Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato

Theoretical and Applied Genetics

Volumn 121, Issue 7, 2010, Pages 1303-1310

  Li, Li ^a   Paulo, Maria João ^a,b   van Eeuwijk, Fred ^b   Gebhardt, Christiane ^a  

^a MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH   (Germany)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION MAPPING; BIOCHEMICAL PATHWAY; BIOLOGICAL MODELS; BISPHOSPHATES; CANDIDATE GENES; CARBOHYDRATE METABOLISM; CHIP COLOR; CHIP QUALITY; COMPLEX TRAITS; CUT-OFF VALUE; DNA MARKERS; EPISTATIC INTERACTIONS; FALSE DISCOVERY RATE; FUNCTIONAL LEVELS; POTATO TUBERS; POTATO VARIETIES; QUANTITATIVE TRAITS; RIBULOSE; STARCH CONTENTS; SUCROSE-PHOSPHATE SYNTHASE; SUGAR CONTENT; TOTAL VARIANCE; TUBER STARCH; VACUOLAR INVERTASE;

ASSOCIATION REACTIONS; CARBOHYDRATES; GENES; MAPPING; METABOLISM; PLANTS (BOTANY); POPULATION STATISTICS; SUGAR (SUCROSE);

STARCH;

BETA FRUCTOFURANOSIDASE; GLUCOSYLTRANSFERASE; RIBULOSEBISPHOSPHATE CARBOXYLASE; STARCH; SUCROSE PHOSPHATE SYNTHASE; SUCROSE-PHOSPHATE SYNTHASE;

ALLELE; ARTICLE; CHEMISTRY; CHROMOSOME MAP; GENETIC MARKER; GENETIC VARIABILITY; GENETICS; METABOLISM; PHENOTYPE; PLANT GENE; POTATO; QUANTITATIVE TRAIT LOCUS; TETRAPLOIDY;

ALLELES; BETA-FRUCTOFURANOSIDASE; CHROMOSOME MAPPING; GENES, PLANT; GENETIC MARKERS; GENETIC VARIATION; GLUCOSYLTRANSFERASES; PHENOTYPE; QUANTITATIVE TRAIT LOCI; RIBULOSE-BISPHOSPHATE CARBOXYLASE; SOLANUM TUBEROSUM; STARCH; TETRAPLOIDY;

SOLANUM TUBEROSUM; TUBER (TRUFFLE);

EID: 78049294150     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-010-1389-3     Document Type: Article

References (42)

