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Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat.
Genome. 2009 Jun; 52(6):576-87.G

Abstract

In hexaploid wheat (Triticum aestivum L.) (AABBDD, C=17 000 Mb), repeat DNA accounts for approximately 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 are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Aegilops tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shotgun sequences were used to search for RJM. Of the 300 RJM primer pairs tested, 269 (90%) amplified single bands from diploid Ae. tauschii. Of these 269 primer pairs, 260 (97%) amplified hexaploid wheat and 9 (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 38 RJM primers mapped on chromosome 6D, 31 (82%) were unambiguously mapped to delineated bins of the chromosome 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.

Authors+Show Affiliations

Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA.No 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, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

19483776

Citation

Wanjugi, Humphrey, et al. "Rapid Development of PCR-based Genome-specific Repetitive DNA Junction Markers in Wheat." Genome, vol. 52, no. 6, 2009, pp. 576-87.
Wanjugi H, Coleman-Derr D, Huo N, et al. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome. 2009;52(6):576-87.
Wanjugi, H., Coleman-Derr, D., Huo, N., Kianian, S. F., Luo, M. C., Wu, J., Anderson, O., & Gu, Y. Q. (2009). Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome, 52(6), 576-87. https://doi.org/10.1139/g09-033
Wanjugi H, et al. Rapid Development of PCR-based Genome-specific Repetitive DNA Junction Markers in Wheat. Genome. 2009;52(6):576-87. PubMed PMID: 19483776.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. AU - Wanjugi,Humphrey, AU - Coleman-Derr,Devin, AU - Huo,Naxin, AU - Kianian,Shahryar F, AU - Luo,Ming-Cheng, AU - Wu,Jiajie, AU - Anderson,Olin, AU - Gu,Yong Qiang, PY - 2009/6/2/entrez PY - 2009/6/2/pubmed PY - 2009/9/11/medline SP - 576 EP - 87 JF - Genome JO - Genome VL - 52 IS - 6 N2 - In hexaploid wheat (Triticum aestivum L.) (AABBDD, C=17 000 Mb), repeat DNA accounts for approximately 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 are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Aegilops tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shotgun sequences were used to search for RJM. Of the 300 RJM primer pairs tested, 269 (90%) amplified single bands from diploid Ae. tauschii. Of these 269 primer pairs, 260 (97%) amplified hexaploid wheat and 9 (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 38 RJM primers mapped on chromosome 6D, 31 (82%) were unambiguously mapped to delineated bins of the chromosome 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. SN - 0831-2796 UR - https://www.unboundmedicine.com/medline/citation/19483776/Rapid_development_of_PCR_based_genome_specific_repetitive_DNA_junction_markers_in_wheat_ L2 - https://cdnsciencepub.com/doi/10.1139/g09-033?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub=pubmed DB - PRIME DP - Unbound Medicine ER -