Theoretical and Applied Genetics

, Volume 125, Issue 2, pp 201–210 | Cite as

Mapping QTL for agronomic traits in breeding populations

Review

Abstract

Detection of quantitative trait loci (QTL) in breeding populations offers the advantage that these QTL are of direct relevance for the improvement of crops via knowledge-based breeding. As phenotypic data are routinely generated in breeding programs and the costs for genotyping are constantly decreasing, it is tempting to exploit this information to unravel the genetic architecture underlying important agronomic traits in crops. This review characterizes the germplasm from breeding populations available for QTL detection, provides a classification of the different QTL mapping approaches that are available, and highlights important considerations concerning study design and biometrical models suitable for QTL analysis.

References

  1. Alheit KV, Reif JC, Maurer HP, Hahn V, Weissmann EA et al (2011) Detection of segregation distortion loci in triticale (× Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map. BMC Genomics 12:380PubMedCrossRefGoogle Scholar
  2. Bauer AM, Hoti F, von Korff M, Pillen K, Léon J et al (2009) Advanced backcross-QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML versus a Bayesian model in multi-environmental field trials. Theor Appl Genet 119:105–123PubMedCrossRefGoogle Scholar
  3. Bernardo R (2008) Molecular marker and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48:1649–1664CrossRefGoogle Scholar
  4. Bink MCAM, Uimari P, Sillanpää MJ, Janss LLG, Jansen RC (2002) Multiple QTL mapping in related plant populations via a pedigree-analysis approach. Theor Appl Genet 104:751–762PubMedCrossRefGoogle Scholar
  5. Bink MCAM, Boer MP, ter Braak CJF, Jansen J, Voorrips RE et al (2008) Bayesian analysis of complex traits in pedigreed plant populations. Euphytica 161:85–96CrossRefGoogle Scholar
  6. Blanc G, Charcosset A, Mangin B, Gallais A, Moreau L (2006) Connected populations for detecting quantitative trait loci and testing for epistasis: an application in maize. Theor Appl Genet 113:206–224PubMedCrossRefGoogle Scholar
  7. Bradbury P, Parker T, Hamblin MT, Jannink JL (2011) Assessment of power and false discovery rate in genome-wide association studies using the BarleyCAP germplasm. Crop Sci 51:52–59CrossRefGoogle Scholar
  8. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177PubMedCrossRefGoogle Scholar
  9. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ et al (2009) The genetic architecture of maize flowering time. Science 325:714–718PubMedCrossRefGoogle Scholar
  10. Carlborg Ö, Haley CS (2004) Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5:618–625PubMedCrossRefGoogle Scholar
  11. Coles ND, McMullen MD, Balint-Kurti PJ, Pratt RC, Holland JB (2010) Genetic control of photoperiod sensitivity in maize revealed by joint multiple population analysis. Genetics 184:799–822PubMedCrossRefGoogle Scholar
  12. Dekkers JCM, Hospital F (2002) Multifactorial genetics: the use of molecular genetics in the improvement of agricultural populations. Nat Rev Genet 3:22–32PubMedCrossRefGoogle Scholar
  13. Dudley JW, Johnson GR (2009) Epistatic models improve prediction of performance in corn. Crop Sci 49:763–770CrossRefGoogle Scholar
  14. Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics, 4th edn. Addison Wesley Longman, HarlowGoogle Scholar
  15. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54:357–374CrossRefGoogle Scholar
  16. Ganal MW, Altmann T, Röder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12:211–217PubMedCrossRefGoogle Scholar
  17. Gasbarra D, Pirinen M, Sillanpää MJ, Arjas E (2009) Bayesian quantitative trait locus mapping based on reconstruction of recent genetic histories. Genetics 183:709–721PubMedCrossRefGoogle Scholar
  18. Harjes CE, Rocheford TR, Bai L, Brutnell TP, Bermudez Kandianis C et al (2008) Natural genetic variation in epsilon lycopene cyclase tapped for maize biofortification. Science 319:300–333CrossRefGoogle Scholar
  19. Heckenberger M, Maurer HP, Melchinger AE, Frisch M (2008) The plabsoft database: a comprehensive database management system for integrating phenotypic and genomic data in academic and commercial plant breeding programs. Euphytica 161:173–179CrossRefGoogle Scholar
  20. Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10:156–161PubMedCrossRefGoogle Scholar