1. Alcazar R, Garcia AV, Parker JE, Reymond M (2009) Incremental steps toward incompatibility revealed by Arabidopsis epistatic interactions modulating salicylic acid pathway activation. Proc Natl Acad Sci 106: 334-339.
2. Allison DB, Gadbury GL, Heo M, Fernández JR, Lee C-K, Prolla TA, Weindruch R (2002) A mixture model approach for the analysis of microarray gene expression data. Comput Stat Data Anal 39: 1-20.
3. Burton WG (1969) The sugar balance in some British potato varieties during storage II: the effects of tuber age, previous storage temperature, and intermittent refrigeration upon low-temperature sweetening. Eur Potato J 12: 81-95.
4. Carlborg O, Haley CS (2004) Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5: 618-625.
5. Ducrocq S, Madur D, Veyrieras J-B, Camus-Kulandaivelu L, Kloiber-Maitz M, Presterl T, Ouzunova M, Manicacci D, Charcosset A (2008) Key impact of Vgt1 on flowering time adaptation in maize: evidence from association mapping and ecogeographical information. Genetics 178: 2433-2437.
6. Eckert A, Bower AD, Wegrzyn JL, Pande B, Jermstad KD, Krutovsky KV, St. Clair JB, Neale DB (2009) Association genetics of coastal Douglas-fir (Pseudotsuga menziesii var. menziesii, Pinaceae) I. Cold-hardiness related traits. Genetics. http://genetics. 109. 102350.
7. Ehrenreich IM, Stafford PA, Purugganan MD (2007) The genetic architecture of shoot branching in Arabidopsis thaliana: a comparative assessment of candidate gene associations vs. quantitative trait locus mapping. Genetics 176: 1223-1236.
8. Fisher RA (1918) The correlations between relatives on the supposition of Mendelian inheritance. Trans R Soc Edinb 52: 399-433.
9. Frommer WB, Sonnewald U (1995) Molecular analysis of carbon partitioning in solanaceous species. J Exp Bot 46: 587-607.
10. Gebhardt C, Ballvora A, Walkemeier B, Oberhagemann P, Schüler K (2004) Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol Breed 13: 93-102.
11. Gonzalez-Martinez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB (2007) Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175: 399-409.
12. Gupta P, Rustgi S, Kulwal P (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57: 461-485.
13. Habib A, Brown HD (1957) The role of reducing sugars and amino acids in browning of potato chips. Food Technol 11: 85-89.
14. Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10: 156-161.
15. Huber SC, Huber JL (1992) Role of sucrose-phosphate synthase in sucrose metabolism in leaves. Plant Physiol 99: 1275-1278.
16. Isherwood FA (1973) Starch-sugar interconversion in Solanum tuberosum. Phytochemistry 12: 2579-2591.
17. Jannink J-L (2007) Identifying quantitative trait locus by genetic background interactions in association studies. Genetics 176: 553-561.
18. 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.
19. Li L, Strahwald J, Hofferbert HR, Lubeck J, Tacke E, Junghans H, Wunder J, Gebhardt C (2005) DNA variation at the invertase locus invGE/GF is associated with tuber quality traits in populations of potato breeding clones. Genetics 170: 813-821.
20. Li L, Paulo MJ, Strahwald J, Lübeck J, Hofferbert HR, Tacke E, Junghans H, Wunder J, Draffehn A, van Eeuwijk F, Gebhardt C (2008) Natural DNA variation at candidate loci is associated with potato chip color, tuber starch content, yield and starch yield. Theor Appl Genet 116: 1167-1181.
21. Luo ZW, Hackett CA, Bradshaw JE, McNicol JW, Milbourne D (2001) Construction of a genetic linkage map in tetraploid species using molecular markers. Genetics 157: 1369-1385.
22. Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12: 57-63.
23. Manicacci D, Camus-Kulandaivelu L, Fourmann M, Arar C, Barrault S, Rousselet A, Feminias N, Consoli L, Frances L, Mechin V, Murigneux A, Prioul J-L, Charcosset A, Damerval C (2009) Epistatic interactions between Opaque2 transcriptional activator and its target gene CyPPDK1 control kernel trait variation in maize. Plant Physiol 150: 506-520.
24. Mate CJ, Hudson GS, von Caemmerer S, Evans JR, Andrews TJ (1993) Reduction of ribulose bisphosphate carboxylase activase levels in tobacco (Nicotiana tabacum) by antisense RNA reduces ribulose bisphosphate carboxylase carbamylation and impairs photosynthesis. Plant Physiol 102: 1119-1128.
25. Olsen KO, Halldorsdottir SS, Stinchcomb JR, Weinig C, Schmitt J, Purugganan MD (2004) Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 167: 1361-1369.
26. Pajerowska-Mukhtar K, Stich B, Achenbach U, Ballvora A, Lübeck J, Strahwald J, Tacke E, Hofferbert H-R, Ilarionova E, Bellin D, Walkemeier B, Basekow R, Kersten B, Gebhardt C (2009) Single nucleotide polymorphisms in the Allene Oxide Synthase 2 gene are associated with field resistance to late blight in populations of tetraploid potato cultivars. Genetics 181: 1115-1127.
27. Phillips PC (2008) Epistasis-the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9: 855-867.
28. Portis ARJ (1990) Rubisco activase. Biochim Biophys Acta 1015: 15-28.
29. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
30. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
31. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98: 11479-11484.
32. Saidou A-A, Mariac C, Luong V, Pham J-L, Bezancon G, Vigouroux Y (2009) Association studies identify natural variation at PHYC linked to flowering time and morphological variation in Pearl Millet. Genetics 182: 899-910.
33. Salvucci M, Ogren W (1996) The mechanism of Rubisco activase: insights from studies of the properties and structure of the enzyme. Photosynth Res 47: 1-11.
34. Stitt M, Wilke I, Feil R, Heldt HW (1988) Coarse control of sucrose-phosphate synthase in leaves: alterations of the kinetic properties in response to the rate of photosynthesis and the accumulation of sucrose. Planta 174: 217-230.
35. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440-9445.
36. Stracke S, Haseneyer G, Veyrieras J-B, Geiger H, Sauer S, Graner A, Piepho H-P (2009) Association mapping reveals gene action and interactions in the determination of flowering time in barley. Theor and Appl Genet 118: 259-273.
37. Sturm A, Tang G-Q (1999) The sucrose-cleaving enzymes of plants are crucial for development, growth and carbon partitioning. Trends Plant Sci 4: 401-407.
38. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28: 286-289.
39. Townsend LR, Hope GW (1960) Factors influencing the color of potato chips. Can J Plant Sci 40: 58-64.
40. Tymowska-Lalanne Z, Kreis M, Callow JA (1998) The plant invertases: physiology, biochemistry and molecular biology. In: Advances in botanical research. Academic Press, Dublin, pp 71-117.
41. Winter H, Huber SC, Sharkey T (2000) Regulation of sucrose metabolism in higher plants: localization and regulation of activity of key enzymes. Crit Rev Biochem Mol Biol 35: 253-289.
42. Zrenner R, Schüler K, Sonnewald U (1996) Soluble acid invertase determines the hexose-to-sucrose ratio in cold-stored potato tubers. Planta 198: 246-252.