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Prediction of single-cross hybrid performance in maize using haplotype blocks associated with QTL for grain yield

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Abstract

Marker-based prediction of hybrid performance facilitates the identification of untested single-cross hybrids with superior yield performance. Our objectives were to (1) determine the haplotype block structure of experimental germplasm from a hybrid maize breeding program, (2) develop models for hybrid performance prediction based on haplotype blocks, and (3) compare hybrid performance prediction based on haplotype blocks with other approaches, based on single AFLP markers or general combining ability (GCA), under a validation scenario relevant for practical breeding. In total, 270 hybrids were evaluated for grain yield in four Dent × Flint factorial mating experiments. Their parental inbred lines were genotyped with 20 AFLP primer–enzyme combinations. Adjacent marker loci were combined into haplotype blocks. Hybrid performance was predicted on basis of single marker loci and haplotype blocks. Prediction based on variable haplotype block length resulted in an improved prediction of hybrid performance compared with the use of single AFLP markers. Estimates of prediction efficiency (R 2) ranged from 0.305 to 0.889 for marker-based prediction and from 0.465 to 0.898 for GCA-based prediction. For inter-group hybrids with predominance of general over specific combining ability, the hybrid prediction from GCA effects was efficient in identifying promising hybrids. Considering the advantage of haplotype block approaches over single marker approaches for the prediction of inter-group hybrids, we see a high potential to substantially improve the efficiency of hybrid breeding programs.

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References

  • Anderson EC, Novembre J (2003) Finding haplotype block boundaries by using the minimum-description-length principle. Am J Hum Genet 73:336–354

    Article  PubMed  CAS  Google Scholar 

  • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 57:289–300

    Google Scholar 

  • Bernardo R (1994) Prediction of maize single-cross performance using RFLPs and information from related hybrids. Crop Sci 34:20–25

    Article  Google Scholar 

  • Bernardo R (1996) Best linear unbiased prediction of maize single-cross performance. Crop Sci 36:50–56

    Article  Google Scholar 

  • Bernardo R (1998) Predicting the performance of untested single crosses: trait and marker data. In: Lamkey KR, Staub JE (eds) Concepts and breeding of heterosis in crop plants. Crop Science Society of America, Madison, pp 117–127

    Google Scholar 

  • Bernardo R (1999) Marker-assisted best linear unbiased prediction of single-cross performance. Crop Sci 39:1277–1282

    Article  Google Scholar 

  • Charcosset A, Essioux L (1994) The effect of population-structure on the relationship between heterosis and heterozygosity at marker loci. Theor Appl Genet 89:336–343

    Article  Google Scholar 

  • Cochran WG, Cox GM (1957) Experimental designs. Wiley, New York

    Google Scholar 

  • Cockerham CC (1967) Prediction of double crosses from single crosses. Der Züchter 37:160–169

    Google Scholar 

  • Comstock RE, Robinson HF (1952) Estimation of average dominance of genes. In: Gowen JW (ed) Heterosis. ISU Press, Ames, pp 494–516

    Google Scholar 

  • Dijkstra EW (1959) A note on two problems in connexion with graphs. Numer Math 1:269–271

    Article  Google Scholar 

  • Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374

    Article  PubMed  CAS  Google Scholar 

  • Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D (2002) The structure of haplotype blocks in the human genome. Science 296:2225–2229

    Article  PubMed  CAS  Google Scholar 

  • Gardner CO, Eberhart SA (1966) Analysis and interpretation of the variety cross diallel and related populations. Biometrics 22:439–452

    Article  PubMed  CAS  Google Scholar 

  • Guo SW, Thompson EA (1992) Performing the exact test of Hardy–Weinberg proportion for multiple alleles. Biometrics 48:361–372

    Article  PubMed  CAS  Google Scholar 

  • Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136:1447–1455

    PubMed  CAS  Google Scholar 

  • Jansen RC, Jannink JL, Beavis WD (2003) Mapping quantitative trait loci in plant breeding populations: use of parental haplotype sharing. Crop Sci 43:829–834

    Article  CAS  Google Scholar 

  • Johnson GCL, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RCJ, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SCL, Clayton DG, Todd JA (2001) Haplotype tagging for the identification of common disease genes. Nat Genetics 29:233–237

    Article  CAS  Google Scholar 

  • Maurer HP, Knaak C, Melchinger AE, Ouzunova M, Frisch M (2006) Linkage disequilibrium between SSR markers in six pools of elite lines of an European breeding program for hybrid maize. Maydica 51:269–279

