QTL mapping of yield and fiber traits based on a four-way cross population in Gossypium hirsutum L.

  • Hongde Qin
  • Wangzhen Guo
  • Yuan-Ming Zhang
  • Tianzhen ZhangEmail author
Original Paper


Four-way cross (4WC) involving four different inbred lines frequently appears in the cotton breeding programs. However, linkage analysis and quantitative trait loci (QTL) mapping with molecular markers in cotton has largely been applied to populations derived from a cross between two inbred lines, and few results of QTL dissection were conducted in a 4WC population. In this study, an attempt was made to construct a linkage map and identify QTL for yield and fiber quality traits in 4WC derived from four different inbred lines in Gossypium hirsutum L. A linkage map was constructed with 285 SSR loci and one morphological locus, covering 2113.3 cM, approximately 42% of the total recombination length of the cotton genome. A total of 31 QTL with 5.1–25.8% of the total phenotypic variance explained were detected. Twenty-four common QTL across environments showed high stability, and six QTL were environment-specific. Several genomic segments affecting multiple traits were identified. The advantage of QTL mapping using a 4WC were discussed. This study presents the first example of QTL mapping using a 4WC population in upland cotton. The results presented here will enhance the understanding of the genetic basis of yield and fiber quality traits and enable further marker-assisted selection in cultivar populations in upland cotton.


Quantitative Trait Locus Quantitative Trait Locus Mapping Upland Cotton Significant Quantitative Trait Locus Lint Yield 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was financially supported in part by grants from the State Key Basic Research and Development Plan of China (2006CB101708), The National Natural Foundation for Outstanding Youth (30025029), High-tech program 863 (2006AA100105), The Changjiang Scholars and Innovative Research Team in University of MOE, China (IRT0432) and the 111 Project (B08025).


