Quantitative trait loci mapped to single-nucleotide resolution in yeast

Nature Genetics

Volumn 37, Issue 12, 2005, Pages 1333-1340

  Deutschbauer, Adam M ^a   Davis, Ronald W ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA POLYMORPHISM; FUNGAL GENE; GENE IDENTIFICATION; GENE INTERACTION; GENE MAPPING; GENE SEGREGATION; GENETIC ENGINEERING; GENETIC EPISTASIS; GENETIC HETEROGENEITY; GENETIC VARIABILITY; MISSENSE MUTATION; MORPHOLOGICAL TRAIT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; REGULATOR GENE; SACCHAROMYCES CEREVISIAE; SINGLE NUCLEOTIDE POLYMORPHISM; SPOROGENESIS;

BASE SEQUENCE; CARRIER PROTEINS; CHROMOSOME MAPPING; EPISTASIS, GENETIC; GENES, FUNGAL; MOLECULAR SEQUENCE DATA; MUTATION, MISSENSE; NUCLEOTIDES; QUANTITATIVE TRAIT LOCI; REPRESSOR PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SPORES, FUNGAL;

SACCHAROMYCES CEREVISIAE;

EID: 28444467392     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1674     Document Type: Article

References (43)

1. Mackay, T.F. The genetic architecture of quantitative traits. Annu. Rev. Genet. 35, 303-339 (2001).
2. Glazier, A.M., Nadeau, J.H. & Aitman, T.J. Finding genes that underlie complex traits. Science 298, 2345-2349 (2002).
3. Page, G.P., George, V., Go, R.C., Page, P.Z. & Allison, D.B. "Are we there yet?": Deciding when one has demonstrated specific genetic causation in complex diseases and quantitative traits. Am. J. Hum. Genet. 73, 711-719 (2003).
4. Flint, J. & Mott, R. Finding the molecular basis of quantitative traits: successes and pitfalls. Nat. Rev. Genet. 2, 437-445 (2001).
5. Risch, N.J. Searching for genetic determinants in the new millennium. Nature 405, 847-856 (2000).
6. Esposito, R.E. & Klapholz, S. Meiosis and Ascospore Development (Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1981).
7. Winzeler, E.A. et al. Direct allelic variation scanning of the yeast genome. Science 281, 1194-1197 (1998).
8. Goffeau, A. et al. Life with 6000 genes. Science 274, 546, 563-567 (1996).
9. Steinmetz, L.M. et al. Dissecting the architecture of a quantitative trait locus in yeast. Nature 416, 326-330 (2002).
10. Mewes, H.W., Albermann, K., Heumann, K., Liebl, S. & Pfeiffer, F. MIPS: a database for protein sequences, homology data and yeast genome information. Nucleic Acids Res. 25, 28-30 (1997).
11. Cliften, P. et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71-76 (2003).
12. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E.S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254 (2003).
13. Hirschhorn, J.N. & Daly, M.J. Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet. 6, 95-108 (2005).
14. The International HapMap Consortium. The International HapMap Project. Nature 426, 789-796 (2003).
15. Winzeler, E.A. et al. Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays. Genetics 163, 79-89 (2003).
16. McCusker, J.H., Clemons, K.V., Stevens, D.A. & Davis, R.W. Genetic characterization of pathogenic Saccharomyces cerevisiae isolates. Genetics 136, 1261-1269 (1994).
17. Carlborg, O. & Haley, C.S. Epistasis: too often neglected in complex trait studies? Nat. Rev. Genet. 5, 618-625 (2004).
18. Brem, R.B. & Kruglyak, L. The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc. Natl. Acad. Sci. USA 102, 1572-1577 (2005).
19. Farrall, M. Quantitative genetic variation: a post-modern view. Hum. Mol. Genet. 13, R1-R7 (2004).
20. Singer, J.B. et al. Genetic dissection of complex traits with chromosome substitution strains of mice. Science 304, 445-448 (2004).
21. Tabor, H.K., Risch, N.J. & Myers, R.M. Opinion: Candidate-gene approaches for studying complex genetic traits: practical considerations. Nat. Rev. Genet. 3, 391-397 (2002).
22. Mitchell, A.P. & Herskowitz, I. Activation of meiosis and sporulation by repression of the RME1 product in yeast. Nature 319, 738-742 (1986).
23. Du, L.L. & Novick, P. Pag1p, a novel protein associated with protein kinase Cbk1p, is required for cell morphogenesis and proliferation in Saccharomyces cerevisiae. Mol. Biol. Cell 13, 503-514 (2002).
24. Wickner, R.B. MKT1, a nonessential Saccharomyces cerevisiae gene with a temperature-dependent effect on replication of M2 double-stranded RNA. J. Bacteriol. 169, 4941-4945 (1987).
25. Tadauchi, T., Inada, T., Matsumoto, K. & Irie, K. Posttranscriptional regulation of HO expression by the Mkt1-Pbp1 complex. Mol. Cell. Biol. 24, 3670-3681 (2004).
26. Chu, S. et al. The transcriptional program of sporulation in budding yeast. Science 282, 699-705 (1998).
27. Primig, M. et al. The core meiotic transcriptome in budding yeasts. Nat. Genet. 26, 415-423 (2000).
28. Briza, P. et al. Systematic analysis of sporulation phenotypes in 624 non-lethal homozygous deletion strains of Saccharomyces cerevisiae. Yeast 19, 403-422 (2002).
29. Deutschbauer, A.M., Williams, R.M., Chu, A.M. & Davis, R.W. Parallel phenotypic analysis of sporulation and postgermination growth in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 99, 15530-15535 (2002).
30. Enyenihi, A.H. & Saunders, W.S. Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics 163, 47-54 (2003).
31. Brachmann, C.B. et al. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14, 115-132 (1998).
32. Goldstein, A.L. & McCusker, J.H. Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15, 1541-1553 (1999).
33. Storici, F., Lewis, L.K. & Resnick, M.A. In vivo site-directed mutagenesis using oligonucleotides. Nat. Biotechnol. 19, 773-776 (2001).
34. Guthrie, C. & Fink, G.R. (eds.). Guide to Yeast Genetics and Molecular and Cell Biology (Academic, San Diego, 1991).
35. Codon, A.C., Gasent-Ramirez, J.M. & Benitez, T. Factors which affect the frequency of sporulation and tetrad formation in Saccharomyces cerevisiae baker's yeasts. Appl. Environ. Microbiol. 61, 630-638 (1995).
36. Herskowitz, I. & Jensen, R.E. Putting the HO gene to work: practical uses for mating-type switching. Methods Enzymol. 194, 132-146 (1991).
37. Rozen, S. & Skaletsky, H. Primer3 on the WWW for general users and for biologist programmers, in Bioinformatics Methods and Protocols: Methods in Molecular Biology (eds. Krawetz, S. & Misener, S.) 365-386 (Humana Press, Totowa, New Jersey, 2000).
38. Gordon, D., Abajian, C. & Green, P. Consed: a graphical tool for sequence finishing. Genome Res. 8, 195-202 (1998).
39. Winzeler, E.A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906 (1999).
40. Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391 (2002).
41. Gray, M., Kupiec, M. & Honigberg, S.M. Site-specific genomic (SSG) and random domain-localized (RDL) mutagenesis in yeast. BMC Biotechnol. 4, 7 (2004).
42. Jorgensen, P. et al. High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants. Genetics 162, 1091-1099 (2002).
43. Issel-Tarver, L. et al. Saccharomyces Genome Database. Methods Enzymol. 350, 329-346 (2002).