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Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends

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Abstract

Fine mapping and positional cloning will eventually improve with the anchoring of additional markers derived from genomic clones such as BACs. From 2,603 new BAC-end genomic sequences from Gossypium hirsutum Acala ‘Maxxa’, 1,316 PCR primer pairs (designated as MUSB) were designed to flank microsatellite or simple sequence repeat motif sequences. Most (1164 or 88%) MUSB primer pairs successfully amplified DNA from three species of cotton with an average of three amplicons per marker and 365 markers (21%) were polymorphic between G. hirsutum and G. barbadense. An interspecific RIL population developed from the above two entries was used to map 433 marker loci and 46 linkage groups with a genetic distance of 2,126.3 cM covering approximately 45% of the cotton genome and an average distance between two loci of 4.9 cM. Based on genome-specific chromosomes identified in G. hirsutum tetraploid (A and D), 56.9% of the coverage was located on the A subgenome while 39.7% was assigned to the D subgenome in the genetic map, suggesting that the A subgenome may be more polymorphic and recombinationally active than originally thought. The linkage groups were assigned to 23 of the 26 chromosomes. This is the first genetic map in which the linkage groups A01 and A02/D03 have been assigned to specific chromosomes. In addition the MUSB-derived markers from BAC-end sequences markers allows fine genetic and QTL mapping of important traits and for the first time provides reconciliation of the genetic and physical maps. Limited QTL analyses suggested that loci on chromosomes 2, 3, 12, 15 and 18 may affect variation in fiber quality traits. The original BAC clones containing the newly mapped MUSB that tag the QTLs provide critical DNA regions for the discovery of gene sequences involved in biological processes such as fiber development and pest resistance in cotton.

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Acknowledgements

We would like to gratefully acknowledge Cotton Inc. for its support on this project under a Cotton Incorporated Fellowship (Cary, NC) for James Frelichowski. The sequences of these markers are made public through the Cotton Microsatellite Database (CMD, http://www.mainlab.clemson.edu/cmd/projects/) as part of a community-wide initiative to increase coverage of the cotton genome. Names are necessary to report factually in available data; however, the USDA neither guarantees nor warrants the standard of products or service, and the use of the name by the USDA implies no approval of the products or service to the exclusion of others that may also be suitable. This research was supported in part, by Cotton Incorporated Project Number 05-704 (to MU) under the C.I. Fellowship program.

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Authors and Affiliations

  1. USDA-ARS, W.I.C.S. Res. Unit, Cotton Enhancement Program, Shafter, CA, USA

    James E. Frelichowski Jr & Mauricio Ulloa

  2. Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA

    Michael B. Palmer, Dorrie Main & Jeffrey P. Tomkins

  3. Cotton Incorporated, Cary, NC, USA

    Roy G. Cantrell

  4. Texas A&M University, College Station, TX, USA

    David M. Stelly

  5. USDA-ARS, College Station, TX, USA

    John Yu & Russell J. Kohel

  6. 17053 N. Shafter Ave, Shafter, CA, 93263, USA

    Mauricio Ulloa

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  1. James E. Frelichowski Jr
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  2. Michael B. Palmer
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  3. Dorrie Main
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  4. Jeffrey P. Tomkins
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  7. John Yu
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  9. Mauricio Ulloa
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Correspondence to Mauricio Ulloa.

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Frelichowski, J.E., Palmer, M.B., Main, D. et al. Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends. Mol Genet Genomics 275, 479–491 (2006). https://doi.org/10.1007/s00438-006-0106-z

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