Optimum design of family structure and allocation of resources in association mapping with lines from multiple crosses

Heredity

Volumn 110, Issue 1, 2013, Pages 71-79

  Liu, W ^a,b   Maurer, H P ^b   Reif, J C ^b   Melchinger, A E ^b   Utz, H F ^b   Tucker, M R ^c   Ranc, N ^d   Della Porta, G ^e   Wurschum T ^b  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b UNIVERSITY OF HOHENHEIM   (Germany)

^c UNIVERSITY OF ADELAIDE   (Australia)

^d Syngenta Seeds SAS   (France)

^e Syngenta Seeds SpA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY ASSESSMENT; BIOMARKER; EXPERIMENTAL DESIGN; FAMILY STRUCTURE; GENETIC VARIATION; GENOTYPE; LIFE HISTORY TRAIT; PHENOTYPE; POPULATION SIZE; QUANTITATIVE ANALYSIS; RESOURCE ALLOCATION; SAMPLING;

ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; CROSS BREEDING; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETICS; GENOTYPE; METHODOLOGY; PLANT; PLANT SEED; POPULATION GENETICS; QUANTITATIVE TRAIT LOCUS; REPRODUCIBILITY;

COMPUTER SIMULATION; CROSSES, GENETIC; GENETIC ASSOCIATION STUDIES; GENETICS, POPULATION; GENOTYPE; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; PLANTS; QUANTITATIVE TRAIT LOCI; REPRODUCIBILITY OF RESULTS; SEEDS;

EID: 84871087348     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2012.63     Document Type: Article

References (35)

1. Beavis WD (1994). The power and deceit of QTL experiments: lessons from comparative QTL studies. 49th Annual Corn and Sorghum Industry Research Conference. ASTA: Washington, DC, pp 250-266.
2. Beavis WD (1998). QTL analyses: power, precision and accuracy. Molecular Dissection of Complex Traits. edited by Paterson. AHCRC PressBoca Raton FL pp 145-162.
3. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C et al. (2009). The genetic architecture of maize flowering time. Science 325: 714-718.
4. Falconer DS, Mackay TFC (1996). Introduction to Quantitative Genetics, 4th edn. Longman House: London.
5. Hallauer AR, Miranda JB (1981). Quantitative Genetics in Maize Breeding. Iowa State University Press: Ames, IA.
6. Hamblin MT, Buckler ES, Jannink JL (2011). Population genetics of genomics-based crop improvement methods. Trends Genet 27: 98-106.
7. Holland JB (2007). Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10: 156-161.
8. Holm S (1979). A simple sequentially rejective bonferroni test procedure. Scand J Stat 6: 65-70.
9. Knapp SJ, Bridges WC (1990). Using molecular markers to estimate quantitative trait locus parameters: power and genetic variances for unreplicated and replicated progeny. Genetics 126: 769-777.
10. Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD et al. (2009). A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5: e1000551.
11. Lande R, Thompson R (1990). Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124: 743-756.
12. Liu W, Gowda M, Steinhoff J, Maurer HP, Wurschum T, Longin CF et al. (2011). Association mapping in an elite maize breeding population. Theor Appl Genet 123: 847-858.
13. Liu W, Reif JC, Ranc N, Della Porta G, Wurschum T (2012). Comparison of biometrical approaches for QTL detection in multiple segregating families. Theor Appl Genet 125: 987-998.
14. Longin CFH, Utz HF, Reif JC, Wegenast T, Schipprack W, Melchinger AE (2007). Hybrid maize breeding with doubled haploids: III. Efficiency of early testing prior to doubled haploid production in two-stage selection for testcross performance. Theor Appl Genet 115: 519-527.
15. Maurer HP, Melchinger AE, Frisch M (2008). Population genetic simulation and data analysis with Plabsoft. Euphytica 161: 133-139.
16. McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li HH, Sun Q (2009). Genetic properties of the maize nested association mapping population. Science 325: 737-740.
17. Melchinger AE, Utz HF, Schon CC (1998). Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects. Genetics 149: 383-403.
18. Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE et al. (2009). Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21: 2194-2202.
19. Reif JC, Liu W, Gowda M, Maurer HP, Mohring J, Fischer S et al. (2010). Genetic basis of agronomically important traits in sugar beet (Beta vulgaris L.) investigated with joint linkage association mapping. Theor Appl Genet 121: 1489-1499.
20. SAS Institute. Inc (2008). SAS User's Guide, Version 9 2. SAS Institute: Cary, NC.
21. Schon 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.
22. Schwarz G (1978). Estimating the dimension of a model. Ann Stat 6: 461-464.
23. Searle SR (1971). Linear Models. Wiley: New York.
24. Stich B, Yu J, Melchinger AE, Piepho HP, Utz HF, Maurer HP et al. (2007). Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy. Genetics 176: 563-570.
25. Stich B (2009). Comparison of mating designs for establishing nested association mapping populations in maize and Arabidopsis thaliana. Genetics 183: 1525-1534.
26. Stich B, Utz HF, Piepho HP, Maurer HP, Melchinger AE (2010). Optimum allocation of resources for QTL detection using a nested association mapping strategy in maize. Theor Appl Genet 120: 553-561.
27. Utz HF, Melchinger AE (1994). Comparison of different approaches to interval mapping of quantitative trait loci. pp 195-204, inBiometrics in plant breeding: applications of molecular markers. Proceedings of the Ninth Meeting of the EUCARPIA Section Biometrics in Plant Breeding. edited by Van Ooijen JW, Jansen J) (CPRO-DLO: Wageningen, Netherlands.
28. Utz HF, Melchinger AE, Schon 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.
29. Valdar W, Holmes CC, Mott R, Flint J (2009). Mapping in structured populations by resample model averaging. Genetics 182: 1263-1277.
30. Verhoeven KJF, Jannink JL, McIntyre LM (2006). Using mating designs to uncover QTL and the genetic architecture of complex traits. Heredity 96: 139-149.
31. Wurschum T (2012). Mapping QTL for agronomic traits in breeding populations. Theor Appl Genet 125: 201-210.
32. Wurschum T, Liu W, Gowda M, Maurer HP, Fischer S, Schechert A et al. (2012). Comparison of biometrical models for joint linkage association mapping. Heredity 108: 332-340.
33. Wu R, Ma CX, Casella G (2002). Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations. Genetics 160: 779-792.
34. Yu J, Holland JB, McMullen MD, Buckler ES (2008). Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.
35. Zhao Y, Gowda M, Liu W, Wurschum T, Maurer HP, Longin FH et al. (2012). Accuracy of genomic selection in European maize elite breeding populations. Theor Appl Genet 124: 769-776.