    Google Scholar 

  • Melchinger AE (1999) Genetic diversity and heterosis. In: Coors JG, Pandey S (eds) The genetics and exploitation of heterosis in crops. ASA-CSSA, Madison, pp 99–118

    Google Scholar 

  • Melchinger AE, Geiger HH, Seitz G, Schmidt GA (1987) Optimum prediction of three-way crosses from single crosses in forage maize (Zea mays L.). Theor Appl Genet 74:339–345

    Article  Google Scholar 

  • Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, Nguyen BTN, Norris MC, Sheehan JB, Shen NP, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SPA, Cox DR (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294:1719–1723

    Article  PubMed  CAS  Google Scholar 

  • Peleman J, van Wijk R, Van Oeveren J, Van Schaik R (2000) Linkage map integration: an integrated genetic map of Zea mays L. In: Proceedings of plant and animal genome conference VIII, San Diego, US, 9–12 Jan 2000. Poster P472

  • Piepho HP, Gauch HG (2001) Marker pair selection for mapping quantitative trait loci. Genetics 157:433–444

    PubMed  CAS  Google Scholar 

  • R Development Core Team (2004) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria

  • Schrag TA, Melchinger AE, Sorensen AP, Frisch M (2006) Prediction of single-cross hybrid performance for grain yield and grain dry matter content in maize using AFLP markers associated with QTL. Theor Appl Genet 113:1037–1047

    Article  PubMed  CAS  Google Scholar 

  • Stich B, Maurer HP, Melchinger AE, Frisch M, Heckenberger M, van der Voort JR, Peleman J, Sorensen AP, Reif JC (2006) Comparison of linkage disequilibrium in elite European maize inbred lines using AFLP and SSR markers. Mol Breed 17:217–226

    Article  CAS  Google Scholar 

  • Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp mays L.). Proc Natl Acad Sci USA 98:9161–9166

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW, Melchinger AE, Lübberstedt T, Xia XC, Stam P, Zabeau M, Kuiper M (1999) Two high-density AFLP (R) linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor Appl Genet 99:921–935

    Article  CAS  Google Scholar 

  • Vuylsteke M, Kuiper M, Stam P (2000) Chromosomal regions involved in hybrid performance and heterosis: their AFLP (R)-based identification and practical use in prediction models. Heredity 85:208–218

    Article  PubMed  CAS  Google Scholar 

  • Zaykin D, Zhivotovsky L, Weir BS (1995) Exact tests for association between alleles at arbitrary numbers of loci. Genetica 96:169–178

    Article  PubMed  CAS  Google Scholar 

  • Zhang K, Deng M, Chen T, Waterman MS, Sun F (2002) A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci USA 99:7335–7339

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This project was supported by the German Research Foundation DFG in the framework program “Heterosis in Plants” (research grants FR 1615/3-1 and 3-3). We thank Dr. J. Muminovic for helpful comments on this manuscript. The staff at the Plant Breeding Research Station at Eckartsweier and Hohenheim is gratefully acknowledged for conducting the field experiments.

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Authors and Affiliations

  1. Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593, Stuttgart, Germany

    Tobias A. Schrag, Hans Peter Maurer, Albrecht E. Melchinger & Matthias Frisch

  2. Bioinformatics Unit of the Institute for Crop Production and Grassland Research, University of Hohenheim, 70599, Stuttgart, Germany

    Hans-Peter Piepho

  3. Keygene, P.O. Box 216, 6700 AE, Wageningen, The Netherlands

    Johan Peleman

Authors
  1. Tobias A. Schrag
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  2. Hans Peter Maurer
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  3. Albrecht E. Melchinger
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  4. Hans-Peter Piepho
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  5. Johan Peleman
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  6. Matthias Frisch
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Corresponding author

Correspondence to Albrecht E. Melchinger.

Additional information

Communicated by H. C. Becker.

Tobias A. Schrag and Hans Peter Maurer contributed equally to this work.

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Schrag, T.A., Maurer, H.P., Melchinger, A.E. et al. Prediction of single-cross hybrid performance in maize using haplotype blocks associated with QTL for grain yield. Theor Appl Genet 114, 1345–1355 (2007). https://doi.org/10.1007/s00122-007-0521-5

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  • DOI: https://doi.org/10.1007/s00122-007-0521-5

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