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Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat.
Proc Natl Acad Sci U S A. 2005 Dec 27; 102(52):19243-8.PN

Abstract

The current view of wheat genome composition is that genes are compartmentalized into gene-rich and gene-poor regions. This model can be tested by analyzing randomly selected bacterial artificial chromosome (BAC) clones for gene content, followed by placement of these BACs onto physical and genetic maps. Map localization could be difficult for BACs that consist entirely of repeated elements. We therefore developed a technique where repeat junctions are used to generate unique markers. Four BAC clones from hexaploid wheat variety Chinese Spring were randomly selected and sequenced at 4- to 6-fold redundancy. About 50% of the BAC sequences corresponded to previously identified repeats, mainly LTR-retrotransposons, whereas most of the remaining DNA consisted of sequences with unknown origin or function. The average gene content was <1%, although each BAC contained one or two identified genes. Repeat boundaries were amplified and used to map each clone to a chromosome arm. Extrapolation from wheat-rice comparative knowledge suggests that three of the four BAC clones originate from "gene-rich" regions of the wheat genome. Nevertheless, because these BACs carry only a single gene (two BACs) or two genes (one BAC), the predicted gene density is approximately 1 gene per 75 kb, which is considerably lower than previously estimated gene densities (one gene per 5-20 kb) for gene-rich regions in wheat. This analysis of randomly selected wheat BAC clones suggests that genes are more evenly distributed in wheat than previously believed and substantiates the need for large-scale random BAC sequencing to determine wheat genome organization.

Authors+Show Affiliations

Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA. kdevos@uga.eduNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article

Language

eng

PubMed ID

16357197

Citation

Devos, Katrien M., et al. "Analysis and Mapping of Randomly Chosen Bacterial Artificial Chromosome Clones From Hexaploid Bread Wheat." Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 52, 2005, pp. 19243-8.
Devos KM, Ma J, Pontaroli AC, et al. Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. Proc Natl Acad Sci U S A. 2005;102(52):19243-8.
Devos, K. M., Ma, J., Pontaroli, A. C., Pratt, L. H., & Bennetzen, J. L. (2005). Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. Proceedings of the National Academy of Sciences of the United States of America, 102(52), 19243-8.
Devos KM, et al. Analysis and Mapping of Randomly Chosen Bacterial Artificial Chromosome Clones From Hexaploid Bread Wheat. Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):19243-8. PubMed PMID: 16357197.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. AU - Devos,Katrien M, AU - Ma,Jianxin, AU - Pontaroli,Ana C, AU - Pratt,Lee H, AU - Bennetzen,Jeffrey L, Y1 - 2005/12/15/ PY - 2005/12/17/pubmed PY - 2006/2/7/medline PY - 2005/12/17/entrez SP - 19243 EP - 8 JF - Proceedings of the National Academy of Sciences of the United States of America JO - Proc Natl Acad Sci U S A VL - 102 IS - 52 N2 - The current view of wheat genome composition is that genes are compartmentalized into gene-rich and gene-poor regions. This model can be tested by analyzing randomly selected bacterial artificial chromosome (BAC) clones for gene content, followed by placement of these BACs onto physical and genetic maps. Map localization could be difficult for BACs that consist entirely of repeated elements. We therefore developed a technique where repeat junctions are used to generate unique markers. Four BAC clones from hexaploid wheat variety Chinese Spring were randomly selected and sequenced at 4- to 6-fold redundancy. About 50% of the BAC sequences corresponded to previously identified repeats, mainly LTR-retrotransposons, whereas most of the remaining DNA consisted of sequences with unknown origin or function. The average gene content was <1%, although each BAC contained one or two identified genes. Repeat boundaries were amplified and used to map each clone to a chromosome arm. Extrapolation from wheat-rice comparative knowledge suggests that three of the four BAC clones originate from "gene-rich" regions of the wheat genome. Nevertheless, because these BACs carry only a single gene (two BACs) or two genes (one BAC), the predicted gene density is approximately 1 gene per 75 kb, which is considerably lower than previously estimated gene densities (one gene per 5-20 kb) for gene-rich regions in wheat. This analysis of randomly selected wheat BAC clones suggests that genes are more evenly distributed in wheat than previously believed and substantiates the need for large-scale random BAC sequencing to determine wheat genome organization. SN - 0027-8424 UR - https://www.unboundmedicine.com/medline/citation/16357197/Analysis_and_mapping_of_randomly_chosen_bacterial_artificial_chromosome_clones_from_hexaploid_bread_wheat_ L2 - http://www.pnas.org/cgi/pmidlookup?view=long&amp;pmid=16357197 DB - PRIME DP - Unbound Medicine ER -