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. 2013;9(8):e1003693. doi: 10.1371/journal.pgen.1003693. Epub 2013 Aug 15.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Cell Cycle Proteins / genetics*
  • Chromosome Mapping
  • Genetic Linkage
  • Genetic Variation
  • Hot Temperature
  • Quantitative Trait Loci / genetics*
  • RNA / genetics
  • RNA Processing, Post-Transcriptional / genetics*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / genetics*

Substances

  • Cell Cycle Proteins
  • NCS2 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • RNA

Grant support

This work has been supported by a predoctoral fellowship from the VIB and KU Leuven Research Fund to YY, SBO grants (IWT 50148 and IWT 90043) from IWT-Flanders, the EC 7th Framework program (NEMO project), IOF-Knowledge platform (IKP/10/002 ZKC 1836) and BOF-Program financing (project NATAR) to JMT and by the Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’, Ghent University to LC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.