Dataset Information

Rapid Identification of Major QTLS Associated With Near- Freezing Temperature Tolerance in Saccharomyces cerevisiae.

ABSTRACT: Temperatures had a strong effect on many life history traits, including growth, development and reproduction. At near-freezing temperatures (0-4°C), yeast cells could trigger series of biochemical reactions to respond and adapt to the stress, protect them against sever cold and freeze injury. Different Saccharomyces cerevisiae strains vary greatly in their ability to grow at near-freezing temperatures. However, the molecular mechanisms that allow yeast cells to sustain this response are not yet fully understood and the genetic basis of tolerance and sensitivity to near-freeze stress remains unclear. Uncovering the genetic determinants of this trait is, therefore, of is of significant interest. In order to investigate the genetic basis that underlies near-freezing temperature tolerance in S. cerevisiae, we mapped the major quantitative trait loci (QTLs) using bulk segregant analysis (BSA) in the F2 segregant population of two Chinese indigenous S. cerevisiae strains with divergent tolerance capability at 4°C. By genome-wide comparison of single-nucleotide polymorphism (SNP) profiles between two bulks of segregants with high and low tolerance to near-freezing temperature, a hot region located on chromosome IV was identified tightly associated with the near-freezing temperature tolerance. The Reciprocal hemizygosity analysis (RHA) and gene deletion was used to validate the genes involved in the trait, showed that the gene NAT1 plays a role in the near-freezing temperature tolerance. This study improved our understanding of the genetic basis of the variability of near-freezing temperature tolerance in yeasts. The superior allele identified could be used to genetically improve the near-freezing stress adaptation of industrial yeast strains.

SUBMITTER: Feng L

PROVIDER: S-EPMC6141824 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Rapid Identification of Major QTLS Associated With Near- Freezing Temperature Tolerance in Saccharomyces cerevisiae.

Feng Li L Jia He H Qin Yi Y Song Yuyang Y Tao Shiheng S Liu Yanlin Y

Frontiers in microbiology 20180911

Temperatures had a strong effect on many life history traits, including growth, development and reproduction. At near-freezing temperatures (0-4°C), yeast cells could trigger series of biochemical reactions to respond and adapt to the stress, protect them against sever cold and freeze injury. Different Saccharomyces cerevisiae strains vary greatly in their ability to grow at near-freezing temperatures. However, the molecular mechanisms that allow yeast cells to sustain this response are n ...[more]

PMID: 30254614

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Project description:BackgroundWinter freezing temperature impacts alfalfa (Medicago sativa L.) persistence and seasonal yield and can lead to the death of the plant. Understanding the genetic mechanisms of alfalfa freezing tolerance (FT) using high-throughput phenotyping and genotyping is crucial to select suitable germplasm and develop winter-hardy cultivars. Several clones of an alfalfa F1 mapping population (3010 x CW 1010) were tested for FT using a cold chamber. The population was genotyped with SNP markers identified using genotyping-by-sequencing (GBS) and the quantitative trait loci (QTL) associated with FT were mapped on the parent-specific linkage maps. The ultimate goal is to develop non-dormant and winter-hardy alfalfa cultivars that can produce extended growth in the areas where winters are often mild.ResultsAlfalfa FT screening method optimized in this experiment comprises three major steps: clone preparation, acclimation, and freezing test. Twenty clones of each genotype were tested, where 10 samples were treated with freezing temperature, and 10 were used as controls. A moderate positive correlation (r ~ 0.36, P < 0.01) was observed between indoor FT and field-based winter hardiness (WH), suggesting that the indoor FT test is a useful indirect selection method for winter hardiness of alfalfa germplasm. We detected a total of 20 QTL associated with four traits; nine for visual rating-based FT, five for percentage survival (PS), four for treated to control regrowth ratio (RR), and two for treated to control biomass ratio (BR). Some QTL positions overlapped with WH QTL reported previously, suggesting a genetic relationship between FT and WH. Some favorable QTL from the winter-hardy parent (3010) were from the potential genic region for a cold tolerance gene CBF. The BLAST alignment of a CBF sequence of M. truncatula, a close relative of alfalfa, against the alfalfa reference showed that the gene's ortholog resides around 75 Mb on chromosome 6.ConclusionsThe indoor freezing tolerance selection method reported is useful for alfalfa breeders to accelerate breeding cycles through indirect selection. The QTL and associated markers add to the genomic resources for the research community and can be used in marker-assisted selection (MAS) for alfalfa cold tolerance improvement.