  21. Jannink JL, Bink M, Jansen RC (2001) Using complex plant pedigrees to map valuable genes. Trends Plant Sci 6:337–342PubMedCrossRefGoogle Scholar
  22. Jansen RC (2007) Quantitative trait loci in inbred lines. In: Handbook of Statistical Genetics, 3rd edn. Wiley, New York. ISBN: 978-0-470-05830-5Google Scholar
  23. Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136:1447–1455PubMedGoogle Scholar
  24. Jansen RC, Jannink JL, Beavis WD (2003) Mapping quantitative trait loci in plant breeding populations: use of parental haplotype sharing. Crop Sci 43:829–834CrossRefGoogle Scholar
  25. Lander ES, Schork NJ (1994) Genetic dissection of complex traits. Science 265:2037–2048PubMedCrossRefGoogle Scholar
  26. Li L, Paulo MJ, Van Eeuwijk F, Gebhardt C (2010) Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato. Theor Appl Genet 121:1303–1310PubMedCrossRefGoogle Scholar
  27. Li H, Bradbury P, Ersoz E, Buckler ES, Wang J (2011) Joint QTL linkage mapping for multiple-cross mating design sharing one common parent. PLoS ONE 6(3):e17573. doi:10.1371/journal.pone.0017573 PubMedCrossRefGoogle Scholar
  28. Liu W, Gowda M, Steinhoff J, Maurer HP, Würschum T et al (2011) Association mapping in an elite maize breeding population. Theor Appl Genet 123:847–858PubMedCrossRefGoogle Scholar
  29. Liu W, Maurer HP, Reif JC, Cossic F, Würschum T (2012a) Optimum design of family structure and allocation of resources in association mapping with lines from multiple crosses (in review)Google Scholar
  30. Liu W, Reif JC, Cossic F, Würschum T (2012b) Comparison of biometrical approaches for QTL detection in multiple segregating populations. Theor Appl Genet (accepted)Google Scholar
  31. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Assoc, SunderlandGoogle Scholar
  32. Mackay TFC, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10:565–577PubMedCrossRefGoogle Scholar
  33. Malosetti M, Van der Linden CG, Vosman B, Van Eeuwijk FA (2007) A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato. Genetics 175:879–889PubMedCrossRefGoogle Scholar
  34. Malosetti M, Van Eeuwijk FA, Boer MP, Casas AM, Elía M et al (2011) Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs. Theor Appl Genet 122:1605–1616PubMedCrossRefGoogle Scholar
  35. Massman J, Cooper B, Horsley R, Neate S, Dill-Macky R et al (2011) Genome-wide association mapping of fusarium head blight resistance in contemporary barley breeding germplasm. Mol Breeding 27:439–454CrossRefGoogle Scholar
  36. McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H et al (2009) Genetic properties of the maize nested association mapping population. Science 325:737–740PubMedCrossRefGoogle Scholar
  37. Melchinger AE, Orsini E, Schön CC (2012) QTL mapping under truncation selection in homozygous lines derived from biparental crosses. Theor Appl Genet 124:543–553Google Scholar
  38. Meuwissen THE, Karlsen A, Lien S, Olsaker I, Goddard ME (2002) Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping. Genetics 161:373–379PubMedGoogle Scholar
  39. Miedaner T, Wilde F, Korzun V, Ebmeyer E, Schmolke M et al (2009) Marker selection for Fusarium head blight resistance based on quantitative trait loci (QTL) from two European sources compared to phenotypic selection in winter wheat. Euphytica 166:219–227CrossRefGoogle Scholar
  40. Miedaner T, Würschum T, Maurer HP, Korzun V, Ebmeyer E, Reif JC (2011) Association mapping for Fusarium head blight resistance in soft European winter wheat. Mol Breed 28:647–655Google Scholar
  41. Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z et al (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21:2194–2202PubMedCrossRefGoogle Scholar
  42. Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456:720–723PubMedCrossRefGoogle Scholar
  43. Parisseaux B, Bernardo R (2004) In silico mapping of quantitative trait loci in maize. Theor Appl Genet 109:508–514PubMedCrossRefGoogle Scholar
  44. Phillips PC (2008) Epistasis—the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9:855–867PubMedCrossRefGoogle Scholar
  45. Powell JE, Visscher PM, Goddard ME (2010) Reconciling the analysis of IBD abd IBS in complex trait studies. Nat Rev Genet 11:800–805PubMedCrossRefGoogle Scholar
  46. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA et al (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904–909PubMedCrossRefGoogle Scholar
