Four linked genes participate in controlling sporulation efficiency in budding yeast - PubMed (original) (raw)
Four linked genes participate in controlling sporulation efficiency in budding yeast
Giora Ben-Ari et al. PLoS Genet. 2006.
Abstract
Quantitative traits are conditioned by several genetic determinants. Since such genes influence many important complex traits in various organisms, the identification of quantitative trait loci (QTLs) is of major interest, but still encounters serious difficulties. We detected four linked genes within one QTL, which participate in controlling sporulation efficiency in Saccharomyces cerevisiae. Following the identification of single nucleotide polymorphisms by comparing the sequences of 145 genes between the parental strains SK1 and S288c, we analyzed the segregating progeny of the cross between them. Through reciprocal hemizygosity analysis, four genes, RAS2, PMS1, SWS2, and FKH2, located in a region of 60 kilobases on Chromosome 14, were found to be associated with sporulation efficiency. Three of the four "high" sporulation alleles are derived from the "low" sporulating strain. Two of these sporulation-related genes were verified through allele replacements. For RAS2, the causative variation was suggested to be a single nucleotide difference in the upstream region of the gene. This quantitative trait nucleotide accounts for sporulation variability among a set of ten closely related winery yeast strains. Our results provide a detailed view of genetic complexity in one "QTL region" that controls a quantitative trait and reports a single nucleotide polymorphism-trait association in wild strains. Moreover, these findings have implications on QTL identification in higher eukaryotes.
Conflict of interest statement
Competing interests. The authors have declared that no competing interests exist.
Figures
Figure 1. Distribution of Sporulation Efficiencies of Diploid Segregants Obtained from the Crosses S288c × SK1
Generation of diploid segregants is described in Materials and Methods. Sporulation efficiencies and standard errors of parents and hybrids are in italics. Assessment of sporulation was carried out after 7 d on solid sporulation medium. Equal amounts of DNA from 21 segregants at each of the two “tails” were pooled to generate the “high” and “low” DNA pools (gray bars).
Figure 2. Sequences of DNA Pools
Shown are short sequences with known SNPs. The upper part shows reconstruction of mixtures of DNA of the strains SK1 and S288c, testing the ability to evaluate reliable allele frequencies of SNPs in DNA pools. DNA of strains SK1 and S288c were pooled at various ratios and a short genomic region containing a known SNP in the gene SPS18 was sequenced. The two alleles could clearly be distinguished even in pools with allele ratios of 8:2 and 9:1. The signal height of the DNA pool sequence was found to be a very good estimator for the allele frequency (correlation coefficient r = 0.99, p < 0.0001). The figure contains sequences of the “high” and “low” DNA pools from the genes RAS2 and YNL100W and from polymorphic DNA segments flanking the candidate region on Chromosome 14. In each sequence, the SNP position is labeled by a black box or arrow (the SNP in the promoter of RAS2 is in position −52).
Figure 3. Hybridization of DNA from Parents and Pools of Segregants (“Low Tail” and “High Tail”) to Affymetrix S98 Microarrays
For each chromosome, the top horizontal line (green) represents hybridizations of S288c DNA and the second line (red) represents hybridizations of SK1 DNA. The third and the fourth horizontal lines represent the hybridizations of the “low” and the “high” pools, respectively. Each horizontal array (comprised of four lines) represents a given yeast chromosome and the physical genomic positions along the chromosome. The small vertical bars represent probes containing polymorphisms between strains SK1 and S288c (alleles are colored according to their parental colors). The small vertical bars on the third and fourth lines of each chromosome represent the inherited allele in the pools: green is S288c and red is SK1. Inheritance of a mixture of alleles is marked either yellow (composition closer to S288c) or pink (closer to SK1). Three regions show consistent inherited differences in allele frequencies between the low and the high pools (boxes). These regions are located on Chromosome 2 (95–157 kb from the left end), Chromosome 7 (500–612 kb), and Chromosome 14 (400–585 kb).
Figure 4. Effects of Reciprocal Hemizygosity and of Allele Replacements on Sporulation
(A) Sporulation efficiency of pairs of hybrid strains (S288c × SK1) with single-gene heterozygous deletions. Strains deleted for the S288c allele (only the SK1 allele is present) are presented by black bars and the isogenic strains deleted for the corresponding SK1 allele (only the S288c allele is present) are presented as diagonally hatched bars. The non-deleted hybrid is presented for reference (gray bar). (B) Sporulation efficiency of double-gene and four-gene deletion mutants. Every pair consisted of two isogenic hybrid strains (S288c × SK1), each with two (or four) hemizygosities: One strain had deletions of the two (or four) sporulation-promoting alleles (empty bars) and the other had deletions of the corresponding sporulation-inhibiting alleles (bars with horizontal lines). (C) Sporulation of the four-gene deletion mutants. In the hybrid strain containing the four sporulation-promoting alleles (left microscopic image), almost all cells formed asci, whereas in the strain with the sporulation-inhibiting alleles (right image), most of the cells did not form asci. The genotypes of the two “reciprocal” strains are given below each image. (D) Sporulation efficiencies of a diploid S288c strain and two isogenic allele-replacement strains, one containing the two SWS2 alleles from strain SK1 and the other containing the two RAS2 alleles from SK1. A fourth isogenic strain contains, homozygotically, only a single additional A in the promoter poly-A stretch of RAS2, as found in strain SK1. For each strain, sporulation was assessed four times. The average sporulation efficiencies and their confidence intervals (p = 0.95) are shown.
