African Journal of

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12340

Full Length Research Paper

Linkage disequilibrium and association mapping of drought tolerance in cotton (Gossypium hirsutum L.) germplasm population from diverse regions of Pakistan

Abdelhafiz Adam Dahab
  • Abdelhafiz Adam Dahab
  • Environmental and Natural Resources Research Institute (ENRRI), National Centre for Research (NCR), Khartoum, Sudan.
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Muhammad Saeed
  • Muhammad Saeed
  • Department of Botany, Government College University, Faisalabad, Pakistan.
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Nada Babiker Hamza
  • Nada Babiker Hamza
  • Commission for Biotechnology and Genetic Engineering, National Centre for Research, Khartoum, Sudan.
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Bahaeldeen Babiker Mohamed
  • Bahaeldeen Babiker Mohamed
  • Environmental and Natural Resources Research Institute (ENRRI), National Centre for Research (NCR), Khartoum, Sudan.
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Tayyab Husnain
  • Tayyab Husnain
  • Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan.
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  •  Received: 22 November 2015
  •  Accepted: 01 February 2016
  •  Published: 16 November 2016


Drought stress is a major abiotic stress that limits crop production. Molecular association mapping techniques through linkage disequilibrium (LD) can be effectively used to tag genomic regions involved in drought stress tolerance. With the association mapping approach, 90 genotypes of cotton Gossypium hirsutum, from diverse regions of Pakistan were used. The morpho-physiological traits of all genotypes were evaluated in greenhouse under well-watered and drought stress conditions. Mean squares from analysis of variance for all morpho-physiological traits revealed highly significant variations (P≤0.05) between water levels and genotypes. Cotton varieties were screened for polymorphism with 180 simple sequence repeat (SSR) markers. Out of these 180 SSR markers, 95 were polymorphic. Genotyping of the selected 95 SSR primer pairs generated 57.5% polymorphism, and the number of polymorphic alleles per primer was 2.10. Population structure, linkage disequilibrium, and association mapping between pairs of SSR marker loci were studied. The significance of pairwise LD (P≤0.005) among all possible SSR loci was evaluated at significant threshold values (R2≥0.05); 7.1% of the SSR marker pairs showed significant pairwise LD in 90 accessions of G. hirsutum. Also we observed a significant (R2) LD between 13 pairs of SSR loci; each pair within the same chromosome in a range of 180 cM between NAU1230 and NAU3095 loci in chromosome (D5) and 1.612 cM between NAU462 and NAU3414 in chromosome A9. This indicates tight linkage between two alleles on the same chromosome. Markers, NAU3414, NAU2691, NAU1141 and NAU1190 were associated with more than single traits under drought treatments. Highest phenotypic variance explaining (R2) was ascribed to NAU3011 chromosome D13 significantly (p£0.001) associated with root length under drought treatment.

Key words: Cotton Gossypium hirsutum, drought stress, association mapping, linkage disequilibrium (LD), simple sequence repeats (SSRs).


QTL, Quantitative trait loci; SSR, simple sequence repeat; TASSEL, trait analysis by association, evolution and linkage; GLM, general linear model; PL, plant length, PFW, plant fresh weight, SL, shoot length, RL, root length, SFW, shoot fresh weight, SDW, shoot dry weight, RDW, root dry weight, RFW, root fresh weight, RSR, root shoot ratio; RWC, relative water contents; LD, linkage disequilibrium.