Genetic Mapping of MAPK-Mediated Complex Traits Across

1. SegerR, KrebsEG (1995) The MAPK signaling cascade. FASEB J 9: 726–735.

2. O'RourkeSM, HerskowitzI, O'SheaEK (2002) Yeast go the whole HOG for the hyperosmotic response. Trends in Genetics 18: 405–412.

3. ChenRE, ThornerJ (2007) Function and regulation in MAPK signaling pathways: lessons learned from the yeast Saccharomyces cerevisiae. Biochim Biophys Acta 1773: 1311–1340.

4. WaltermannC, KlippE (2010) Signal integration in budding yeast. Biochemical Society transactions 38: 1257–1264.

5. WagnerEF, NebredaAR (2009) Signal integration by JNK and p38 MAPK pathways in cancer development. Nat Rev Cancer 9: 537–549.

6. SaklatvalaJ (2004) The p38 MAP kinase pathway as a therapeutic target in inflammatory disease. Current Opinion Pharmacology 4: 372–377.

7. LevinDE (2005) Cell wall integrity signaling in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 69: 262–291.

8. KvitekDJ, WillJL, GaschAP (2008) Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genetics 4: e1000223.

9. LitiG, CarterDM, MosesAM, WarringerJ, PartsL, et al. (2009) Population genomics of domestic and wild yeasts. Nature 458: 337–341.

10. WarringerJ, ZörgöE, CubillosFA, ZiaA, GjuvslandA, et al. (2011) Trait variation in yeast is defined by population history. PLoS Genetics 7: e1002111.

11. BahnYS, XueC, IdnurmA, RutherfordJC, HeitmanJ, et al. (2007) Sensing the environment: lessons from fungi. Nat Rev Microbiol 5: 57–69.

12. WuX, ChiX, WangP, ZhengD, DingR, et al. (2010) The evolutionary rate variation among genes of HOG-signaling pathway in yeast genomes. Biology direct 5: 46.

13. BremRB, StoreyJD, WhittleJ, KruglyakL (2005) Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 436: 701–703.

14. BremRB, YvertG, ClintonR, KruglyakL (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752–755.

15. PerlsteinEO, RuderferDM, RobertsDC, SchreiberSL, KruglyakL (2007) Genetic basis of individual differences in the response to small-molecule drugs in yeast. Nat Genet 39: 496–502.

16. SteinmetzLM, SinhaH, RichardsDR, SpiegelmanJI, OefnerPJ, et al. (2002) Dissecting the architecture of a quantitative trait locus in yeast. Nature 416: 326–330.

17. BloomJS, EhrenreichIM, LooWT, LiteTL, KruglyakL (2013) Finding the sources of missing heritability in a yeast cross. Nature 494: 234–237.

18. MichelmoreRW, ParanI, KesseliRV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci U S A 88: 9828–9832.

19. BrauerMJ, ChristiansonCM, PaiDA, DunhamMJ (2006) Mapping novel traits by array-assisted bulk segregant analysis in Saccharomyces cerevisiae. Genetics 173: 1813–1816.

20. EhrenreichIM, TorabiN, JiaY, KentJ, MartisS, et al. (2010) Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 464: 1039–1042.

21. AlbertFW, TreuschS, ShockleyAH, BloomJS, KruglyakL (2014) Genetics of single-cell protein abundance variation in large yeast populations. Nature 506: 494–497.

22. CubillosFA, PartsL, SalinasF, BergstromA, ScovacricchiE, et al. (2013) High-resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics 195: 1141–1155.

23. EhrenreichIM, BloomJ, TorabiN, WangX, JiaY, et al. (2012) Genetic architecture of highly complex chemical resistance traits across four yeast strains. PLoS Genet 8: e1002570.

24. TongAH, BooneC (2006) Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol Biol 313: 171–192.

25. PearceDA, ShermanF (1999) Toxicity of copper, cobalt, and nickel salts is dependent on histidine metabolism in the yeast Saccharomyces cerevisiae. J Bacteriol 181: 4774–4779.

26. Joseph-StraussD, ZenvirthD, SimchenG, BarkaiN (2007) Spore germination in Saccharomyces cerevisiae: global gene expression patterns and cell cycle landmarks. Genome Biol 8: R241.

27. SchachererJ, ShapiroJA, RuderferDM, KruglyakL (2009) Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458: 342–345.

28. VerhoevenKJ, JanninkJL, McIntyreLM (2006) Using mating designs to uncover QTL and the genetic architecture of complex traits. Heredity (Edinb) 96: 139–149.

29. SalomePA, BombliesK, LaitinenRA, YantL, MottR, et al. (2011) Genetic architecture of flowering-time variation in Arabidopsis thaliana. Genetics 188: 421–433.

30. HuangW, RichardsS, CarboneMA, ZhuD, AnholtRR, et al. (2012) Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proc Natl Acad Sci U S A 109: 15553–15559.