Figure 5. Sequence Comparisons of Part of the RAS2 Promoter in Ten Winery Strains
The published [27] assessment of sporulation efficiency are: H, high; M, moderate; L, low. Our assessment of sporulation efficiency (percent) is under “Spo.” The first codon of the open reading frame (ATG) is marked by “Start.” The black arrowhead indicates the deletion of adenine in the poly-A stretch. Based on their DNA sequences, the ten winery strains are closely related to each other and to strain S288c, whereas they differ from SK1 in many SNPs throughout the genome, by approximately 1 in 150 bp [26].
Similar articles
- Quantitative trait loci mapped to single-nucleotide resolution in yeast.
Deutschbauer AM, Davis RW. Deutschbauer AM, et al. Nat Genet. 2005 Dec;37(12):1333-40. doi: 10.1038/ng1674. Epub 2005 Nov 6. Nat Genet. 2005. PMID: 16273108 - Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast.
Schlecht U, Erb I, Demougin P, Robine N, Borde V, van Nimwegen E, Nicolas A, Primig M. Schlecht U, et al. Mol Biol Cell. 2008 May;19(5):2193-207. doi: 10.1091/mbc.e07-12-1242. Epub 2008 Feb 27. Mol Biol Cell. 2008. PMID: 18305101 Free PMC article. - Sporulation genes associated with sporulation efficiency in natural isolates of yeast.
Tomar P, Bhatia A, Ramdas S, Diao L, Bhanot G, Sinha H. Tomar P, et al. PLoS One. 2013 Jul 17;8(7):e69765. doi: 10.1371/journal.pone.0069765. Print 2013. PLoS One. 2013. PMID: 23874994 Free PMC article. - Regulation of sporulation in the yeast Saccharomyces cerevisiae.
Piekarska I, Rytka J, Rempola B. Piekarska I, et al. Acta Biochim Pol. 2010;57(3):241-50. Acta Biochim Pol. 2010. PMID: 20842291 Review. - The molecular basis of phenotypic variation in yeast.
Fay JC. Fay JC. Curr Opin Genet Dev. 2013 Dec;23(6):672-7. doi: 10.1016/j.gde.2013.10.005. Epub 2013 Nov 21. Curr Opin Genet Dev. 2013. PMID: 24269094 Free PMC article. Review.
Cited by
- QTL mapping reveals novel genes and mechanisms underlying variations in H2S production during alcoholic fermentation in Saccharomyces cerevisiae.
De Guidi I, Serre C, Noble J, Ortiz-Julien A, Blondin B, Legras JL. De Guidi I, et al. FEMS Yeast Res. 2024 Jan 9;24:foad050. doi: 10.1093/femsyr/foad050. FEMS Yeast Res. 2024. PMID: 38124683 Free PMC article. - Use of Time-Lapse Microscopy and Stage-Specific Nuclear Depletion of Proteins to Study Meiosis in S. Cerevisiae.
Cairo G, MacKenzie A, Tsuchiya D, Lacefield S. Cairo G, et al. J Vis Exp. 2022 Oct 11;(188):10.3791/64580. doi: 10.3791/64580. J Vis Exp. 2022. PMID: 36314815 Free PMC article. - Meiotic cDNA libraries reveal gene truncations and mitochondrial proteins important for competitive fitness in Saccharomyces cerevisiae.
Sing TL, Conlon K, Lu SH, Madrazo N, Morse K, Barker JC, Hollerer I, Brar GA, Sudmant PH, Ünal E. Sing TL, et al. Genetics. 2022 May 31;221(2):iyac066. doi: 10.1093/genetics/iyac066. Genetics. 2022. PMID: 35471663 Free PMC article. - Domestication reprogrammed the budding yeast life cycle.
De Chiara M, Barré BP, Persson K, Irizar A, Vischioni C, Khaiwal S, Stenberg S, Amadi OC, Žun G, Doberšek K, Taccioli C, Schacherer J, Petrovič U, Warringer J, Liti G. De Chiara M, et al. Nat Ecol Evol. 2022 Apr;6(4):448-460. doi: 10.1038/s41559-022-01671-9. Epub 2022 Feb 24. Nat Ecol Evol. 2022. PMID: 35210580 - Infection by dsRNA viruses is associated with enhanced sporulation efficiency in Saccharomyces cerevisiae.
Travers Cook TJ, Skirgaila C, Martin OY, Buser CC. Travers Cook TJ, et al. Ecol Evol. 2022 Jan 22;12(1):e8558. doi: 10.1002/ece3.8558. eCollection 2022 Jan. Ecol Evol. 2022. PMID: 35127053 Free PMC article.
References
- Mauricio R. Mapping quantitative trait loci in plants: Uses and caveats for evolutionary biology. Nat Rev Genet. 2001;2:370–381. - PubMed
- Darvasi A. Experimental strategies for the genetic dissection of complex traits in animal models. Nat Genet. 1998;18:19–24. - PubMed
- Mackay TF. Quantitative trait loci in Drosophila . Nat Rev Genet. 2001;2:11–20. - PubMed
- Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, et al. Dissecting the architecture of a quantitative trait locus in yeast. Nature. 2002;416:326–330. - PubMed
- El-Din El-Assal S, Alonso-Blanco C, Peeters AJ, Raz V, Koornneef M. A QTL for flowering time in Arabidopsis reveals a novel allele of CRY2 . Nat Genet. 2001;29:435–440. - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases
Research Materials