  1. Burton JW (1987) Quantitative genetics: results relevant to soybean breeding. In: Wilcox JR (ed) Soybeans: improvement, production and uses, 2nd edn. ASA, CSSA and SSSA, Madison, pp 211–247Google Scholar
  2. Cahaner A, Hillel J (1980) Estimating heritability and genetic correlation between traits from generations F2 and F3 of selffertilizing species: a comparison of three methods. Theor Appl Genet 58:33–38CrossRefGoogle Scholar
  3. Chen FQ, Foodlad MR, Hyman J, St.Clair DA, Beelaman RB (1999) Mapping of QTL for lycopene and other fruit traits in a Lycopersicum esculentum × L. pimpinefolium cross and comparison of QTL across tomato species. Mol Breed 5:283–299CrossRefGoogle Scholar
  4. Fryxell PA (1992) A revised taxonomic interpretation of Gossypium L. (Malvaceae). Rheedea 2:108–165Google Scholar
  5. Guo WZ, Cai CP, Wang CB, Han ZG, Song XL, Wang K, Niu XW, Wang C, Lu KY, Shi S, Zhang TZ (2007) A microsatellite-based, gene-rich linkage map reveals genome structure, function, and evolution in Gossypium. Genetics 176:527–541PubMedCrossRefGoogle Scholar
  6. Han ZG, Guo WZ, Song XL, Zhang TZ (2004) Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton. Mol Genet Genomics 272:308–327PubMedCrossRefGoogle Scholar
  7. Han ZG, Wang CB, Song XL, Guo WZ, Gou JY, Li CH, Cheng XY, Zhang TZ (2006) Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet 112:430–439PubMedCrossRefGoogle Scholar
  8. Huang ZK (1996) The cultivars and their pedigree of cotton in China. China Agriculture Press, BeijingGoogle Scholar
  9. Kimber G (1961) Basis of the diploid-like meiotic behavior of polyploid cotton. Nature 191:98–99CrossRefGoogle Scholar
  10. Knott SA, Neale DB, Sewell MM, Haley CS (1997) Multiple marker mapping of quantitative trait loci in an outbred pedigree of loblolly pine. Theor Appl Genet 94:810–820CrossRefGoogle Scholar
  11. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175Google Scholar
  12. Lacape JM, Nguyen TB, Thibivilliers S, Bojinov B, Courtois B, Cantrell RG, Burr B, Hau B (2003) A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum × Gossypium barbadense backcross population. Genome 46:612–626PubMedCrossRefGoogle Scholar
  13. Lander ES, Kruglyak L (1995) Genetic disstection of complex traits guidelines for interpreting and reporting linkage results. Nat Genetics 11:241–247CrossRefGoogle Scholar
  14. Lin YR, Schertz KF, Paterson AH (1995) Comparative analysis of QTL affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population. Genetics 141:391–411PubMedGoogle Scholar
  15. Lu Y, Curtiss J, Percy RG, Cantrell RG, Zhang JF (2005) Discovery of single nucleotide polymorphisim in selected fiber genes in cultivated tetraploid cotton. In: Proceedings of the Beltwide cotton conference, New Orleans, LA, USA, 5–9 January 2005. National Cotton Council of America, Memphis, TN, USAGoogle Scholar
  16. Luís FA, Natal AV (2004) Heritability and correlations among traits in four-way soybean crosses. Euphytica 136:81–91CrossRefGoogle Scholar
  17. Mei M, Syed NH, Gao S, Thaxton PM, Smith CW, Stelly DM, Chen ZJ (2004) Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theor Appl Genet 108:280–291PubMedCrossRefGoogle Scholar
  18. Meredith WR Jr (1992) Improving fiber strength through genetics and breeding. In: Benedict CR, Jividen GM (eds) Proceedings of cotton fiber cellulose: structure, function, and utilization conference, Savannah, GA, USA, 28–31 October 1992. Natl. Cotton Counc., Memphis, TN, USA, pp 289–302Google Scholar
  19. McCouch SR, Cho YG, Yano PE, Blinstrub M, Morishima H, Kinoshita T (1997) Report on QTL nomenclature. Rice Genet Newslett 14:11–13Google Scholar
  20. Nguyen TB, Giband M, Brottier P, Risterucci AM, Lacape JM (2004) Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers. Theor Appl Genet 109:167–175PubMedCrossRefGoogle Scholar
  21. Paterson AH, Brubaker CL, Wendel JF (1993) A rapid method for extraction of cotton (Gossypium spp) genomic DNA suitable for RFLP or PCR analysis. Plan Mol Biol Rep 11:122–127CrossRefGoogle Scholar
  22. Peng JH, Ronin YF, Fahima T, Röder MS, Li YC, Nevo ER, Korol A (2003) Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci 100(5):2489–2494PubMedCrossRefGoogle Scholar
  23. Qin HD, Zhang TZ (2008) Genetic linkage mapping based on SSR marker with a four-way cross population in Gossypium hirsutum L. J Nanjing Agri Univ (in press)Google Scholar
  24. Qureshi SN, Saha S, Kantety RV, Jenkins JN (2004) EST-SSR: a new class of genetic markers in cotton. J Cotton Sci 8:112–123Google Scholar
