Genome-wide association mapping reveals epistasis and genetic interaction networks in sugar beet

Theoretical and Applied Genetics

Volumn 123, Issue 1, 2011, Pages 109-118

  Würschum, Tobias ^a   Maurer, Hans Peter ^a   Schulz, Britta ^b   Möhring, Jens ^a   Reif, Jochen Christoph ^a  

^a UNIVERSITY OF HOHENHEIM   (Germany)

^b KWS SAAT SE Co KGaA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION MAPPING; COMPLEX TRAITS; EPISTATIC INTERACTIONS; GENE NETWORKS; GENETIC ARCHITECTURE; GENETIC INTERACTION; GENETIC LOCUS; GENETIC NETWORKS; GENOME-WIDE ASSOCIATION; HIGHER ORDER; LARGE POPULATION; MAIN EFFECT; MATRIX; MIXED MODELS; PHYSIOLOGICAL TRAIT; POPULATION STRATIFICATION; QUANTITATIVE TRAITS;

GENES; SUGAR BEETS; SUGARS;

ASSOCIATION REACTIONS;

ARTICLE; BEET; BIOLOGICAL MODEL; BREEDING; CHROMOSOME MAP; CROSS BREEDING; GENETIC ASSOCIATION; GENETIC EPISTASIS; GENETICS; GENOTYPE; METHODOLOGY; PHENOTYPE; QUANTITATIVE TRAIT LOCUS;

BETA VULGARIS; BREEDING; CHROMOSOME MAPPING; CROSSES, GENETIC; EPISTASIS, GENETIC; GENETIC ASSOCIATION STUDIES; GENOTYPE; MODELS, GENETIC; PHENOTYPE; QUANTITATIVE TRAIT LOCI;

BETA VULGARIS SUBSP. VULGARIS;

EID: 79958136814     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-011-1570-3     Document Type: Article

References (37)

1. Bernardo R (1993) Estimation of coefficient of coancestry using molecular markers in maize. Theor Appl Genet 85: 1055-1062.
2. Brem RB, Kruglyak L (2005) The landscape of genetic complexity across 5. 700 gene expression traits in yeast. Proc Natl Acad Sci USA 102: 1572-1577.
3. Carlborg Ö, Haley CS (2004) Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5: 618-625.
4. Carlborg Ö, Jacobsson L, Ahgren P, Siegel P, Andersson L (2006) Epistasis and the release of genetic variation during long-term selection. Nat Genet 38: 418-420.
5. Chao S, Zhang W, Dubcovsky J, Sorrells ME (2007) Evaluation of genetic diversity and genome-wide linkage disequilibrium among U. S. wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Sci 47: 1018-1030.
6. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED et al (2010) The genetic landscape of a cell. Science 327: 425-431.
7. Draycott AP (2006) Sugar beet, 1st edn. Blackwell, Oxford.
8. Eshed Y, Zamir D (1996) Less-than-additive epistatic interactions of quantitative trait loci in tomato. Genetics 143: 1807-1817.
9. Gilmour AR, Gogel BJ, Cullis BR, Thompson R (2006) ASReml User Guide Release 2. 0 VSN International Ltd, Hermel HempsteadHempstead, UK.
10. He X, Qian W, Wang Z, Li Y, Zhang J (2010) Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks. Nat Genet 42: 272-276.
11. Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38: 226-231.
12. Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6: 65-70.
13. Kraakman ATW, Niks RE, van den Berg PMMM, Stam P, van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168: 435-446.
14. Li Z, Pinson SR, Park WD, Paterson AH, Stansel JW (1997) Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145: 453-465.
15. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Assoc., Sunderland.
16. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
17. Maurer HP, Melchinger AE, Frisch M (2008) Population genetic simulation and data analysis with Plabsoft. Euphytica 161: 133-139.
18. 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.
19. Montooth KL, Marden JH, Clark AG (2003) Mapping determinants of variation in energy metabolism, respiration and flight in Drosophila. Genetics 165: 623-635.
20. Phillips PC (2008) Epistasis-the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9: 855-867.
21. 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: 904-909.
22. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N et al (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
23. Schneider K, Schäfer-Pregl R, Borchardt C, Salamini F (2002) Mapping QTLs for sucrose content, yield and quality in a sugar beet population fingerprinted by EST-related markers. Theor Appl Genet 104: 1107-1113.
24. St Onge RP, Mani R, Oh J, Proctor M, Fung E et al (2007) Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nat Genet 39: 199-206.
25. Stich B, Melchinger AE, Frisch M, Maurer HP, Heckenberger M et al (2005) Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet 111: 723-730.
26. Stich B, Melchinger AE, Heckenberger M, Möhring J, Schechert A et al (2008a) Association mapping in multiple segregating populations of sugar beet (Beta vulgaris L.). Theor Appl Genet 117: 1167-1179.
27. Stich B, Möhring J, Piepho HP, Heckenberger M, Buckler ES et al (2008b) Comparison of mixed-model approaches for association mapping. Genetics 178: 1745-1754.
28. Stich B, Yu J, Melchinger AE, Piepho HP, Utz HF et al (2008c) Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy. Genetics 176: 563-570.
29. Stram DO, Lee JW (1994) Variance components testing in longitudinal mixed effects model. Biometrics 50: 1171-1177.
30. Tong AH, Lesage G, Bader GD, Ding H, Xu H et al (2004) Global mapping of the yeast genetic interaction network. Science 303: 808-813.
31. 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.
32. Weber WE, Borchardt DC, Koch G (2000) Marker analysis for quantitative traits in sugar beet. Plant Breed 119: 97-106.
33. Weir BS (1996) Genetic data analysis II, 2nd edn. Sinauer Associates, Sunderland.
34. Wright S (1978) Evolution and genetics of populations, variability within and among natural populations, vol 4. The University of Chicago Press, Chicago, p 91.
35. Xu S, Jia Z (2007) Genomewide analysis of epistatic effects for quantitative traits in barley. Genetics 175: 1955-1963.
36. 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: 203-208.
37. 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: e4.