Complex genetic interactions in a quantitative trait locus

PLoS Genetics

Volumn 2, Issue 2, 2006, Pages 140-147

  Sinha, Himanshu ^a   Nicholson, Bradly P ^a   Steinmetz, Lars M ^b   McCusker, John H ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL STRAIN; DNA HYBRIDIZATION; DNA POLYMORPHISM; GENE DELETION; GENE INTERACTION; GENETIC ANALYSIS; GENETIC IDENTIFICATION; HEMIZYGOSITY; HIGH TEMPERATURE; MARKER GENE; NONHUMAN; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; SACCHAROMYCES CEREVISIAE; 3' UNTRANSLATED REGION; BIOLOGICAL MODEL; CHROMOSOME; CHROMOSOME MAP; FUNGAL GENE; GENETIC LINKAGE; GENETIC POLYMORPHISM; GENETICS; METABOLISM; PLASMID; TEMPERATURE;

BACTERIA (MICROORGANISMS); SACCHAROMYCES CEREVISIAE;

3' UNTRANSLATED REGIONS; CHROMOSOME MAPPING; CHROMOSOMES, FUNGAL; GENE DELETION; GENES, FUNGAL; LINKAGE (GENETICS); MODELS, GENETIC; PHENOTYPE; PLASMIDS; POLYMORPHISM, GENETIC; QUANTITATIVE TRAIT LOCI; SACCHAROMYCES CEREVISIAE; TEMPERATURE;

EID: 33645789591     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020013     Document Type: Article

References (49)

1. Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, et al. (2002) Dissecting the architecture of a quantitative trait locus in yeast. Nature 416: 326-330.
2. Kroymann J, Mitchell-Olds T (2005) Epistasis and balanced polymorphism in.uencing complex trait variation. Nature 435: 95-98.
3. Carlborg O, Haley CS (2004) Epistasis: Too often neglected in complex trait studies? Nat Rev Genet 5: 618-625.
4. Barton NH, Keightley PD (2002) Understanding quantitative genetic variation. Nat Rev Genet 3: 11-21.
5. Glazier AM, Nadeau JH, Aitman TJ (2002) Finding genes that underlie complex traits. Science 298: 2345-2349.
6. Mackay TF (2001) The genetic architecture of quantitative traits. Ann Rev Genet 35: 303-339.
7. Flint J, Mott R (2001) Finding the molecular basis of quantitative traits: Successes and pitfalls. Nat Rev Genet 2: 437-445.
8. Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes: Past successes for mendelian disease, future approaches for complex disease. Nat Genet 33 (Suppl): 228-237.
9. Doerge RW (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet 3: 43-52.
10. Jansen RC (2003) Studying complex biological systems using multifactorial perturbation. Nat Rev Genet 4: 145-151.
11. Hoh J, Ott J (2003) Mathematical multi-locus approaches to localizing complex human trait genes. Nat Rev Genet 4: 701-709.
12. Borevitz JO, Chory J (2004) Genomics tools for QTL analysis and gene discovery. Curr Opin Plant Biol 7: 132-136.
13. Steinmetz LM, Davis RW (2004) Maximizing the potential of functional genomics. Nat Rev Genet 5: 190-201.
14. Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, et al. (2005) Saccharomyces Genome Database. Available at: http://www.yeastgenome.org. Accessed 31 August 2005.
15. Guldener U, Munsterkotter M, Kastenmuller G, Strack N, van Helden J, et al. (2005) CYGD: The Comprehensive Yeast Genome Database. Nucleic Acids Res 33: D364-D368.
16. Stepp JD, Huang K, Lemmon SK (1997) The yeast adaptor protein complex, AP-3, is essential for the efficient delivery of alkaline phosphatase by the alternate pathway to the vacuole. J Cell Biol 139: 1761-1774.
17. Moreau V, Galan JM, Devilliers G, Haguenauer-Tsapis R, Winsor B (1997) The yeast actin-related protein Arp2p is required for the internalization step of endocytosis. Mol Biol Cell 8: 1361-1375.
18. Tang HY, Munn A, Cai M (1997) EH domain proteins Pan1p and End3p are components of a complex that plays a dual role in organization of the cortical actin cytoskeleton and endocytosis in Saccharomyces cerevisiae. Mol Cell Biol 17: 4294-4304.
19. Tong AHY, Lesage G, Bader GD, Ding H, Xu H, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303: 808-813.
20. Tadauchi T, Inada T, Matsumoto K, Irie K (2004) Posttranscriptional regulation of HO expression by the Mkt1-Pbp1 complex. Mol Cell Biol 24: 3670-3681.
21. +-ATPase-defective yeast: Identification of six new END genes. J Cell Biol 127: 373-386.
22. Benedetti H, Raths S, Crausaz F, Riezman H (1994) The END3 gene encodes a protein that is required for the internalization step of endocytosis and for actin cytoskeleton organization in yeast. Mol Biol Cell 5: 1023-1037.
23. Altshuler D, Brooks LD, Chakravarti A, Collins FS, Daly MJ, et al. (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
24. Kuersten S, Goodwin EB (2003) The power of the 39 UTR: Translational control and development. Nat Rev Genet 4: 626-637.
25. Gray NK, Wickens M (1998) Control of translation initiation in animals. Annu Rev Cell Dev Biol 14: 399-458.
26. Gonsalvez GB, Urbinati CR, Long RM (2005) RNA localization in yeast: Moving towards a mechanism. Biol Cell 97: 75-86.
27. Madaule P, Axel R, Myers AM (1987) Characterization of two members of the rho gene family from the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 84: 779-783.
28. Wickner RB (1987) MKT1, a nonessential Saccharomyces cerevisiae gene with a temperature-dependent effect on replication of M2 double-stranded RNA. J Bacteriol 169: 4941-4945.
29. Deutschbauer AM, Davis RW (2005) Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nat Genet 37: 1333-1340.
30. Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K (2002) A comprehensive review of genetic association studies. Genet Med 4: 45-61.
31. McCusker JH, Clemons KV, Stevens DA, Davis RW (1994) Genetic characterization of pathogenic Saccharomyces cerevisiae isolates. Genetics 136: 1261-1269.
32. Rose MD, Winston F, Hieter P (1990) Methods in yeast genetics: A laboratory course manual. Cold Spring Harbor (New York): Cold Spring Harbor Laboratory. 198 p.
33. Chattoo BB, Sherman F, Azubalis DA, Fjellstedt TA, Mehnert D, et al. (1979) Selection of lys2 mutants of the yeast Saccharomyces cerevisiae by the utilization of α-aminoadipate. Genetics 93: 51-65.
34. Wach A, Brachat A, Pohlmann R, Philippsen P (1994) New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10: 1793-1808.
35. Goldstein AL, McCusker JH (1999) Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15: 1541-1553.
36. Codon A, Gasent-Ramirez J, Benitez T (1995) Factors which affect the frequency of sporulation and tetrad formation in Saccharomyces cerevisiae baker's yeasts. Appl Environ Microbiol 61: 630-638.
37. Gietz RD, Schiestl RH, Willems AR, Woods RA (1995) Studies on the transformation of intact yeast cells by the LiAc/SS-DNA/PEG procedure. Yeast 11: 355-360.
38. Niedenthal RK, Riles L, Johnston M, Hegemann JH (1996) Green fluorescent protein as a marker for gene expression and subcellular localization in budding yeast. Yeast 12: 773-786.
39. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, et al., editors (2004) Current protocols in molecular biology. Hoboken (New Jersey): John Wiley & Sons.
40. Sokal RR, Rohlf FJ (2000) Biometry: The principles and practice of statistics in biological research. New York: W. H. Freeman and Company. 887 p.
41. Rothstein R (1991) Targeting, disruption, replacement, and allele rescue: Integrative DNA transformation in yeast. Methods Enzymol 194: 281-301.
42. Sikorski RS, Hieter P (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
43. Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57: 267-272.
44. Sambrook J, Russell DW (2001) Molecular cloning: A laboratory manual. Volume 1. Cold Spring Harbor (New York): Cold Spring Harbor Laboratory Press. 680 p.
45. Ito-Harashima S, McCusker JH (2004) Positive and negative selection LYS5MX gene replacement cassettes for use in Saccharomyces cerevisiae. Yeast 21: 53-61.
46. Huang J, Lee SH, Lin C, Medici R, Hack E, et al. (1990) Expression in yeast of the T-urf13 protein from Texas male-sterile maize mitochondria confers sensitivity to methomyl and to Texas-cytoplasm-specific fungal toxins. EMBO J 9: 339-347.
47. Soderholm J, Bevis BJ, Glick BS (2001) Vector for pop-in/pop-out gene replacement in Pichia pastoris. Biotechniques 31: 306 310,-312.
48. Storici F, Lewis LK, Resnick MA (2001) In vivo site-directed mutagenesis using oligonucleotides. Nat Biotechnol 19: 773-776.
49. Goldstein AL, Pan X, McCusker JH (1999) Heterologous URA3MX cassettes for gene replacement in Saccharomyces cerevisiae. Yeast 15: 507-511.