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Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population

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Abstract

There is an immediate need for a high-density genetic map of cotton anchored with fiber genes to facilitate marker-assisted selection (MAS) for improved fiber traits. With this goal in mind, genetic mapping with a new set of microsatellite markers [comprising both simple (SSR) and complex (CSR) sequence repeat markers] was performed on 183 recombinant inbred lines (RILs) developed from the progeny of the interspecific cross Gossypium hirsutum L. cv. TM1 × Gossypium barbadense L. Pima 3-79. Microsatellite markers were developed using 1557 ESTs-containing SSRs (≥10 bp) and 5794 EST-containing CSRs (≥12 bp) obtained from ~14,000 consensus sequences derived from fiber ESTs generated from the cultivated diploid species Gossypium arboreum L. cv AKA8401. From a total of 1232 EST-derived SSR (MUSS) and CSR (MUCS) primer-pairs, 1019 (83%) successfully amplified PCR products from a survey panel of six Gossypium species; 202 (19.8%) were polymorphic between the G. hirsutum L. and G. barbadense L. parents of the interspecific mapping population. Among these polymorphic markers, only 86 (42.6%) showed significant sequence homology to annotated genes with known function. The chromosomal locations of 36 microsatellites were associated with 14 chromosomes and/or 13 chromosome arms of the cotton genome by hypoaneuploid deficiency analysis, enabling us to assign genetic linkage groups (LG) to specific chromosomes. The resulting genetic map consists of 193 loci, including 121 new fiber loci not previously mapped. These fiber loci were mapped to 19 chromosomes and 11 LG spanning 1277 cM, providing approximately 27% genome coverage. Preliminary quantitative trait loci analysis suggested that chromosomes 2, 3, 15, and 18 may harbor genes for traits related to fiber quality. These new PCR-based microsatellite markers derived from cotton fiber ESTs will facilitate the development of a high-resolution integrated genetic map of cotton for structural and functional study of fiber genes and MAS of genes that enhance fiber quality.

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Acknowledgements

This research was supported, in part, by Cotton Incorporated Project Nos. 03-398 and 03-321CA (to M.U.) and the NSF Plant Genome Research Program (DBI 9872630 to T.A.W). We would like to thank James Frelichowski, Ravinder Gill and Gregory Allen for running agarose gels. We would like to gratefully acknowledge Cotton Inc. for its support on this project. We also would like to acknowledge the U.S.-Egypt Joint Cotton Project (BIO7-001-015) for providing partial support of Magdy S. Alabady at the USDA-ARS, WICS, Cotton Enhancement Program.

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Authors and Affiliations

  1. Biotechnology Department, Sakata Seed America, Inc., Salinas, CA, 93907, USA

    Young-Hoon Park

  2. Department of Plant Sciences, University of California, Davis, CA, 95616, USA

    Magdy S. Alabady, Brad Sickler & Thea A. Wilkins

  3. USDA-ARS, Germplasm Research Unit, College Station, TX, 77845, USA

    John Yu & Russell J. Kohel

  4. Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA

    David M. Stelly

  5. Plant Biotechnology Research Laboratory, Faculty of Agriculture, Cairo University, Cairo, Egypt

    Magdy S. Alabady & Osama M. El-Shihy

  6. Cotton Incorporated, Cary, NC, 27513, USA

    Roy G. Cantrell

  7. WCIS Research Unit, Cotton Enhancement Program, USDA-ARS, 17053 N. Shafter Ave., Shafter, CA, 93263, USA

    Mauricio Ulloa

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  1. Young-Hoon Park
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  2. Magdy S. Alabady
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  3. Mauricio Ulloa
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  6. John Yu
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  8. Russell J. Kohel
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  9. Osama M. El-Shihy
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  10. Roy G. Cantrell
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Correspondence to Mauricio Ulloa.

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Communicated by R. Hagemann

Names are necessary to report factually on 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.

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Park, YH., Alabady, M.S., Ulloa, M. et al. Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol Genet Genomics 274, 428–441 (2005). https://doi.org/10.1007/s00438-005-0037-0

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