, Volume 195, Issue 1, pp 143–156 | Cite as

Molecular tagging of QTLs for fiber quality and yield in the upland cotton cultivar Acala-Prema

  • Ning Zhiyuan
  • Hong Chen
  • Hongxian Mei
  • Tianzhen ZhangEmail author


Cotton is a high-value per acre crop that is produced as a raw material for the textile industry. With the development of new technologies in the textile industry, much attention has been paid to fiber quality in conjunction with yield. The introgression cultivar “Acala Prema” is extensively planted in the Carolina/USA for its good fiber qualities, high yields and tolerance to Verticillium wilt. To conduct QTL mapping for fiber quality and yield in Acala-Prema, we developed a population of 180 recombinant inbred lines (RILs) from a single seed derived from a cross between this line and Chinese cultivar 86-1. We examined the yield performance of the RILs in five Chinese environments and fiber qualities in seven Chinese environments. A genetic linkage map comprising 279 loci was constructed using this RIL population, chiefly with SSR markers, and QTLs were repeatedly identified across diverse environments using the composite interval mapping method. A total of 86 nonredundant QTLs for yield and its components and fiber qualities were independently detected in five or seven environments; Prema alleles were responsible for the increase in trait values for 46 QTLs, while 86-1 was responsible for 40 QTLs. Notably, we detected the stable fiber strength QTL qFS-D3-1, which explained 4.51–17.55 % of PV, with LOD scores ranging from 2.83 to 7.09, and the fiber length qFL-D11-1, which explained 10.02–25.34 % of the PV. Eighteen environment epistatic QTLs were also detected. The QTLs detected in this study provide new information for improving fiber quality and may be especially valuable for marker-assisted selection.


QTL mapping Fiber strength Fiber length Recombinant inbred lines Cotton breeding 



Quantitative trait locus/loci


Recombinant inbred line


Simple sequence repeat


Expressed sequence tag



This work financially supported in part by Grants from the China National 973 Program (2011CB109300), 863 (2011AA10A102, 2012AA101108-04-04), and the Priority Academic Program Development of Jiangsu Higher Education Institutions.

Supplementary material

10681_2013_990_MOESM1_ESM.docx (58 kb)
Supplementary material 1 (DOCX 58 kb)


