Skip to main content
SpringerLink
Log in

Differential gene expression and associated QTL mapping for cotton yield based on a cDNA-AFLP transcriptome map in an immortalized F2

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

cDNA-AFLP techniques have found new applications in recent years. Currently, the methodology is used to establish differential gene expression and construct linkage maps. In the present study, a transcriptome map based on cDNA-AFLP techniques was constructed using an immortalized F2 (IF2) population of 171 lines. The lines were derived from intercrosses between 180 recombinant inbred lines (RILs) of the cotton hybrid Xiangzamian 2 (Gossypium. hirsutum L.). A total of 302 transcriptome-derived fragments (TDFs) were mapped onto 26 linkage groups that covered 2,477.06 cM in length with an average distance of 8.23 cM between two markers. Seventy-one QTL for yield and yield component traits were detected by CIM procedures based on four environments, with 13 QTL identified in at least two environments. Some TDFs co-located with yield QTL were subsequently sequenced and analyzed by online homology searches. Potential candidate genes for yield and yield component traits were found to encode proteins involved in DNA replication, transcription, translation, and biosynthesis regulation. Furthermore, genes regulating metabolic processes signal transduction, transport, and structural components of organelles were identified. Correlation analysis between expression patterns of TDFs and trait performance detected six TDFs positively correlated to both yield and yield heterosis: six TDFs positively correlated to yield, and seven TDFs to yield heterosis. These TDFs have potential for cloning the functional genes responsible for each corresponding trait and have future value in marker-assisted selection.

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.

Fig. 1

Similar content being viewed by others

Abbreviations

QTL:

Quantitative trait locus/loci

RIL:

Recombinant inbred line

IF2 :

Immortalized F2

cDNA-AFLP:

cDNA amplified fragment length polymorphism

TDFs:

Transcriptome derived fragments

References

  • Abdalla AM, Reddy OUK, El-Zik KM, Pepper AE (2001) Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP. Theor Appl Genet 102:222–229

    Article  CAS  Google Scholar 

  • Altschul SF, Madden TL, SchaVer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • An CF, Saha S, Jenkins JN, ScheZer BE, Wilkins TA, Stelly DM (2007) Transcriptome profiling, sequence characterization, and SNP based chromosomal assignment of the EXPANSIN genes in cotton. Mol Genet Genomics 278:539–553

    Article  PubMed  CAS  Google Scholar 

  • An CF, Saha S, Jenkins JN, Ma DP, ScheZer BE, Kohel RJ, John ZY, Stelly DM (2008) Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization, and linkage mapping. Theor Appl Genet 116:1015–1026

    Article  PubMed  CAS  Google Scholar 

  • Bachem C, van der Hoeven RS, de Bruijn SM, Vreugdenhil D, Zabeau M, Visser RG (1996) Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J 9:745–753

    Article  PubMed  CAS  Google Scholar 

  • Bachem C, Oomen R, Visser R (1998) Transcript imaging with cDNA-AFLP: a step by step protocol. Plant Mol Biol Rep 16:157–173

    Article  CAS  Google Scholar 

  • Basten CJ, Weir BS, Zeng ZB (2001) QTL Cartographer, Version 1.15. Department of Statistics. North Carolina State University, Raleigh

    Google Scholar 

  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2008) GenBank. Nucleic Acids Res 36(Database issue):D25–D30

    PubMed  CAS  Google Scholar 

  • Breyne P, Zabeau M (2001) Genome-wide expression of plant cell cycle modulated genes. Curr Opin Plant Biol 4:136–142

    Article  PubMed  CAS  Google Scholar 

  • Breyne P, Dreesen R, Cannoot B, Rombaut D, Vandepoele K, Rombauts S, Vandeerhaeghen R, Inzé D, Zabeau M (2003) Quantitative cDNA-AFLP analysis for genome-wide expression studies. Mol Gen Genomics 269:173–179

