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Molecular characterization of the Gossypium Diversity Reference Set of the US National Cotton Germplasm Collection

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Abstract

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A core marker set containing markers developed to be informative within a single commercial cotton species can elucidate diversity structure within a multi-species subset of the Gossypium germplasm collection.

Abstract

An understanding of the genetic diversity of cotton (Gossypium spp.) as represented in the US National Cotton Germplasm Collection is essential to develop strategies for collecting, conserving, and utilizing these germplasm resources. The US collection is one of the largest world collections and includes not only accessions with improved yield and fiber quality within cultivated species, but also accessions possessing sources of abiotic and biotic stress resistance often found in wild species. We evaluated the genetic diversity of a subset of 272 diploid and 1,984 tetraploid accessions in the collection (designated the Gossypium Diversity Reference Set) using a core set of 105 microsatellite markers. Utility of the core set of markers in differentiating intra-genome variation was much greater in commercial tetraploid genomes (99.7 % polymorphic bands) than in wild diploid genomes (72.7 % polymorphic bands), and may have been influenced by pre-selection of markers for effectiveness in the commercial species. Principal coordinate analyses revealed that the marker set differentiated interspecific variation among tetraploid species, but was only capable of partially differentiating among species and genomes of the wild diploids. Putative species-specific marker bands in G. hirsutum (73) and G. barbadense (81) were identified that could be used for qualitative identification of misclassifications, redundancies, and introgression within commercial tetraploid species. The results of this broad-scale molecular characterization are essential to the management and conservation of the collection and provide insight and guidance in the use of the collection by the cotton research community in their cotton improvement efforts.

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Acknowledgments

The authors wish to acknowledge the contributions of S. Simpson of the USDA-ARS Genomics and Bioinformatics Research Unit who managed the whole process of the PCRs from setting up and proofing the plates to monitoring the data output. Without Ms. Simpson’s efforts and diligence this project could not have been completed. The authors also recognize the contributions of members of the USDA-ARS cotton breeding, genetics, and genomics project teams for their valuable technical assistance. This research project was supported by funding from Cotton Incorporated and USDA CRIS Nos. 6202-21000-031-00D (L.H., J.Y., J.F., R.P.), 6435-21000-016-00D (D.F.), 5347-21000-011-00D (M.G.), and 6402-21310-003-00D (B.S.). Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. The USDA is an equal opportunity provider and employer.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The authors note that this research is performed and reported in accordance with the ethical standards for scientific conduct in the United States of America.

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Authors and Affiliations

  1. Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX, USA

    Lori L. Hinze, John Z. Yu, James Frelichowski & Richard G. Percy

  2. Cotton Fiber Bioscience Research Unit, Southern Regional Research Center, USDA-ARS, New Orleans, LA, USA

    David D. Fang

  3. Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA

    Michael A. Gore

  4. Genomics and Bioinformatics Research Unit, Jamie Whitten Delta States Research Center, USDA-ARS, Stoneville, MS, USA

    Brian E. Scheffler

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  1. Lori L. Hinze
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  2. David D. Fang
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  3. Michael A. Gore
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  4. Brian E. Scheffler
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  6. James Frelichowski
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Correspondence to Richard G. Percy.

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Communicated by Alan H. Schulman.

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Hinze, L.L., Fang, D.D., Gore, M.A. et al. Molecular characterization of the Gossypium Diversity Reference Set of the US National Cotton Germplasm Collection. Theor Appl Genet 128, 313–327 (2015). https://doi.org/10.1007/s00122-014-2431-7

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