  1. Aguado A, Santos B, Blanco C, Romero F (2008) Study of gene effects for cotton yield and Verticillium wilt tolerance in cotton plant (Gossypium hirsutum L.). Field Crops Res 107:78–86CrossRefGoogle Scholar
  2. Aguado A, De Los Santos B, Gamane D, García del Moral LF, Romero F (2010) Gene effects for cotton-fiber traits in cotton plant (Gossypium hirsutum L.) under Verticillium conditions. Field Crops Res 116:209–217CrossRefGoogle Scholar
  3. Bowman D, Gutierrez O, Percy R, Calhoun D, May O (2006) Pedigrees of upland and pima cotton cultivars released between 1970 and 2005. Miss Agric For Exp Station Tech Bull 1155:57Google Scholar
  4. Cantrell R, Hughs E, Lu Y, Zhang J (2005) Molecular marker diversity and field performance in commercial cotton cultivars evaluated in the Southwestern USA. Crop Sci 45:1483–1490CrossRefGoogle Scholar
  5. Chen H, Qian N, Guo W, Song Q, Li B, Deng F, Dong C, Zhang T (2009) Using three overlapped RILs to dissect genetically clustered QTL for fiber strength on Chro. D8 in upland cotton. Theor Appl Genet 119:605–612PubMedCrossRefGoogle Scholar
  6. Guo W, Cai C, Wang C, Zhao L, Wang L, Zhang T (2008) A preliminary analysis of genome structure and composition in Gossypium hirsutum. BMC Genomics 9:314PubMedCrossRefGoogle Scholar
  7. Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T (2006) Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet 112:430–439PubMedCrossRefGoogle Scholar
  8. He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Zhang YX, Li W (2007) QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum×Gossypium barbadense. Euphytica 153:181–197CrossRefGoogle Scholar
  9. Kohel RJ, Yu J, Park YH, Lazo GR (2001) Molecular mapping and characterization of traits controlling fiber quality in cotton. Euphytica 121:163–172CrossRefGoogle Scholar
  10. Lacape JM, Nguyen TB, Thibivilliers S, Bojinov B, Courtois B, Cantrell R, 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
  11. Lacape JM, Nguyen TB, Courtois B, Belot JL, Roques S, Hau B, Giband M, Gourlot JP, Gawryziak G (2005) QTL analysis of cotton fiber quality using multiple × backcross generations. Crop Sci 45:123–140Google Scholar
  12. Li H, Ribaut J-M, Li Z, Wang J (2008) Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations. Theor Appl Genet 116:243–260PubMedCrossRefGoogle Scholar
  13. Liu R, Wang B, Guo W, Qin Y, Wang L, Zhang Y, Zhang T (2012) Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L. Mol Breed 29:297–311CrossRefGoogle Scholar
  14. Lorieux M, Goffinet B, Perrier X, León DG, Lanaud C (1995) Maximum-likelihood models for mapping genetic markers showing segregation distortion. 1. Backcross populations. Theor Appl Genet 90:73–80PubMedGoogle Scholar
  15. McCouch S, Cho Y, Yano P, Paul E, Blinstrub M (1997) Report on QTL nomenclature. Rice Genet Newslett 14:11–13Google Scholar
  16. Mei M, Syed N, Gao W, Thaxton P, Smith C, Stelly D, Chen Z (2004) Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theor Appl Genet 108:280–291PubMedCrossRefGoogle Scholar
  17. Park Y-H, Alabady M, Ulloa M, Sickler B, Wilkins T, Yu J, Stelly D, Kohel R, El-Shihy O, Cantrell R (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol Genet Genomics 274:428–441PubMedCrossRefGoogle Scholar
  18. Paterson AH, Brubaker CL, Wendel JF (1993) A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Mol Biol Rep 11:122–127CrossRefGoogle Scholar
  19. Paterson AH, Saranga Y, Menz M, Jiang CX, Wright RJ (2003) QTL analysis of genotype × environment interactions affecting cotton fiber quality. Theor Appl Genet (Theoretische und angewandte Genetik) 106:384–396Google Scholar
  20. Shen X, Guo W, Zhu X, Yuan Y, Yu JZ, Kohel RJ, Zhang T (2005) Molecular mapping of QTLs for fiber qualities in three diverse lines in upland cotton using SSR markers. Mol Breed 15:169–181CrossRefGoogle Scholar
  21. Shen X, Guo W, Lu Q, Zhu X, Yuan Y, Zhang T (2006) Genetic mapping of quantitative trait loci for fiber quality and yield trait by RIL approach in upland cotton. Euphytica 155:371–380CrossRefGoogle Scholar
