Skip to main content
SpringerLink
Log in

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

  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

A high-density molecular marker linkage map of cotton based entirely on polymerase chain reaction-based markers is useful for a marker-assisted breeding program. Four kinds of markers—simple sequence repeats (SSRs), sequence-related amplified polymorphism (SRAP), random amplified polymorphic DNA (RAPD), and retrotransposon-microsatellite amplified polymorphism (REMAP)—were used to assay an F2 population from a cross between “Handan208” (Gossypium hirsutum) and “Pima90” (Gossypium barbadense). Sixty-nine F2 plants were used for map construction using 834 SSRs, 437 SRAPs, 107 RAPDs, and 16 REMAPs. Linkage analysis revealed that 1,029 loci could be mapped to 26 linkage groups that extended for 5,472.3 cM, with an average distance between 2 loci of 5.32 cM. The corresponding 69 F2:3 families were grown, arranged in two replicates, and scored for eight phenotypes. Quantitative trait loci (QTL) analysis was performed by means of composite interval mapping using WinQtlCart ver 2.0. A total of 52 distinct QTLs were detected: 4 QTLs for lint index, 8 for seed index, 11 for lint yield, 4 for seed cotton yield, 9 for number of seed per boll, 3 for fiber strength, 5 for fiber length, and 8 for micronaire value. The present map and QTL analysis may provide a useful tool for breeders to transfer desirable traits from G. barbadense to the mainly cultivated species, G. hirsutum.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    CAS  Google Scholar 

  • Basten CJ, Weir BS, Zeng ZB (1994) Zmap—a QTL cartographer. In: Smith C, Gavora JS, Chesnais BBJ, Fairfull W, Gibson JP, Kennedy BW, Burnside EB (eds) Proceedings of the 5th world congress on genetics applied to livestock production, vol. 2. Computing strategies and software. University of Guelph, Guelph, Ont, Canada, pp. 65–66

  • Basten CJ, Weir BS, Zeng ZB (1997) QTL cartographer: reference manual and tutorial for QTL mapping. Department of Statistics, North Carolina State University, Raleigh

    Google Scholar 

  • Castilho A, Vershinin A, Heslop-Harrison JS (2000) Repetitive DNA and the chromosomes in the genome of oil palm (Elaeis guineensis). Ann Bot 85:837–844

    Article  CAS  Google Scholar 

  • Dodds KG, Ball R, Djorovic N, Carson SD (2004) The effect of an imprecise map on interval mapping QTLs. Genet Res 84:47–55

    Article  PubMed  CAS  Google Scholar 

  • Haley C (1999) Advances in quantitative trait locus mapping. In: Dekkers JCM, Lamont SJ, Rothschild MF (eds) From Jay Lush to genomics: visions for animal breeding and genetics, Iowa State University, May 16–18, pp. 47–59

  • 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 272:308–327

    Article  PubMed  CAS  Google Scholar 

  • Hanson RE, Jackson LE, Zwick MS, Crane CF, Islam-Faridi MN, McKnight TD, Wendel JF, Stelly DM, Price HJ (2000) The chromosomal distribution of a copia-like retrotransposon in cotton (Gossypium hirsutum L.). Chromosome Res 8:73–76

    Article  PubMed  CAS  Google Scholar 

  • He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Feng CD, Stewart JMcD (2005) Mapping QTLs of traits contributing to yield and analysis of genetic effects in tetraploid cotton. Euphytica 144:141–149

    Article  CAS  Google Scholar 

  • Jiang C, Zeng ZB (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140:1111–1117

    PubMed  CAS  Google Scholar 

  • Jiang CX, Wright RJ, El-Zik K, Paterson AH (1998) Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc Natl Acad Sci USA 95:4419–4424

    Article  PubMed  CAS  Google Scholar 

  • Kohel RJ, Yu J, Park YH, Lazo GR (2001) Molecular mapping and characterization of traits controlling fiber quality in cotton. Euphytica 121:163–172

    Article  CAS  Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • 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 46:612–626

    Article  PubMed  CAS  Google Scholar 

  • Lacape JM, Nguyen TB, Courtois B, Belot JL, Giband M, Gourlot JP, Gawryziak G, Roques S, Hau B (2005) QTL analysis of cotton fiber quality using multiple Gossypium hirsutum × Gossypium barbadense backcross generations. Crop Sci 45:123–140