  47. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100PubMedCrossRefGoogle Scholar
  48. Reif JC, Maurer HP, Korzun V, Ebmeyer E, Miedaner T et al (2011) Mapping QTLs with main and epistatic effects underlying grain yield and heading time in soft winter wheat. Theor Appl Genet 123:283–292PubMedCrossRefGoogle Scholar
  49. Steinhoff J, Liu W, Maurer HP, Würschum T, Longin FH et al (2011) Multiple-line cross QTL-mapping in European elite maize. Crop Sci 51:2505–2516Google Scholar
  50. Steinhoff J, Liu W, Reif JC, Ranc N, Würschum T (2012) Detection of QTL for flowering time in multiple families of elite maize (in review)Google Scholar
  51. Thornsberry JM, Goodman MM, Doebley H, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289PubMedCrossRefGoogle Scholar
  52. Van Eeuwijk FA, Boer M, Totir LR, Bink M, Wright D et al (2010a) Mixed model approaches for the identification of QTLs within a maize hybrid breeding program. Theor Appl Genet 120:429–440PubMedCrossRefGoogle Scholar
  53. Van Eeuwijk FA, Bink MCAM, Chenu K, Chapman SC (2010b) Detection and use of QTL for complex traits in multiple environments. Cur Opin Plant Biol 13:193–205CrossRefGoogle Scholar
  54. Van Inghelandt D, Reif JC, Dhillon BS, Flament P, Melchinger AE (2011) Extent and genome-wide distribution of linkage disequilibrium in commercial maize germplasm. Theor Appl Genet 123:11–20PubMedCrossRefGoogle Scholar
  55. Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530PubMedCrossRefGoogle Scholar
  56. Verhoeven KJF, Jannink JL, McIntyre LM (2006) Using mating designs to uncover QTL and the genetic architecture of complex traits. Heredity 96:139–149PubMedCrossRefGoogle Scholar
  57. Von der Ohe C, Ebmeyer E, Korzun V, Miedaner T (2010) Agronomic and quality performance of winter wheat backcross populations carrying non-adapted Fusarium head blight resistance QTL. Crop Sci 50:2283–2290CrossRefGoogle Scholar
  58. Wang H, Smith KP, Combs E, Blake T, Horsley RD et al (2011) Effect of population size and unbalanced data sets on QTL detection using genome-wide association mapping in barley breeding germplasm. Theor Appl Genet. doi:10.1007/s00122-011-1691-8 Google Scholar
  59. Wu R, Zheng ZB (2001) Joint linkage and linkage disequilibrium mapping in natural populations. Genetics 157:899–909PubMedGoogle Scholar
  60. Würschum T, Maurer HP, Kraft T, Janssen G, Nilsson C et al (2011a) Genome-wide association mapping of agronomic traits in sugar beet. Theor Appl Genet 123:1121–1131PubMedCrossRefGoogle Scholar
  61. Würschum T, Maurer HP, Schulz B, Möhring J, Reif JC (2011b) Genome-wide association mapping reveals epistasis and genetic interaction networks in sugar beet. Theor Appl Genet 123:109–118PubMedCrossRefGoogle Scholar
  62. Würschum T, Maurer HP, Dreyer F, Reif JC (2012a) Effect of inter- and intragenic epistasis on the heritability of complex traits (in review)Google Scholar
  63. Würschum T, Liu W, Gowda M, Maurer HP, Fischer S et al (2012b) Comparison of biometrical models for joint linkage association mapping. Heredity 108:332–340Google Scholar
  64. Würschum T, Liu W, Maurer HP, Abel S, Reif JC (2012c) Dissecting the genetic architecture of agronomic traits in multiple segregating populations in rapeseed (Brassica napus L.). Theor Appl Genet 124:153–161Google Scholar
  65. Yu J, Arbelbide M, Bernardo R (2005) Power of in silico QTL mapping from phenotypic, pedigree, and marker data in a hybrid breeding program. Theor Appl Genet 110:1061–1067PubMedCrossRefGoogle Scholar
  66. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M et al (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208PubMedCrossRefGoogle Scholar
  67. Yu LX, Lorenz A, Rutkoski J, Singh RP, Bhavani S et al (2011) Association mapping and gene–gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor Appl Genet. doi:10.1007/s00122-011-1664-y Google Scholar
  68. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468PubMedGoogle Scholar
  69. Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK et al (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42:355–360PubMedCrossRefGoogle Scholar
  70. Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C et al (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3:e4PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  1. 1.State Plant Breeding InstituteUniversity of HohenheimStuttgartGermany

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