  22. Ulloa M, Meredith WR Jr (2000) Genetic linkage map and QTL analysis of agronomic and fiber quality traits in an intraspecific population. J Cotton Sci 4:161–170Google Scholar
  23. Ulloa M, Saha S, Jenkins JN, Meredith WR Jr, McCarty JC Jr, Stelly DM (2005) Chromosomal assignment of RFLP linkage groups harboring important QTLs on an intraspecific cotton (Gossypium hirsutum L.) Joinmap. J Hered 96:132–144PubMedCrossRefGoogle Scholar
  24. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLsGoogle Scholar
  25. Wang G, Dong J, Paterson A (1995) The distribution of Gossypium hirsutum chromatin in G. barbadense germ plasm: molecular analysis of introgressive plant breeding. Theor Appl Genet 91:1153–1161PubMedCrossRefGoogle Scholar
  26. Wang K, Song X, Han Z, Guo W, Yu JZ, Sun J, Pan J, Kohel RJ, Zhang T (2006) Complete assignment of the chromosomes of Gossypium hirsutum L. by translocation and fluorescence in situ hybridization mapping. Theor Appl Genet 113:73–80PubMedCrossRefGoogle Scholar
  27. Wang B, Guo W, Zhu X, Wu Y, Huang N, Zhang T (2007) QTL mapping of yield and yield components for elite hybrid derived-RILs in upland cotton. J Genet Genomics 34:35–45PubMedCrossRefGoogle Scholar
  28. Wang K, Wang ZW, Li FG, Ye WW, Wang JY, Song GL, Yue Z, Cong L, Shang HH, Zhu SL, Zou CY, Li Q, Yuan YL, Lu CR, Wei HL, Gou CY, Zheng ZQ, Yn Y, Zhang XY, Liu K, Wang B, Song C, Shi N, Kohel RJ, Percy RG, Yu JZ, Zhu YX, Wang J, Yu SX (2012) The draft genome of a diploid cotton Gossypium raimondii. Nat Genet 44:1098–1104PubMedCrossRefGoogle Scholar
  29. Xiao J, Wu K, Fang DD, Stelly DM, Yu J, Cantrell RG (2009) New SSR markers for use in cotton (Gossypium spp.) improvement. J Cotton Sci 13:75–157Google Scholar
  30. Yang C, Guo W, Li G, Gao F, Lin S, Zhang T (2008) QTLs mapping for Verticillium wilt resistance at seedling and maturity stages in Gossypium barbadense L. Plant Sci 174:290–298CrossRefGoogle Scholar
  31. Yu Y, Yuan DJ, Liang SG, Li XM, Wang XQ, Lin ZX, Zhang XL (2011) Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between Gossypium hirsutum and G. barbadense. BMC Genomics 12:15PubMedCrossRefGoogle Scholar
  32. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468PubMedGoogle Scholar
  33. Zhang J, Guo W, Zhang T (2002) Molecular linkage map of allotetraploid cotton (Gossypium hirsutum L.×Gossypium barbadense L.) with a haploid population. Theor Appl Genet 105:1166–1174PubMedCrossRefGoogle Scholar
  34. Zhang T, Yuan Y, Yu J, Guo W, 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
  35. Zhang Z-S, Xiao Y-H, Luo M, Li X-B, Luo X-Y, Hou L, Li D-M, Pei Y (2005) Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.). Euphytica 144:91–99CrossRefGoogle Scholar
  36. Zhang K, Zhang J, Ma J, Tang SY, Liu DJ, Teng ZH, Liu DX, Zhang ZS (2012) Genetic mapping and quantitative trait locus analysis of fiber quality traits using a three-parent composite population in upland cotton (Gossypium hirsutum L.). Mol Breed 29:335–348CrossRefGoogle Scholar
  37. Zhao F, Fang W, Xie D, Zhao Y, Tang Z, Li W, Nie L, Lv S (2012) Proteomic identification of differentially expressed proteins in Gossypium thurberi inoculated with cotton Verticillium dahliae. Plant Sci 185–186:176–184PubMedCrossRefGoogle Scholar
  38. Zhu C, Wang F, Wang J, Li G, Zhang H, Zhang Y (2007) Reconstruction of linkage maps in the distorted segregation populations of backcross, doubled haploid and recombinant inbred lines. Chin Sci Bull 52:1648–1653CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Ning Zhiyuan
    • 1
  • Hong Chen
    • 2
  • Hongxian Mei
    • 1
  • Tianzhen Zhang
    • 1
    Email author
  1. 1.State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOE Hybrid Cotton R&D Engineering CenterNanjing Agricultural UniversityNanjingChina
  2. 2.Cotton Research InstituteXinjiang Academy of Agricultural and Reclamation SciencesShiheziChina

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