    CAS  Google Scholar 

  • Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199

    PubMed  CAS  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg I (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  PubMed  CAS  Google Scholar 

  • Li Z, Pinzon SR, Park WD, Paterson AH, Stansel JW (1997) Epistasis for three grain yield in rice (Oryza sativa L.). Genetics 145:453–465

    PubMed  CAS  Google Scholar 

  • Lin ZX, He DH, Zhang XL, Nie YC, Guo XP, Feng CD, Stewart JMcD (2005) Linkage map construction and mapping QTLs for cotton fiber quality using SRAP, SSR and RAPD. Plant Breed 124:180–187

    Article  CAS  Google Scholar 

  • Lincoln S, Daly M, Lander ES (1992) Constructing genetic maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report, 2nd edn. Whitehead Institute, Cambridge

  • Liu S, Saha S, Stelly D, Burr B, Cantrell RG (2000) Chromosomal assignment of microsatellite loci in cotton. J Hered 91:326–332

    Article  PubMed  CAS  Google Scholar 

  • Manninen O, Kalendar R, Robinson J, Schulman AH (2000) Application of BARE-1 retrotransposon markers to map a major resistance gene for net blotch in barley. Mol Gen Genet 264:325–334

    Article  PubMed  CAS  Google Scholar 

  • Mei M, Syed NH, Gao W, Thaxton PM, Smith CW, Stelly DM, Chen ZJ (2004) Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theor Appl Genet 108:280–291

    Article  PubMed  CAS  Google Scholar 

  • 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 109:167–175

    Article  PubMed  CAS  Google Scholar 

  • Paterson AH, Brubaker CL, Wendel JF (1993) A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP and PCR analysis. Plant Mol Biol Rep 11:112–127

    Google Scholar 

  • Paterson AH, Saranga Y, Menz M, Jiang CX, Wright RJ (2003) QTL analysis of genotype × environment interactions affecting cotton fiber quality. Theor Appl Genet 106:384–396

    PubMed  CAS  Google Scholar 

  • Reinisch AJ, Dong JM, Brubaker CL, Stelly DM, Wendel JF, Paterson AH (1994) A detailed RFLP map of cotton Gossypium hirsutum × Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138:829–847

    PubMed  CAS  Google Scholar 

  • Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516–1517

    Article  PubMed  CAS  Google Scholar 

  • Rong J, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA, Ding X, Garza JJ, Marler BS, Park C, Pierce GJ, Rainey KM, Rastogi VK, Schulze SR, Trolinder NL, Wendel JF, Wilkins TA, Williams-Coplin TD, Wing RA, Wright RJ, Zhao X, Zhu L, 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 166:389–417

    Article  PubMed  CAS  Google Scholar 

  • Saha S, Karaca M, Jenkins JN, Zipf AE, Ramesh OU, Kantety RV (2003) Simple sequence repeats as useful resources to study transcribed genes of cotton. Euphytica 130:355–364

    Article  CAS  Google Scholar 

  • Sankar AA, Moore GA (2001) Evaluation of inter-simple sequence repeat analysis for mapping in Citrus and extension of the genetic linkage map. Theor Appl Genet 102:206–214

    Article  CAS  Google Scholar 

  • Saranga Y, Menz M, Jiang CX, Wright RJ, Yakir D, Paterson AH (2001) Genomic dissection of genotype × environment interactions conferring adaptation of cotton to arid conditions. Genome Res 11:1988–1995

    Article  PubMed  CAS  Google Scholar 

  • SAS Institute Inc. (1999) SAS user’s guide, release 8.01 Edition. SAS Institute Inc., Cary

    Google Scholar 

  • Shappley ZW (1996) Construction of RFLP linkage groups and mapping of quantitative trait loci in upland cotton (Gossypium hirsutum L.). PhD dissertation, Mississippi State University (dissertation abstract AAG9711761)

  • Shappley ZW, Jenkins JN, Watson CE Jr, Kahler AL, Meredith WR Jr (1996) Establishment of molecular markers and linkage groups in two F2 populations of upland cotton. Theor Appl Genet 92:915–919

    Article  CAS  Google Scholar 

  • Shappley ZW, Jenkins JN, Zhu J, McCarty JC Jr (1998a) Quantitative trait loci associated with agronomic and fiber traits of upland cotton. J Cotton Sci 2:153–163