    CAS  Google Scholar 

  • Brugmans B, Fernández del Carmen A, Bachem CW, van Os H, van Eck HJ, Visser RG (2002) A novel method for the construction of genome wide transcriptome maps. Plant J 31(2):211–222

    Article  PubMed  CAS  Google Scholar 

  • Chee PW, Rong J, Williams-Coplin D, Schulze SR, Paterson AH (2004) EST derived PCR-based markers for functional gene homologues in cotton. Genome 47:449–462

    Article  PubMed  CAS  Google Scholar 

  • Chee P, Draye X, Jiang CX, Decanini L, Delmonte T, Bredhauer R, Smith CW, Paterson AH (2005) Molecular dissection of interspecific variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: I. Fiber elongation. Theor Appl Genet 111:757–763

    Article  PubMed  CAS  Google Scholar 

  • Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971

    PubMed  CAS  Google Scholar 

  • Drost DR, Benedict CI, Arthur Berg A, Evandro Novaes E, Novaes CR, Yu QB, Dervinis C, Maia JM, Yap J, Miles B, Kirst M (2010) Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus. PNAS 107(18):8492–8497

    Article  PubMed  CAS  Google Scholar 

  • Ewing RM, Kahla AB, Poirot O, Lopez F, Audic S, Claverie JM (1999) Large scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res 9:950–959

    Article  PubMed  CAS  Google Scholar 

  • Fan SY, Le JG, Cheng GJ, Wu CJ (2008) Construction of Chinese Cabbage-pak-choi transcriptome map with cDNA-AFLP techniques. Sci Agri Sinica 41(6):1735–1741

    CAS  Google Scholar 

  • Fernández-del-Carmen A, Celis-Gamboa C, Visser RG, Bachem C (2007) Targeted transcript mapping for agronomic traits in potato. J Exp Bot 58:2761–2774

    Article  PubMed  Google Scholar 

  • Frelichowski JE, Palmer M, Main D, Tomkins JP, Cantrell RG, Stelly DM, Yu J, Kohel RJ, Ulloa M (2006) Genetic mapping of microsatellites derived from BAC-end sequences of Gossypium hirsutum Acala ‘Maxxa’. Mol Genet Genom 275(5):479–491

    Article  CAS  Google Scholar 

  • Guo WZ, Ma GJ, Zhu YC, Yi CX, Zhang TZ (2006) Molecular tagging and mapping of quantitative trait loci for lint percentage and morphological marker genes in Upland cotton. J Integ Plant Biol 48(3):320–326

    Article  CAS  Google Scholar 

  • Guo WZ, Cai CP, Wang CB, Han ZG, Song XL, Wang K, Niu XW, Wang C, Lu KY, Shi B, Zhang TZ (2007) A microsatellite-based, generich linkage map reveals genome structure, function and evolution in Gossypium. Genetics 176(1):527–541

    Article  PubMed  CAS  Google Scholar 

  • Han ZG, Guo WZ, Song XL, Zhang TZ (2004) Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton. Mol Gen Genet 272:308–327

    CAS  Google Scholar 

  • Han Z, Wang C, Song X, Guo WZ, Gou J, Li C, Chen X, Zhang TZ (2006) Characteristics, development and mapping of Gossypium hirsutun derived EST-SSR in allotetraploid cotton. Theor Appl Genet 112:430–439

    Article  PubMed  CAS  Google Scholar 

  • 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 153:181–197

    Article  CAS  Google Scholar 

  • Hovav R, Udall JA, Hovav E, Rapp R, Flagel L, Wendel JF (2008) A majority of cotton genes are expressed in single-celled fiber. Planta 227:319–329

    Article  PubMed  CAS  Google Scholar 

  • Hua JP, Xing YZ, Xu CG, Sun XL, Yu SB, Zhang QF (2002) Genetic dissection of an elite rice hybrid revealed that heterozygotes are not always advantageous for performance. Genetics 162:1885–1895