31. BremRB, KruglyakL (2005) The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci U S A 102: 1572–1577.

32. Lynch M, Walsh B (1998) Genetics and Analysis of Quantitative Traits: Sinauer Associates.

33. EdwardsMD, GiffordDK (2012) High-resolution genetic mapping with pooled sequencing. BMC Bioinformatics 13 Suppl 6: S8.

34. CubillosFA, BilliE, ZorgoE, PartsL, FargierP, et al. (2011) Assessing the complex architecture of polygenic traits in diverged yeast populations. Mol Ecol 20: 1401–1413.

35. SinhaH, DavidL, PasconRC, Clauder-MunsterS, KrishnakumarS, et al. (2008) Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast. Genetics 180: 1661–1670.

36. YangY, Foulquie-MorenoMR, ClementL, ErdeiE, TangheA, et al. (2013) QTL analysis of high thermotolerance with superior and downgraded parental yeast strains reveals new minor QTLs and converges on novel causative alleles involved in RNA processing. PLoS Genet 9: e1003693.

37. MackayTF, StoneEA, AyrolesJF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10: 565–577.

38. MarquezJA, SerranoR (1996) Multiple transduction pathways regulate the sodium-extrusion gene PMR2/ENA1 during salt stress in yeast. FEBS Lett 382: 89–92.

39. Daran-LapujadeP, DaranJM, LuttikMA, AlmeringMJ, PronkJT, et al. (2009) An atypical PMR2 locus is responsible for hypersensitivity to sodium and lithium cations in the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D. FEMS Yeast Res 9: 789–792.

40. WilkeningS, LinG, FritschES, TekkedilMM, AndersS, et al. (2013) An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae. Genetics

41. LoewithR, JacintoE, WullschlegerS, LorbergA, CrespoJL, et al. (2002) Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control. Mol Cell 10: 457–468.

42. ReinkeA, ChenJC, AronovaS, PowersT (2006) Caffeine targets TOR complex I and provides evidence for a regulatory link between the FRB and kinase domains of Tor1p. J Biol Chem 281: 31616–31626.

43. TorresJ, Di ComoCJ, HerreroE, De La Torre-RuizMA (2002) Regulation of the cell integrity pathway by rapamycin-sensitive TOR function in budding yeast. J Biol Chem 277: 43495–43504.

44. AudhyaA, EmrSD (2003) Regulation of PI4,5P2 synthesis by nuclear-cytoplasmic shuttling of the Mss4 lipid kinase. EMBO J 22: 4223–4236.

45. BroachJR (1991) RAS genes in Saccharomyces cerevisiae: signal transduction in search of a pathway. Trends Genet 7: 28–33.

46. KaidaD, YashirodaH, Toh-eA, KikuchiY (2002) Yeast Whi2 and Psr1-phosphatase form a complex and regulate STRE-mediated gene expression. Genes Cells 7: 543–552.

47. KellisM, PattersonN, EndrizziM, BirrenB, LanderES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241–254.

48. SmithC, GreigD (2010) The cost of sexual signaling in yeast. Evolution 64: 3114–3122.

49. ZorgoE, ChwialkowskaK, GjuvslandAB, GarreE, SunnerhagenP, et al. (2013) Ancient evolutionary trade-offs between yeast ploidy states. PLoS Genet 9: e1003388.

50. LangGI, MurrayAW, BotsteinD (2009) The cost of gene expression underlies a fitness trade-off in yeast. Proc Natl Acad Sci U S A 106: 5755–5760.

51. YvertG, BremRB, WhittleJ, AkeyJM, FossE, et al. (2003) Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 35: 57–64.

52. DohlmanHG, SongJ, MaD, CourchesneWE, ThornerJ (1996) Sst2, a negative regulator of pheromone signaling in the yeast Saccharomyces cerevisiae: expression, localization, and genetic interaction and physical association with Gpa1 (the G-protein alpha subunit). Mol Cell Biol 16: 5194–5209.

53. McCleanMN, ModyA, BroachJR, RamanathanS (2007) Cross-talk and decision making in MAP kinase pathways. Nat Genet 39: 409–414.

54. PattersonJC, KlimenkoES, ThornerJ (2010) Single-cell analysis reveals that insulation maintains signaling specificity between two yeast MAPK pathways with common components. Sci Signal 3: ra75.

55. KingEG, MerkesCM, McNeilCL, HooferSR, SenS, et al. (2012) Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Res 22: 1558–1566.

56. YalcinB, FlintJ, MottR (2005) Using progenitor strain information to identify quantitative trait nucleotides in outbred mice. Genetics 171: 673–681.

57. IqbalZ, CaccamoM, TurnerI, FlicekP, McVeanG (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat Genet 44: 226–232.

58. FossEJ, RadulovicD, ShafferSA, RuderferDM, BedalovA, et al. (2007) Genetic basis of proteome variation in yeast. Nat Genet 39: 1369–1375.

59. SwinnenS, SchaerlaekensK, PaisT, ClaesenJ, HubmannG, et al. (2012) Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis. Genome Res 22: 975–984.

