Cross-validation in association mapping and its relevance for the estimation of QTL parameters of complex traits

Heredity

Volumn 112, Issue 4, 2014, Pages 463-468

  Wurschum T ^a   Kraft, T ^b  

^a UNIVERSITY OF HOHENHEIM   (Germany)

^b Syngenta Seeds AB   (Sweden)

Author keywords

association mapping; cross validation; predictive power; QTL position; sugar beet

Indexed keywords

DATA SET; GENETIC STRUCTURE; GENOME; LIFE HISTORY TRAIT; MAPPING; POPULATION SIZE; PRECISION; SUGAR BEET;

BETA VULGARIS SUBSP. VULGARIS;

BEET; CHROMOSOME MAP; CROSS BREEDING; GENETICS; PHENOTYPE; QUANTITATIVE TRAIT LOCUS;

BETA VULGARIS; CHROMOSOME MAPPING; CROSSES, GENETIC; PHENOTYPE; QUANTITATIVE TRAIT LOCI;

EID: 84896489705     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2013.126     Document Type: Article

References (33)

1. Allison DB, Fernadez JR, Heo M, Zhu S, Etzel C, Beasley TM et al. (2002). Bias in estimates of quantitative-trait-locus effect in genome scans: Demonstration of the phenomenon and a method-of-moments procedure for reducing bias. Am J Hum Genet 70: 575-585
2. Beavis WD (1998). QTL analyses: Power, precision and accuracy. Paterson AH edited by Molecular Dissection of Complex Traits. CRC Press: Boca Raton, FL, USA, pp 145-162
3. Benjamini Y, Hochberg Y (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc 57: 289-300
4. Berger GL, Liu S, Hall MD, Brooks WS, Chao S, Muehlbauer GJ et al. (2013). Marker-trait associations in Virginia Tech winter barley identified using genome-wide mapping. Theor Appl Genet 126: 693-710
5. Bernardo R (1993). Estimation of coefficient of coancestry using molecular markers in maize. Theor Appl Genet 85: 1055-1062
6. 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
7. Gilmour AR, Gogel BJ, Cullis BR, Thompson R (2006). ASReml User Guide Release 2.0. VSN International Ltd: Hermel Hempstead, U.K.
8. Ingvarsson PK, Garcia MV, Luquez V, Hall D, Jannson S (2008). Nucleotide polymorphism and phenotypic associations within and around the phtyochrome B2 locus in European aspen (Populus tremula, Salicaceae). Genetics 178: 2217-2226
9. Kollers S, Rodemann B, Ling J, Korzun V, Ebmeyer E, Argillier O et al. (2013). Whole genome association mapping of fusarium head blight resistance in European winter wheat (Triticum aestivum L.). PLoS One 8: E57500
10. Kraakman ATW, Niks RE, PMMM Van den Berg, Stam P, Van Eeuwijk FA (2004). Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168: 435-446
11. Kulwal P, Ishikawa G, Benscher D, Feng Z, Yu L-X, Jadhav A et al. (2012). Association mapping for pre-harvest sprouting resistance in white winter wheat. Theor Appl Genet 125: 793-805
12. Liu W, Gowda M, Steinhoff J, Maurer HP, Würschum T, Longin CF et al. (2011). Association mapping in an elite maize breeding population. Theor Appl Genet 123: 847-858
13. Liu W, Maurer HP, Reif JC, Melchinger AE, Utz HF, Tucker MR et al. (2013). Optimum design of family structure and allocation of resources in association mapping with lines from multiple crosses. Heredity 110: 71-79
14. Melchinger AE, Utz HF, Schön CC (1998). Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and larger bias in estimates of QTL effects. Genetics 149: 383-403
15. Reif JC, Gowda M, Maurer HP, Longin CFH, Korzun V, Ebmeyer E et al. (2011a). Association mapping for quality traits in soft winter wheat. Theor Appl Genet 122: 961-970
16. Reif JC, Maurer HP, Korzun V, Ebmeyer E, Miedaner T, Würschum T (2011b). Mapping QTLs with main and epistatic effects underlying grain yield and heading time in soft winter wheat. Theor Appl Genet 123: 283-292
17. 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
18. Sillanpää MJ, Arjas E (1998). Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148: 1373-1388
19. 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
20. Snowdon RJ, Wittkop B, Rezaidad A, Hasan M, Lipsa F, Stein A et al. (2010). Regional association analysis delineates a sequenced chromosome region influencing antinutritive seed meal compounds in oilseed rape. Genome 53: 917-928
21. Stich B, Melchinger AE, Heckenberger M, Möhring J, Schechert A, Piepho HP (2008). Association mapping in multiple segregating populations of sugar beet (Beta vulgaris L.). Theor Appl Genet 117: 1167-1179
22. 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
23. Wang M, Jiang N, Jia T, Leach L, Cockram J, Comadran J et al. (2012a). Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor Appl Genet 124: 233-246
24. Wang X, Zhang C, Li L, Fritsche S, Endrigkeit J, Zhang W et al. (2012b). Unraveling the genetic basis of seed tocopherol content and composition in rapeseed (Brassica napus L.). PLoS One 7: E50038
25. Würschum T, Maurer HP, Kraft T, Janssen G, Nilsson C, Reif JC (2011a). Genome-wide association mapping of agronomic traits in sugar beet. Theor Appl Genet 123: 1121-1131
26. 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
27. Würschum T (2012). Mapping QTL for agronomic traits in breeding populations. Theor Appl Genet 125: 201-210
28. Würschum T, Liu W, Maurer HP, Abel S, Reif JC (2012a). Dissecting the genetic architecture of agronomic traits in multiple segregating populations in rapeseed (Brassica napus L.). Theor Appl Genet 124: 153-161
29. Würschum T, Liu W, Gowda M, Maurer HP, Fischer S, Schechert A et al. (2012b). Comparison of biometrical models for joint linkage association mapping. Heredity 108: 332-340
30. Xu S (2003). The theoretical basis of the Beavis effect. Genetics 165: 2259-2268
31. Yu J, Pressoir G, Briggs WH, Vroh BiI, Yamasaki M, Doebley JF et al. (2006). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208
32. Zhou H, Steffenson B (2013). Genome-wide association mapping reveals genetic architecture of durable spot blotch resistance in US barley breeding germplasm. Mol Breeding 32: 139-154
33. Zö llner S, Pritchard JK (2007). Overcoming the winner's curse: Estimating penetrance parameters from case-control data. Am J Hum Genet 80: 605-615