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

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Revealing QTLs with a minor effect in complex traits remains difficult. Initial strategies had limited success because of interference by major QTLs and epistasis. New strategies focused on eliminating major QTLs in subsequent mapping experiments. Since genetic analysis of superior segregants from natural diploid strains usually also reveals QTLs linked to the inferior parent, we have extended this strategy for minor QTL identification by eliminating QTLs in both parent strains and repeating the QTL mapping with pooled-segregant whole-genome sequence analysis. We first mapped multiple QTLs responsible for high thermotolerance in a natural yeast strain, MUCL28177, compared to the laboratory strain, BY4742. Using single and bulk reciprocal hemizygosity analysis we identified MKT1 and PRP42 as causative genes in QTLs linked to the superior and inferior parent, respectively. We subsequently downgraded both parents by replacing their superior allele with the inferior allele of the other parent. QTL mapping using pooled-segregant whole-genome sequence analysis with the segregants from the cross of the downgraded parents, revealed several new QTLs. We validated the two most-strongly linked new QTLs by identifying NCS2 and SMD2 as causative genes linked to the superior downgraded parent and we found an allele-specific epistatic interaction between PRP42 and SMD2. Interestingly, the related function of PRP42 and SMD2 suggests an important role for RNA processing in high thermotolerance and underscores the relevance of analyzing minor QTLs. Our results show that identification of minor QTLs involved in complex traits can be successfully accomplished by crossing parent strains that have both been downgraded for a single QTL. This novel approach has the advantage of maintaining all relevant genetic diversity as well as enough phenotypic difference between the parent strains for the trait-of-interest and thus maximizes the chances of successfully identifying additional minor QTLs that are relevant for the phenotypic difference between the original parents.

Vyšlo v časopise: 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(8): e32767. doi:10.1371/journal.pgen.1003693
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003693

Souhrn

Zdroje

1. Paterson AH (1998) Molecular dissection of complex traits. Boca Raton, Fla.: CRC Press. 305 p.

2. LitiG, LouisEJ (2012) Advances in quantitative trait analysis in yeast. PLoS Genet 8: e1002912.

3. SwinnenS, TheveleinJM, NevoigtE (2012) Genetic mapping of quantitative phenotypic traits in Saccharomyces cerevisiae. FEMS Yeast Res 12 : 215–227.

4. GoffeauA, BarrellBG, BusseyH, DavisRW, DujonB, et al. (1996) Life with 6000 genes. Science 274 : 546, 563–547.

5. ManceraE, BourgonR, BrozziA, HuberW, SteinmetzLM (2008) High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454 : 479–485.

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

7. DiezmannS, DietrichFS (2011) Oxidative stress survival in a clinical Saccharomyces cerevisiae isolate is influenced by a major quantitative trait nucleotide. Genetics 188 : 709–722.

8. MarulloP, AigleM, BelyM, Masneuf-PomaredeI, DurrensP, et al. (2007) Single QTL mapping and nucleotide-level resolution of a physiologic trait in wine Saccharomyces cerevisiae strains. FEMS Yeast Res 7 : 941–952.

9. HuXH, WangMH, TanT, LiJR, YangH, et al. (2007) Genetic dissection of ethanol tolerance in the budding yeast Saccharomyces cerevisiae. Genetics 175 : 1479–1487.

10. 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.

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

12. Ben-AriG, ZenvirthD, ShermanA, DavidL, KlutsteinM, et al. (2006) Four linked genes participate in controlling sporulation efficiency in budding yeast. PLoS Genet 2: e195.

13. GatbontonT, ImbesiM, NelsonM, AkeyJM, RuderferDM, et al. (2006) Telomere length as a quantitative trait: genome-wide survey and genetic mapping of telomere length-control genes in yeast. PLoS Genet 2: e35.

14. NogamiS, OhyaY, YvertG (2007) Genetic complexity and quantitative trait loci mapping of yeast morphological traits. PLoS Genet 3: e31.

15. DimitrovLN, BremRB, KruglyakL, GottschlingDE (2009) Polymorphisms in multiple genes contribute to the spontaneous mitochondrial genome instability of Saccharomyces cerevisiae S288C strains. Genetics 183 : 365–383.

16. EhrenreichIM, GerkeJP, KruglyakL (2009) Genetic dissection of complex traits in yeast: insights from studies of gene expression and other phenotypes in the BYxRM cross. Cold Spring Harb Symp Quant Biol 74 : 145–153.

17. BullardJH, MostovoyY, DudoitS, BremRB (2010) Polygenic and directional regulatory evolution across pathways in Saccharomyces. Proc Natl Acad Sci U S A 107 : 5058–5063.

