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Four linked genes participate in controlling sporulation efficiency in budding yeast.

Ben-Ari G, Zenvirth D, Sherman A, David L, Klutstein M, Lavi U, Hillel J, Simchen G - PLoS Genet. (2006)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel.

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.

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Related in: MedlinePlus

Hybridization of DNA from Parents and Pools of Segregants (“Low Tail” and “High Tail”) to Affymetrix S98 MicroarraysFor 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).
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pgen-0020195-g003: Hybridization of DNA from Parents and Pools of Segregants (“Low Tail” and “High Tail”) to Affymetrix S98 MicroarraysFor 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).

Mentions: A genome-wide discovery of SNPs, based on hybridization of genomic DNA to Affymetrix S98 yeast microarrays [25] was carried out using these two DNA pools. We compared probe intensities between five SK1 DNA hybridizations and five S288c hybridizations. As a result, we identified ~4,000 probes containing polymorphisms between these parental strains. Both the “high” and the “low” DNA pools were then hybridized to microarrays to identify differences in frequency of SNP's alleles. We detected three candidate regions, on Chromosomes 2, 7, and 14, each larger than 50 kb (with at least 20 differentiating SNPs). The SK1 allele was highly frequent in the “high” pool and the S288c allele in the “low” pool (Figure 3). The region detected on Chromosome 14 contained the genes RAS2 and YNL100W, also detected by sequencing of the DNA pools (Figure 2).


Four linked genes participate in controlling sporulation efficiency in budding yeast.

Ben-Ari G, Zenvirth D, Sherman A, David L, Klutstein M, Lavi U, Hillel J, Simchen G - PLoS Genet. (2006)

Hybridization of DNA from Parents and Pools of Segregants (“Low Tail” and “High Tail”) to Affymetrix S98 MicroarraysFor 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).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1636695&req=5

pgen-0020195-g003: Hybridization of DNA from Parents and Pools of Segregants (“Low Tail” and “High Tail”) to Affymetrix S98 MicroarraysFor 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).
Mentions: A genome-wide discovery of SNPs, based on hybridization of genomic DNA to Affymetrix S98 yeast microarrays [25] was carried out using these two DNA pools. We compared probe intensities between five SK1 DNA hybridizations and five S288c hybridizations. As a result, we identified ~4,000 probes containing polymorphisms between these parental strains. Both the “high” and the “low” DNA pools were then hybridized to microarrays to identify differences in frequency of SNP's alleles. We detected three candidate regions, on Chromosomes 2, 7, and 14, each larger than 50 kb (with at least 20 differentiating SNPs). The SK1 allele was highly frequent in the “high” pool and the S288c allele in the “low” pool (Figure 3). The region detected on Chromosome 14 contained the genes RAS2 and YNL100W, also detected by sequencing of the DNA pools (Figure 2).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel.

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.

Show MeSH
Related in: MedlinePlus