assigned to individual chromosomes of the hexaploid D genome. Among the thirty eight RJM primers mapped on chromosome 6D, 31 (82 %) were unambiguously mapped to delineated bins of the chromosome 6D using various wheat deletion lines. Our results suggest that the unique RJM derived from the diploid D genome could facilitate genetic, physical, and radiation mapping of the hexaploid wheat D genome. ----------------------------------------------------------------------------