Molecular Genetics and Genomics

, Volume 289, Issue 6, pp 1347–1367 | Cite as

Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. × G. barbadense L.) RIL population

  • John Z. YuEmail author
  • Mauricio Ulloa
  • Steven M. Hoffman
  • Russell J. Kohel
  • Alan E. Pepper
  • David D. Fang
  • Richard G. Percy
  • John J. Burke
Original Paper


A quantitative trait locus (QTL) mapping was conducted to better understand the genetic control of plant architecture (PA), yield components (YC), and fiber properties (FP) in the two cultivated tetraploid species of cotton (Gossypium hirsutum L. and G. barbadense L.). One hundred and fifty-nine genomic regions were identified on a saturated genetic map of more than 2,500 SSR and SNP markers, constructed with an interspecific recombinant inbred line (RIL) population derived from the genetic standards of the respective cotton species (G. hirsutum acc. TM-1 × G. barbadense acc. 3-79). Using the single nonparametric and MQM QTL model mapping procedures, we detected 428 putative loci in the 159 genomic regions that confer 24 cotton traits in three diverse production environments [College Station F&B Road (FB), TX; Brazos Bottom (BB), TX; and Shafter (SH), CA]. These putative QTL loci included 25 loci for PA, 60 for YC, and 343 for FP, of which 3, 12, and 60, respectively, were strongly associated with the traits (LOD score ≥ 3.0). Approximately 17.7 % of the PA putative QTL, 32.9 % of the YC QTL, and 48.3 % of the FP QTL had trait associations under multiple environments. The At subgenome (chromosomes 1–13) contributed 72.7 % of loci for PA, 46.2 % for YC, and 50.4 % for FP while the Dt subgenome (chromosomes 14–26) contributed 27.3 % of loci for PA, 53.8 % for YC, and 49.6 % for FP. The data obtained from this study augment prior evidence of QTL clusters or gene islands for specific traits or biological functions existing in several non-homoeologous cotton chromosomes. DNA markers identified in the 159 genomic regions will facilitate further dissection of genetic factors underlying these important traits and marker-assisted selection in cotton.


Cotton (Gossypium spp.) DNA markers Plant architecture (PA) Yield components (YC) Fiber properties (FP) Quantitative trait loci (QTLs) 



J. Z. Yu, M. Ulloa, and S. M. Hoffman contributed equally to the work. This research was supported by U. S. Department of Agriculture, Agricultural Research Service projects 6202-21000-030-00D, 5303-21220-003-00D, and Cotton Incorporated fellowship to S. M. Hoffman (project 02-260). The authors thank J. Harris for his assistance in maintaining the TM-1 × 3-79 RIL mapping population, S. Young for his check on output analyses of comparative data sets, and J. Frelichowski for his assistance in field study and his review of the manuscript. Mention of trade names or commercial products in this manuscript is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture that is an equal opportunity provider and employer.

Supplementary material

438_2014_930_MOESM1_ESM.docx (88 kb)
Supplementary material 1 (DOCX 88 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2014

Authors and Affiliations

  • John Z. Yu
    • 1
    Email author
  • Mauricio Ulloa
    • 2
  • Steven M. Hoffman
    • 1
    • 3
  • Russell J. Kohel
    • 1
  • Alan E. Pepper
    • 3
  • David D. Fang
    • 4
  • Richard G. Percy
    • 1
  • John J. Burke
    • 2
  1. 1.USDA-ARSSouthern Plains Agricultural Research CenterCollege StationUSA
  2. 2.USDA-ARSPlant Stress and Germplasm Development Research UnitLubbockUSA
  3. 3.Texas A&M University, Biology DepartmentCollege StationUSA
  4. 4.USDA-ARSCotton Fiber Bioscience Research UnitNew OrleansUSA

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