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

19. CarlborgO, HaleyCS (2004) Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5 : 618–625.

20. SmithEN, KruglyakL (2008) Gene-environment interaction in yeast gene expression. PLoS Biol 6: e83.

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

22. 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.

23. LorenzK, CohenBA (2012) Small -⁠ and large-effect quantitative trait locus interactions underlie variation in yeast sporulation efficiency. Genetics 192 : 1123–1132.

24. PartsL, CubillosFA, WarringerJ, JainK, SalinasF, et al. (2011) Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res 21 : 1131–1138.

25. ClaesenJ, ClementL, ShkedyZ, Foulquié-MorenoMR, BurzykowskiT (2013) Simultaneous mapping of multiple gene loci with pooled segregants. PLoS ONE 8 (2) e55133.

26. BenjaminiY, YekutieliD (2001) The control of the false discovery rate in multiple testing under dependency. The Annals of Statistics 29 : 1165–1188.

27. SinhaH, NicholsonBP, SteinmetzLM, McCuskerJH (2006) Complex genetic interactions in a quantitative trait locus. PLoS Genet 2: e13.

28. RiesebergLH, ArcherMA, WayneRK (1999) Transgressive segregation, adaptation and speciation. Heredity 83 : 363–372.

29. BartonNH, TurelliM (1989) Evolutionary quantitative genetics: how little do we know? Annu Rev Genet 23 : 337–370.

30. DemoginesA, SmithE, KruglyakL, AlaniE (2008) Identification and dissection of a complex DNA repair sensitivity phenotype in Baker's yeast. PLoS Genet 4: e1000123.

31. FlintJ, MottR (2001) Finding the molecular basis of quantitative traits: successes and pitfalls. Nat Rev Genet 2 : 437–445.

32. BenjaphokeeS, KoedrithP, AuesukareeC, AsvarakT, SugiyamaM, et al. (2012) CDC19 encoding pyruvate kinase is important for high-temperature tolerance in Saccharomyces cerevisiae. N Biotechnol 29 : 166–176.

33. ShahsavaraniH, SugiyamaM, KanekoY, ChuenchitB, HarashimaS (2011) Superior thermotolerance of Saccharomyces cerevisiae for efficient bioethanol fermentation can be achieved by overexpression of RSP5 ubiquitin ligase. Biotechnol Adv 30 : 1289–1300.

34. McLeanMR, RymondBC (1998) Yeast pre-mRNA splicing requires a pair of U1 snRNP-associated tetratricopeptide repeat proteins. Mol Cell Biol 18 : 353–360.

35. NeubauerG, GottschalkA, FabrizioP, SeraphinB, LuhrmannR, et al. (1997) Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc Natl Acad Sci U S A 94 : 385–390.

36. KambachC, WalkeS, YoungR, AvisJM, de la FortelleE, et al. (1999) Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Cell 96 : 375–387.

37. Pomeranz KrummelDA, OubridgeC, LeungAK, LiJ, NagaiK (2009) Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. Nature 458 : 475–480.

38. DeutschbauerAM, DavisRW (2005) Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nat Genet 37 : 1333–1340.

39. TadauchiT, InadaT, MatsumotoK, IrieK (2004) Posttranscriptional regulation of HO expression by the Mkt1-Pbp1 complex. Mol Cell Biol 24 : 3670–3681.

40. BrachmannCB, DaviesA, CostGJ, CaputoE, LiJ, et al. (1998) 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.

41. ShermanF, HicksJ (1991) Micromanipulation and dissection of asci. Methods Enzymol 194 : 21–37.

42. Johnston JR (1994) Molecular genetics of yeast: a practical approach. New York: IRL Press at Oxford University Press. xxiv, 275 p. p.

43. DohmJC, LottazC, BorodinaT, HimmelbauerH (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36: e105.

44. van de WielMA, BrosensR, EilersPH, KumpsC, MeijerGA, et al. (2009) Smoothing waves in array CGH tumor profiles. Bioinformatics 25 : 1099–1104.

45. McCarthyDJ, SmythGK (2009) Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics 25 : 765–771.

46. WinzelerEA, ShoemakerDD, AstromoffA, LiangH, AndersonK, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285 : 901–906.

47. WachA, BrachatA, PohlmannR, PhilippsenP (1994) New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10 : 1793–1808.

48. ShepherdA, PiperPW (2010) The Fps1p aquaglyceroporin facilitates the use of small aliphatic amides as a nitrogen source by amidase-expressing yeasts. FEMS Yeast Res 10 : 527–534.