On the prospects of whole-genome association mapping in Saccharomyces cerevisiae

Genetics

Volumn 191, Issue 4, 2012, Pages 1345-1353

  Connelly, Caitlin F ^a   Akey, Joshua M ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; MITOCHONDRIAL DNA;

ANALYTICAL ERROR; ARTICLE; FUNGAL GENOME; FUNGAL STRAIN; FUNGUS CULTURE; GENE DOSAGE; GENE MAPPING; GENE SEQUENCE; GENETIC ASSOCIATION; NONHUMAN; POPULATION GENETICS; POPULATION STRUCTURE; PRIORITY JOURNAL; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; COMPUTER SIMULATION; DNA, MITOCHONDRIAL; GENE DOSAGE; GENETIC HETEROGENEITY; GENOME-WIDE ASSOCIATION STUDY; MODELS, GENETIC; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SACCHAROMYCES CEREVISIAE;

EID: 84865066039     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.141168     Document Type: Article

References (27)

1. Atwell, S., Y. S. Huang, B. J. Vilhjálmsson, G. Willems, M. Horton et al., 2010 Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
2. Bokyo, A. R., P. Quignon, L. Li, J. J. Schoenebeck, J. D. Degenhardt et al., 2010 A simple genetic architecture underlies morphological variation in dogs. PLoS Biol. 8: e1000451.
3. Edwards, A., J. Ayroles, E. Stone, M. Carbone, R. Lyman et al., 2009 A transcriptional network associated with natural variation in Drosophila aggressive behavior. Genome Biol. 10: R76.
4. Felsenstein, J., 1989 PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
5. Hindorff, L. A., P. Sethupathy, H. A. Junkins, E. M. Ramos, J. P. Mehta et al., 2009 Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA 106: 9362-9367.
6. Kang, H. M., N. A. Zaitlen, C. M. Wade, A. Kirby, D. Heckerman et al., 2008 Efficient control of population structure in model organism association mapping. Genetics 178: 1709-1723.
7. Lander, E. S., and N. J. Schork, 1994 Genetic dissection of complex traits. Science 265: 2037-2048.
8. Lecrenier, N., and F. Foury, 2000 New features of mitochondrial DNA replication system in yeast and man. Gene 246: 37-48.
9. Ling, F., and T. Shibata, 2002 Recombination-dependent mtDNA partitioning: in vivo role of Mhr1p to promote pairing of homologous DNA. EMBO J. 21: 4730-4740.
10. Liti, G., D. M. Carter, A. M. Moses, J. Warringer, L. Parts et al., 2009 Population genomics of domestic and wild yeasts. Nature 458: 337-341.
11. Lockshon, D., S. G. Zweifel, L. L. Freeman-Cook, H. E. Lorimer, B. J. Brewer et al., 1995 A role for recombination junctions in the segregation of mitochondrial DNA in yeast. Cell 81: 947-955.
12. Mehmood, T., H. Martens, S. Sæbø, J. Warringer, and L. Snipen, 2011 Mining for genotype-phenotype relations in Saccharomyces using partial least squares. BMC Bioinformatics 12: 318.
13. Merker, R., and H. Klein, 2002 HPR1 affects ribosomal DNA recombination and cell life span in Saccharomyces cerevisiae. Mol. Cell. Biol. 22: 421-429.
14. Muller, L., J. Lucas, D. Georgianna, and J. Mccusker, 2011 Genome-wide association analysis of clinical vs. nonclinical origin provides insights into Saccharomyces cerevisiae pathogenesis. Mol. Ecol. 20: 4085-4097.
15. Patterson, N., A. Price, and D. Reich, 2006 Population structure and eigenanalysis. PLoS Genet. 2: e190.
16. Price, A., N. Patterson, R. Plenge, M. Weinblatt, N. Shadick et al., 2006 Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38: 904-909.
17. Pritchard, J. K., M. Stephens, N. A. Rosenberg, and P. Donnelly, 2000 Association mapping in structured populations. Am. J. Hum. Genet. 67: 170-181.
18. Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. Ferreira et al., 2007 PLINK: a tool set for whole-genome association and population-based linkage analyses, Am. J. Hum. Genet. 81: 559-575.
19. Risch, N., and K. Merikangas, 1996 The future of genetic studies of complex human diseases. Science 273: 1516-1517.
20. Rockman, M. V., and L. Kruglyak, 2009 Recombinational landscape and population genomics of Caenorhabditis elegans. PLoS Genet. 5: e1000419.
21. Rose, M. D., F. Winston, and P. Hieter, 1990 Methods in Yeast Genetics: A Laboratory Course Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
22. Skelly, D., J. Ronald, and J. Akey, 2009 Inherited variation in gene expression. Annu. Rev. Genomics Hum. Genet. 10: 313-332.
23. Schacherer, J., J. A. Shapiro, D. M. Ruderfer, and L. Kruglyak, 2009 Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458: 342-345.
24. Threadgill, D., K. Hunter, and R. Williams, 2002 Genetic dissection of complex and quantitative traits: from fantasy to reality via a community effort. Mamm. Genome 13: 175-178.
25. Yu, J., G. Pressoir, W. Briggs, I. Vroh Bi, M. Yamasaki et al., 2006 A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38: 203-208.
26. Zelenaya-Troitskaya, O., S. M. Newman, K. Okamoto, P. S. Perlman, and R. A. Butow, 1998 Functions of the high mobility group protein, Abf2p, in mitochondrial DNA segregation, recombination and copy number in Saccharomyces cerevisiae. Genetics 148: 1763-1776.
27. Zhang, K., and L. Lin, 2003 HaploBlockFinder: haplotype block analyses. Bioinformatics 19: 1300-1301.