Comparison of biometrical approaches for QTL detection in multiple segregating families

Theoretical and Applied Genetics

Volumn 125, Issue 5, 2012, Pages 987-998

  Liu, Wenxin ^a,b   Reif, Jochen C ^b   Ranc, Nicolas ^c   Porta, Giovanni Della ^d   Würschum, Tobias ^b  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b UNIVERSITY OF HOHENHEIM   (Germany)

^c Syngenta Seeds SAS   (France)

^d Syngenta Seeds SpA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION MAPPING; CROSS VALIDATION; DATA SETS; EPISTATIC INTERACTIONS; GENETIC MAP; HIGH MARKER DENSITY; LARGE POPULATION; LINKAGE MAPPING; MAIN EFFECT; MODEL AVERAGING; QTL MAPPING; RESAMPLES;

PROFITABILITY;

MAPPING;

PLANT DNA;

ARTICLE; CHROMOSOME MAP; COMPARATIVE STUDY; GENETIC LINKAGE; GENETIC MARKER; GENETICS; GROWTH, DEVELOPMENT AND AGING; MAIZE; PHENOTYPE; PLANT CHROMOSOME; PLANT GENE; POLYMERASE CHAIN REACTION; QUANTITATIVE TRAIT LOCUS;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA, PLANT; GENES, PLANT; GENETIC LINKAGE; GENETIC MARKERS; PHENOTYPE; POLYMERASE CHAIN REACTION; QUANTITATIVE TRAIT LOCI; ZEA MAYS;

ZEA MAYS;

EID: 84865595131     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-012-1889-4     Document Type: Article

References (39)

1. 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: 206-224.
2. Broman KW, Sen S (2009) A guide to QTL mapping with R/qtl. Springer Science + Business Media, LLC.
3. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ et al (2009) The genetic architecture of maize flowering time. Science 325: 714-718.
4. Carlborg Ö, Haley CS (2004) Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5: 618-625.
5. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
6. 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: 799-822.
7. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54: 357-374.
8. Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38: 226-231.
9. Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10: 156-161.
10. Holland JB, Portyanko VA, Hoffmann DL, Lee M (2002) Genomic regions controlling vernalization and photoperiod responses in oat. Theor Appl Genet 105: 113-126.
11. Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6: 65-70.
12. Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447-1455.
13. 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: 847-858.
14. Liu W, Maurer HP, Reif JC, Melchinger AE, Utz HF et al (2012) Optimum design of family structure and allocation of resources in association mapping with lines from multiple crosses (in review).
15. Lu Y, Zhang S, Shah T, Xie C, Hao Z, Li X et al (2010) Joint linkage-linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize. Proc Natl Acad Sci USA 107: 19585-19590.
16. Maurer HP, Melchinger AE, Frisch M (2008) Population genetic simulation and data analysis with Plabsoft. Euphytica 161: 133-139.
17. 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: 2194-2202.
18. Piepho HP (2000) Optimal marker density for interval mapping in a backcross population. Heredity 84: 437-440.
19. Reif JC, Liu W, Gowda M, Maurer HP, Möhring J et al (2010) Genetic basis of agronomically important traits in sugar beet (Beta vulgaris L.) Investigated with joint linkage association mapping. Theor Appl Genet 8: 1489-1495.
20. Reif JC, Gowda M, Maurer HP, Longin CFH, Korzun V et al (2011a) Association mapping for quality traits in soft winter wheat. Theor Appl Genet 122: 961-970.
21. Reif JC, Maurer HP, Korzun V, Ebmeyer E, Miedaner T et al (2011b) Mapping QTLs with main and epistatic effects underlying grain yield and heading time in soft winter wheat. Theor Appl Genet 123: 283-292.
22. SAS Institute Inc (2008) SAS user's guide, version 9. 2. SAS Institute: Cary, NC, USA.
23. Schön CC, Utz HF, Groh S, Truberg B, Openshaw S, Melchinger AE (2004) Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits. Genetics 167: 485-498.
24. Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6: 461-464.
25. Sillanpää MJ (2011) Overview of techniques to account for confounding due to population stratification and cryptic relatedness in genomic data association analyses. Heredity 106: 511-519.
26. 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: 2505-2516.
27. Utz HF, Melchinger AE, Schön CC (2000) Bias and sampling error of the estimated proportion of genotypic variance explained by quantitative trait loci determined from experimental data in maize using cross validation and validation with independent samples. Genetics 154: 1839-1849.
28. Valdar W, Holmes CC, Mott R, Flint J (2009) Mapping in structured populations by resample model averaging. Genetics 182: 1263-1277.
29. 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: 11-20.
30. Verhoeven KJF, Jannink JL, McLntyre LM (2006) Using mating designs to uncover QTL and the genetic architecture of complex traits. Heredity 96: 139-149.
31. Weir BS (1996) Genetic data analysis II, 2nd edn. Sinauer Associates, Sunderland.
32. Whitt SR, Wilson LM, Tenaillon MD, Gaut BS, Buckler ES (2002) Genetic diversity and selection in the maize starch pathway. Proc Natl Acad Sci 99: 12959-12962.
33. Würschum T (2012) Mapping QTL for agronomic traits in breeding populations. Theor Appl Genet. doi: 10. 1007/s00122-012-1887-6.
34. 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: 1121-1131.
35. 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: 109-118.
36. Würschum T, Liu W, Gowda M, Maurer HP, Fischer S et al (2012a) Comparison of biometrical models for joint linkage association mapping. Heredity 108: 332-340.
37. Würschum T, Liu W, Maurer HP, Abel S, Reif JC (2012b) Dissecting the genetic architecture of agronomic traits in multiple segregating populations in rapeseed (Brassica napus L.). Theor Appl Genet 124: 153-161.
38. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.
39. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.