    CAS  Google Scholar 

  • Shappley ZW, Jenkins JN, Meredith WR, McCarty JC Jr (1998b) An RFLP linkage map of upland cotton (Gossypium hirsutum L.). Theor Appl Genet 97:756–761

    Article  CAS  Google Scholar 

  • Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122–128

    Article  PubMed  CAS  Google Scholar 

  • Stuber CW, Edwards MD, Wendel JF (1987) Molecular marker-facilitated investigations of quantitative trait loci in maize. II. Factors influencing yield and its component traits. Crop Sci 27:639–648

    Article  Google Scholar 

  • Tani N, Takahashi T, Iwata H, Mukai Y, Ujino-Ihara T, Matsumoto A, Yoshimura K, Yoshimaru H, Murai M, Nagasaka K, Tsumura Y (2003) A consensus linkage map for Sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags. Genetics 165:1551–1568

    PubMed  CAS  Google Scholar 

  • Ulloa M, Meredith WR (2000) Genetic linkage map and QTL analysis of agronomic and fiber quality traits in an intraspecific population. J Cotton Sci 4:161–170

    CAS  Google Scholar 

  • Ulloa M, Meredith WR, Shappley ZW, Kahler AL (2002) RFLP genetic linkage maps from F2:3 populations and a joinmap of Gossypium hirsutum. Theor Appl Genet 104:200–208

    Article  PubMed  CAS  Google Scholar 

  • Wendel JF, Albert VA (1992) Phylogenetics of the cotton genus (Gossypium): character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications. Syst Bot 17:115–143

    Article  Google Scholar 

  • Wendel JF, Cronn RC, Johnston JS, Price HJ (2002) Feast and famine in plant genomes. Genetica 115:36–47

    Article  Google Scholar 

  • Yin TM, DiFazio SP, Gunter LE, Riemenschneider D, Tuskan GA (2004) Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map. Theor Appl Genet 109:451–463

    Article  PubMed  CAS  Google Scholar 

  • Yu J, Yong PH, Lazo GR, Kohel RJ (1998) Molecular mapping of the cotton genome: QTL analysis of fiber quality properties. In: Proceedings of Beltwide cotton conferences, San Diego, 5–9 January 1998, 485 pp

  • Zeng ZB (1993) Theoretical basis of separation of multiple linked gene effects on mapping quantitative trait loci. Proc Natl Acad Sci USA 90:10972–10976

    Article  PubMed  CAS  Google Scholar 

  • 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 105:1166–1174

    Article  PubMed  CAS  Google Scholar 

  • 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 106:262–268

    PubMed  CAS  Google Scholar 

  • Zhao XP, Lin YR, Paterson AH (1994) Characterization and genetic mapping of DNA microsatellites from cotton. Plant genome II conference. Town & Country Conference Center, San Diego, January 1994

  • Zhu H, Briceño G, Dovel R, Hayes PM, Liu BH, Liu CT, Ullrich SE (1999) Molecular breeding for grain yield in barley: an evaluation of QTL effects in a spring barley cross. Theor Appl Genet 98:772–779

    Article  Google Scholar 

  • Zuo K, Sun J, Zhang X, Nie Y, Liu J, Feng C (2000) Constructing a linkage map of upland cotton (Gossypium hirsutum L.) using RFLP, RAPD and SSR makers. J Huazhong Agric Univ 19:190–193

    CAS  Google Scholar 

Download references

Acknowledgement

Support from the National Basic Research Program of China (2004CB117301) is appreciated.

Author information

Author notes

  1. Dao-Hua He

    Present address: College of Agronomy, Northwest Sci-Tech University of Agriculture and Forestry, Yangling, Shaanxi, 712100, P.R. China

Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China

    Dao-Hua He, Zhong-Xu Lin, Xian-Long Zhang, Yi-Chun Nie, Xiao-Ping Guo, Yan-Xin Zhang & Wu Li

Authors
  1. Dao-Hua He
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhong-Xu Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xian-Long Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yi-Chun Nie
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xiao-Ping Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yan-Xin Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Wu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xian-Long Zhang.

Rights and permissions

Reprints and permissions

About this article

Cite this article

He, DH., Lin, ZX., Zhang, XL. et al. 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, 181–197 (2007). https://doi.org/10.1007/s10681-006-9254-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10681-006-9254-9

Keywords

Search

Navigation