    PubMed  CAS  Google Scholar 

  • Hua JP, Xing YZ, Wu WR, Xu CG, Sun XL, Zhang QF (2003) Single-locus heterotic effects and dominance-by-dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 100(5):2574–2579

    Article  PubMed  CAS  Google Scholar 

  • Huang XQ, Cöster H, Ganal MW, Röder MS (2003) Advanced backcross QTL analysis for the identification of quantitative trait loci alleles from wild relatives of wheat (Triticum aestivum L.). Theor Appl Genet 106:1379–1389

    PubMed  CAS  Google Scholar 

  • Jiang JX, Zhang TZ (2003) Extraction of total RNA in cotton tissues with CTAB-acidic phenolic method. Cotton Sci 15(3):166–167 (in Chinese)

    Google Scholar 

  • Kendall M (1948) Rank Correlation Methods. Charles Griffin & Company Limited, London

    Google Scholar 

  • Kohel RJ, Yu J, Park Y-H, 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

    Article  Google Scholar 

  • Li, YQ, Zeng ZY, Jing L, Yang FQ, Wan YL (1997) Selection and application of Xiangzamian 2. Crop Research (4):27–29 (in Chinese)

  • Li G, Gao M, Yang B, Quiros CF (2003) Gene for gene alignment between the Brassica and Arabidopsis genomes by direct transcriptome mapping. Theor Appl Genet 107:168–180

    Article  PubMed  CAS  Google Scholar 

  • Lin Z, He D, Zhang X, Nie Y, Guo X, Feng C, Stewart JMcD (2005) Linkage map construction and mapping QTL for cotton fiber quality using SRAP, SSR and RAPD. Plant Breed 124:180–187

    Article  CAS  Google Scholar 

  • Liu HW, Wang XF, Pan YX, Shi RF, Zhang GY, Ma ZY (2009) Mining cotton fiber strength candidate genes based on transcriptome mapping. Chin Sci Bull 54:4651–4657

    Article  CAS  Google Scholar 

  • McCouch SR, Cho YG, Yano PE, Blinstrub M, Morishima H, Kinoshita T (1997) Report on QTL nomenclature. Rice Genet Newslett 14:11–13

    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 

  • Michalak P (2008) Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 91:243–248

    Article  PubMed  CAS  Google Scholar 

  • Pan YX, MA J, Zhang GY, Han GY, Wang XF, Ma ZY (2007) cDNA-AFLP profiling for the fiber development stage of secondary cell wall synthesis and transcriptome mapping in cotton. Chin Sci Bull 52:2358–2364

    Article  CAS  Google Scholar 

  • Park Y-H, Alabady MS, Sickler B, Wilkins TA, Yu J, Stelly DM, Kohel RJ, El-Shihy OM, Cantrell RG, Ulloa M (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line (RIL) cotton population. Mol Genet Genom 274:428–441

    Article  CAS  Google Scholar 

  • Paterson AH, Smith RH (1999) Future horizons: biotechnology for cotton improvement. In: Smith WC (ed) Cotton: origin, history, technology and production. Wiley, USA, pp 415–432

    Google Scholar 

  • Ranik M, Creux NM, Myburg AA (2006) Within-tree transcriptome profiling in wood-forming tissues of a fast-growing Eucalyptus tree. Tree Physiol 26:365–375

    Article  PubMed  CAS  Google Scholar 

  • Reinisch AJ, Dong JM, Brubaker CL, 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 

  • Ren LH, Guo WZ, Zhang TZ (2002) Identification of quantitative trait loci (QTLs) affecting yield and fiber properties in chromosome 16 in cotton using substitution line. Acta Botanica Sinica 44(7):815–820

    CAS  Google Scholar 

  • Ritter E, Ruiz de Galarreta JI, van Eck HJ, Sánchez I (2008) Construction of a potato transcriptome map based on the cDNA–AFLP technique. Theor Appl Genet 116:1003–1013

