, Volume 136, Issue 3, pp 401–417 | Cite as

Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm

  • Ibrokhim Y. Abdurakhmonov
  • Sukumar Saha
  • Jonnie N. Jenkins
  • Zabardast T. Buriev
  • Shukhrat E. Shermatov
  • Brain E. Scheffler
  • Alan E. Pepper
  • John Z. Yu
  • Russell J. Kohel
  • Abdusattor Abdukarimov


Cotton is the world’s leading cash crop, but it lags behind other major crops for marker-assisted breeding due to limited polymorphisms and a genetic bottleneck through historic domestication. This underlies a need for characterization, tagging, and utilization of existing natural polymorphisms in cotton germplasm collections. Here we report genetic diversity, population characteristics, the extent of linkage disequilibrium (LD), and association mapping of fiber quality traits using 202 microsatellite marker primer pairs in 335 G. hirsutum germplasm grown in two diverse environments, Uzbekistan and Mexico. At the significance threshold (r 2 ≥ 0.1), a genome-wide average of LD extended up to genetic distance of 25 cM in assayed cotton variety accessions. Genome wide LD at r 2 ≥ 0.2 was reduced to ~5–6 cM, providing evidence of the potential for association mapping of agronomically important traits in cotton. Results suggest linkage, selection, inbreeding, population stratification, and genetic drift as the potential LD-generating factors in cotton. In two environments, an average of ~20 SSR markers was associated with each main fiber quality traits using a unified mixed liner model (MLM) incorporating population structure and kinship. These MLM-derived significant associations were confirmed in general linear model and structured association test, accounting for population structure and permutation-based multiple testing. Several common markers, showing the significant associations in both Uzbekistan and Mexican environments, were determined. Between 7 and 43% of the MLM-derived significant associations were supported by a minimum Bayes factor at ‘moderate to strong’ and ‘strong to very strong’ evidence levels, suggesting their usefulness for marker-assisted breeding programs and overall effectiveness of association mapping using cotton germplasm resources.


Cotton germplasm Genetic diversity Fiber quality Linkage disequilibrium (LD) Simple sequence repeat (SSR) markers LD-based association mapping 



We acknowledge the Science and Technology Center of Ukraine for the project coordination, and the technical assistance of project participants of P120/P120A. We also thank the administration of Academy of Sciences of Uzbekistan for their continual support of the research efforts. We thank Drs. A. Abdullaev (Uzbek cotton germplasm curator), and S. M. Rizaeva for valuable suggestions on germplasm selection and phenotypic analyses in the Uzbekistan environment. We thank Ms Linda Ballard, Genomics laboratory, USDA ARS at Mississippi for useful suggestions during manuscript edition.


This project was funded by the Office of International Research Programs (OIRP) of United States Department of Agriculture (USDA) in the frame of USDA-Former Soviet Union (FSU) cooperation programs with the research grant of P120/P120A to IYA, RJK, JZY, SS, and AEP.


Mention of trademark or proprietary product does not constitute a guarantee or warranty of the product by the United States Department of Agriculture and does not imply its approval to the exclusion of other products that may also be suitable.

Supplementary material

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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Ibrokhim Y. Abdurakhmonov
    • 1
  • Sukumar Saha
    • 2
  • Jonnie N. Jenkins
    • 2
  • Zabardast T. Buriev
    • 1
  • Shukhrat E. Shermatov
    • 1
  • Brain E. Scheffler
    • 3
  • Alan E. Pepper
    • 4
  • John Z. Yu
    • 5
  • Russell J. Kohel
    • 5
  • Abdusattor Abdukarimov
    • 1
  1. 1.Center of Genomic Technologies, Institute of Genetics and Plant Experimental BiologyAcademy of Sciences of UzbekistanTashkentUzbekistan
  2. 2.Crop Science Research Laboratory, Genetics and Precision AgricultureUSDA-ARSMississippi StateUSA
  3. 3.USDA-ARSStonevilleUSA
  4. 4.Department of BiologyTexas A&M UniversityCollege StationUSA
  5. 5.Crop Germplasm Research UnitUSDA-ARSCollege StationUSA

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