60. WangQM, LiuWQ, LitiG, WangSA, BaiFY (2012) Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity. Mol Ecol 21: 5404–5417.

61. CromieGA, HymaKE, LudlowCL, Garmendia-TorresC, GilbertTL, et al. (2013) Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq. G3 (Bethesda) 3: 2163–2171.

62. ChinBL, FrizzellMA, TimberlakeWE, FinkGR (2012) FASTER MT: Isolation of Pure Populations of a and alpha Ascospores from Saccharomycescerevisiae. G3 (Bethesda) 2: 449–452.

63. AlbertynJ, HohmannS, TheveleinJM, PriorBA (1994) GPD1, which encodes glycerol-3-phosphate dehydrogenase, is essential for growth under osmotic stress in Saccharomyces cerevisiae, and its expression is regulated by the high-osmolarity glycerol response pathway. Mol Cell Biol 14: 4135–4144.

64. Rodriguez-PenaJM, GarciaR, NombelaC, ArroyoJ (2010) The high-osmolarity glycerol (HOG) and cell wall integrity (CWI) signalling pathways interplay: a yeast dialogue between MAPK routes. Yeast 27: 495–502.

65. FuchsBB, MylonakisE (2009) Our paths might cross: the role of the fungal cell wall integrity pathway in stress response and cross talk with other stress response pathways. Eukaryot Cell 8: 1616–1625.

66. MartinDE, HallMN (2005) The expanding TOR signaling network. Curr Opin Cell Biol 17: 158–166.

67. KellisM, BirrenBW, LanderES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617–624.

68. SaulDJ, SudberyPE (1985) Molecular cloning of WHI2, a gene involved in the regulation of cell proliferation in Saccharomyces cerevisiae. J Gen Microbiol 131: 1797–1806.

69. KvitekDJ, SherlockG (2013) Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment. PLoS Genet 9: e1003972.

70. LangGI, RiceDP, HickmanMJ, SodergrenE, WeinstockGM, et al. (2013) Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 500: 571–574.

71. TengX, Dayhoff-BranniganM, ChengWC, GilbertCE, SingCN, et al. (2013) Genome-wide Consequences of Deleting Any Single Gene. Mol Cell

72. MuthuvijayanV, MartenMR (2004) In silico reconstruction of nutrient-sensing signal transduction pathways in Aspergillus nidulans. In Silico Biol 4: 605–631.

73. RodicioR, HeinischJJ (2010) Together we are strong–cell wall integrity sensors in yeasts. Yeast 27: 531–540.

74. TanakaK, TatebayashiK, NishimuraA, YamamotoK, YangHY, et al. (2014) Yeast osmosensors hkr1 and msb2 activate the hog1 MAPK cascade by different mechanisms. Sci Signal 7: ra21.

75. CapaldiAP, KaplanT, LiuY, HabibN, RegevA, et al. (2008) Structure and function of a transcriptional network activated by the MAPK Hog1. Nature Genetics 40: 1300–1306.

76. AlbertiS, GitlerAD, LindquistS (2007) A suite of Gateway cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae. Yeast 24: 913–919.

77. GoldsteinAL, McCuskerJH (1999) Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15: 1541–1553.

78. TrecoDA, WinstonF (2008) Growth and manipulation of yeast. Curr Protoc Mol Biol Chapter 13 Unit 13 12..

79. GietzRD, SchiestlRH (2007) High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat Protoc 2: 31–34.

80. HegemannJH, HeickSB (2011) Delete and repeat: a comprehensive toolkit for sequential gene knockout in the budding yeast Saccharomyces cerevisiae. Methods Mol Biol 765: 189–206.

81. ErdenizN, MortensenUH, RothsteinR (1997) Cloning-free PCR-based allele replacement methods. Genome Res 7: 1174–1183.

82. StuckeyS, MukherjeeK, StoriciF (2011) In vivo site-specific mutagenesis and gene collage using the delitto perfetto system in yeast Saccharomyces cerevisiae. Methods Mol Biol 745: 173–191.

83. StoriciF, LewisLK, ResnickMA (2001) In vivo site-directed mutagenesis using oligonucleotides. Nat Biotechnol 19: 773–776.

84. LeeCK, ArakiN, SowersbyDS, LewisLK (2011) Factors affecting chemical-based purification of DNA from Saccharomyces cerevisiae. Yeast

85. Meyer M, Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010: pdb prot5448.

86. McLarenW, PritchardB, RiosD, ChenY, FlicekP, et al. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26: 2069–2070.

87. CherryJM, HongEL, AmundsenC, BalakrishnanR, BinkleyG, et al. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res 40: D700–705.

88. DanecekP, AutonA, AbecasisG, AlbersCA, BanksE, et al. (2011) The variant call format and VCFtools. Bioinformatics 27: 2156–2158.

89. KentWJ, SugnetCW, FureyTS, RoskinKM, PringleTH, et al. (2002) The human genome browser at UCSC. Genome Res 12: 996–1006.