    Article  PubMed  CAS  Google Scholar 

  • Rong J-K, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA, Ding XL, Garza JJ, Marler BS, Park C-H, 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 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  • Samuelian S, Kleine M, Ruyter-Spira CP, Klein-Lankhorst RM, Jung C (2004) Cloning and functional analyses of a gene from sugar beet up-regulated upon cyst nematode infection. Plant Mol Biol 54:147–156

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Shen XL, Guo WZ, Lu QX, Zhu XF, Yuan YL, Zhang TZ (2007) Genetic mapping of quantitative trait loci for fiber quality and yield trait by RIL approach in Upland cotton. Euphytica 155:371–380

    Article  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 

  • Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277(22):1063–1066

    Article  PubMed  CAS  Google Scholar 

  • Ulloa M, Saha S, Jenkin N, Meredith WR, McCarty JC, Stelly DM (2005) Chromosomal assignment of RFLP linkage groups harboring important QTL on an intraspecific cotton (Gossypium hirsutum L.) joinmap. J Hered 96:132–144

    Article  PubMed  CAS  Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) JoinMap® version 3.0: software for the calculation of genetic linkage maps. Plant Res Int, Wageningen

    Google Scholar 

  • Voorrips RE (2006) MapChart 2.2: software for the graphical presentation of linkage maps and QTLs. Plant Res Int, Wageningen

    Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  PubMed  CAS  Google Scholar 

  • 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 152:367–378

    Article  CAS  Google Scholar 

  • Wang BH, Wu YT, Guo WZ, Zhu XF, Huang NT, Zhang TZ (2007) QTL analysis and epistasis effects dissection of fiber qualities in an elite cotton hybrid grown in second-generation. Crop Sci 47:1384–1392

    Article  CAS  Google Scholar 

  • Williams EJ, Bowles DJ (2004) Coexpression of neighboring genes in the genome of Arabidopsis thaliana. Genome Res 14:1060–1067

    Article  PubMed  CAS  Google Scholar 

  • Wu J, Gutierrez OA, Jenkins JN, McCarty JC, Zhu J (2009) Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of Upland cotton. Euphytica 165:231–245

    Article  Google Scholar 

  • Xie X, Jin F, Song MH, Suh JP, Hwang HG, Kim YG, McCouch SR, Ahn SN (2008) Fine mapping of a yield-enhancing QTL cluster associated with transgressive variation in an Oryza sativa × O. rufipogon cross. Theor Appl Genet 116:613–622

    Article  PubMed  Google Scholar 

  • Yu SX (2010) Progress on Upland cotton sequencing. In: Proceed Plant & Animal Genomes XVIII Conference, Town & Country Convention Center, San Diego, CA. January 9–13, 2010

  • Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468

    PubMed  CAS  Google Scholar 

  • Zhan S, Horrocks J, Lukens LN (2006) Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains. Plant J 45:347–357

    Article  PubMed  CAS  Google Scholar 

  • Zhang J, Guo WZ, Zhang TZ (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 

Download references

Acknowledgments

This work was financially supported in part from the 973 (2011CB109303) and 863 (2009AA101104). We thank Dr. RJ Kohel in USDA-ARS for a critical review of the manuscript and Prof. Yuqiang Li in Hunan Cotton Research Institute for providing breeder-owned parental seeds of XZM2.

Author information

Authors and Affiliations

  1. National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, China

    Renzhong Liu, Baohua Wang, Wangzhen Guo & Tianzhen Zhang

  2. Shandong Cotton Research Center, Jinan, 250100, China

    Renzhong Liu & Liguo Wang

Authors
  1. Renzhong Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Baohua Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wangzhen Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Liguo Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tianzhen Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tianzhen Zhang.

Additional information

Communicated by G. Bryan.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 382 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, R., Wang, B., Guo, W. et al. Differential gene expression and associated QTL mapping for cotton yield based on a cDNA-AFLP transcriptome map in an immortalized F2 . Theor Appl Genet 123, 439–454 (2011). https://doi.org/10.1007/s00122-011-1597-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-011-1597-5

Keywords

Search

Navigation