  25. Rao SQ, Xu SZ (1998) Mapping quantitative trait loci for ordered categorical traits in four-way crosses. Heredity 81:214–224PubMedCrossRefGoogle Scholar
  26. Reddy OUK, Pepper AE, Saha S, Jenkins JN, Brooks T, Bolek Y, El-Zik KM (2001) New dinucleotide and trinucleotide microsatellite marker resources for cotton genome research. J Cotton Sci 5:103–113Google Scholar
  27. Reinisch AJ, Dong JM, Brubaker CL, Wendel JF, Paterson AH (1994) A denseed RFLP map of cotton, Gossypium hirsutum × Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138:829–847PubMedGoogle Scholar
  28. Rong JK, Abbey C, Bowers JE, Brubaker CL, Chang CL, Chee PW, Delmonte TA, Ding XL, Garza JJ, Marler BS, Park CH, Pierce GJ, Rainey KM, Rastogi VK, Schulze SR, Trolinder NL, Wendel JF, Wilkins TA, Williams-Coplin TD, Wing RA, Wright RJ, Zhao XP, Zhu LH, Paterson AH (2004) A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166:389–417PubMedCrossRefGoogle Scholar
  29. Shappley ZW, Jenkins JN, Zhu J, McCarty JC (1998) Quantitative trait loci associated with yield and fiber traits of Upland cotton. J Cotton Sci 4:153–163Google Scholar
  30. Shen XL, Guo WZ, Zhu XF, Yuan YL, Yu JZ, Kohel RJ, Zhang TZ (2005) Molecular mapping of QTL for fiber qualities in three diverse lines in upland cotton using SSR markers. Mol Breed 15:169–181CrossRefGoogle Scholar
  31. Shen XL, Guo WZ, Lu QX, Zhu XF, Yuan YL, Zhang TZ (2006) Genetic mapping of quantitative trait loci for fiber quality and yield trait by RIL approach in Upland cotton. Euphytica 155:371–380CrossRefGoogle Scholar
  32. Smith JD, Kinmam ML (1965) The use of parent–offspring regression as an estimator of heritability. Crop Sci 5:595–596Google Scholar
  33. Stelly DM (1993) Interfacing cytogenetics with the cotton genome mapping effort. In: Proceedings of the Beltwide cotton improvement conference, National Cotton Council of America, Memphis, pp 1545–1550Google Scholar
  34. Ulloa M, Meredith WR Jr (2000) Genetic linkage map and QTL analysis of gronomic and fiber quality traits in an intraspecific population. J Cotton Sci 4:161–170Google Scholar
  35. Ulloa M, Saha S, Jenkins JN, Meredith WR Jr, McCarty JC Jr, Stelly DM (2005) Chromosomal assignment of RFLP linkage groups harboring important QTL on an intraspecific cotton (Gossypium hirsutum L) joinmap. J Hered 96(2):132–144PubMedCrossRefGoogle Scholar
  36. Van Ooijen JW (1999) LOD significance thresholds for QTL analysis in experimental populations of diploid species. Heredity 83:613–624PubMedCrossRefGoogle Scholar
  37. Van Ooijen JW (2004) MapQTL 5.0: Software for the mapping quantitative trait loci in experimental populations. Plant Research International, WageningenGoogle Scholar
  38. Van Ooijen JW, Voorrips RE (2001) JoinMapR Version 3.0: software for the calculation of genetic linkage maps. CPRO-DLO, WageningenGoogle Scholar
  39. Wang BH, Guo WZ, Zhu XF, Wu YT, Huang NT, Zhang TZ (2006) QTL mapping of fiber quality in an elite hybrid derived-RIL population of upland cotton. Euphytica 152(3):367–378CrossRefGoogle Scholar
  40. Wendel JF, Brubaker CL, Percial E (1992) Genetic diversity in gossypium hirsutum and the origin of Upland cotton. Am J Bot 79:1291–1310CrossRefGoogle Scholar
  41. Xu S (1996) Mapping quantitative trait loci using four-way crosses. Genet Res 68:175–181CrossRefGoogle Scholar
  42. Yu JP, Yong-Ha, Lazo GR, Kohel RJ (1998) Molecular mapping of the cotton genome: QTL analysis of fiber quality properties. In: Proceedings of Beltwide cotton conference, San Diego, CA, USA, 5–9 January, Natl Cotton Counc. Am., Memphis, TN, USA, p 485Google Scholar
  43. Zhang J, Wu YT, Guo WZ, Zhang TZ (2000) Fast screening of SSR markers in cotton with PAGE/silver staining. Cotton Sci Sini 12:267–269Google Scholar
  44. Zhang TZ, Yuan YL, Yu JZ, Guo WZ, Kohel RJ (2003) Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection. Theor Appl Genet 106:262–268PubMedGoogle Scholar
  45. Zhang JF, Lu YZ, Yu SX (2005a) Cleaved AFLP (cAFLP), a modified fragment length polymorphism analysis for cotton. Theor Appl Genet 111:1385–1395PubMedCrossRefGoogle Scholar
  46. Zhang ZS, Xiao YH, Luo M, Li XB, Luo XY, Hou L, Li DM, Pei Y (2005b) Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.). Euphytica 144:91–99CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Hongde Qin
    • 1
  • Wangzhen Guo
    • 1
  • Yuan-Ming Zhang
    • 1
  • Tianzhen Zhang
    • 1
    Email author
  1. 1.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research InstituteNanjing Agricultural UniversityNanjingPeople’s Republic of China

Personalised recommendations