Project description:BACKGROUND: Freezing provokes severe yield losses to different fall-sown annual legumes. Understanding the molecular bases of freezing tolerance is of great interest for breeding programs. Medicago truncatula Gaertn. is an annual temperate forage legume that has been chosen as a model species for agronomically and economically important legume crops. The present study aimed to identify positional candidate genes for a major freezing tolerance quantitative trait locus that was previously mapped to M. truncatula chromosome 6 (Mt-FTQTL6) using the LR3 population derived from a cross between the freezing-tolerant accession F83005-5 and the freezing-sensitive accession DZA045-5. RESULTS: The confidence interval of Mt-FTQTL6 was narrowed down to the region comprised between markers MTIC153 and NT6054 using recombinant F7 and F8 lines. A bacterial-artificial chromosome (BAC) clone contig map was constructed in an attempt to close the residual assembly gap existing therein. Twenty positional candidate genes including twelve C-repeat binding factor (CBF)/dehydration-responsive element binding factor 1 (DREB1) genes were identified from BAC-derived sequences and whole-genome shotgun sequences (WGS). CBF/DREB1 genes are organized in a tandem array within an approximately 296-Kb region. Eleven CBF/DREB1 genes were isolated and sequenced from F83005-5 and DZA045-5 which revealed high polymorphism among these accessions. Unique features characterizing CBF/DREB1 genes from M. truncatula, such as alternative splicing and large tandem duplication, are elucidated for the first time. CONCLUSIONS: Overall, twenty genes were identified as potential candidates to explain Mt-FTQTL6 effect. Their future functional characterization will uncover the gene(s) involved in freezing tolerance difference observed between F83005-5 and DZA045-5. Knowledge transfer for breeding improvement of crop legumes is expected. Furthermore, CBF/DREB1 related data will certainly have a large impact on research studies targeting this group of transcriptional activators in M. truncatula and other legume species.

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Project description:BackgroundThe volatile metabolites produced by Saccharomyces cerevisiae during alcoholic fermentation, which are mainly esters, higher alcohols and organic acids, play a vital role in the quality and perception of fermented beverages, such as wine. Although the metabolic pathways and genes behind yeast fermentative aroma formation are well described, little is known about the genetic mechanisms underlying variations between strains in the production of these aroma compounds. To increase our knowledge about the links between genetic variation and volatile production, we performed quantitative trait locus (QTL) mapping using 130 F2-meiotic segregants from two S. cerevisiae wine strains. The segregants were individually genotyped by next-generation sequencing and separately phenotyped during wine fermentation.ResultsUsing different QTL mapping strategies, we were able to identify 65 QTLs in the genome, including 55 that influence the formation of 30 volatile secondary metabolites, 14 with an effect on sugar consumption and central carbon metabolite production, and 7 influencing fermentation parameters. For ethyl lactate, ethyl octanoate and propanol formation, we discovered 2 interacting QTLs each. Within 9 of the detected regions, we validated the contribution of 13 genes in the observed phenotypic variation by reciprocal hemizygosity analysis. These genes are involved in nitrogen uptake and metabolism (AGP1, ALP1, ILV6, LEU9), central carbon metabolism (HXT3, MAE1), fatty acid synthesis (FAS1) and regulation (AGP2, IXR1, NRG1, RGS2, RGT1, SIR2) and explain variations in the production of characteristic sensorial esters (e.g., 2-phenylethyl acetate, 2-metyhlpropyl acetate and ethyl hexanoate), higher alcohols and fatty acids.ConclusionsThe detection of QTLs and their interactions emphasizes the complexity of yeast fermentative aroma formation. The validation of underlying allelic variants increases knowledge about genetic variation impacting metabolic pathways that lead to the synthesis of sensorial important compounds. As a result, this work lays the foundation for tailoring S. cerevisiae strains with optimized volatile metabolite production for fermented beverages and other biotechnological applications.

Project description:BackgroundDecoding of mRNAs is performed by aminoacyl tRNAs (aa-tRNAs). This process is highly accurate, however, at low frequencies (10(-3) - 10(-4)) the wrong aa-tRNA can be selected, leading to incorporation of aberrant amino acids. Although our understanding of what constitutes the correct or cognate aa-tRNA:mRNA interaction is well defined, a functional distinction between near-cognate or single mismatched, and unpaired or non-cognate interactions is lacking.Methodology/principal findingsMisreading of several synonymous codon substitutions at the catalytic site of firefly luciferase was assayed in Saccharomyces cerevisiae. Analysis of the results in the context of current kinetic and biophysical models of aa-tRNA selection suggests that the defining feature of near-cognate aa-tRNAs is their potential to form mini-helical structures with A-site codons, enabling stimulation of GTPase activity of eukaryotic Elongation Factor 1A (eEF1A). Paromomycin specifically stimulated misreading of near-cognate but not of non-cognate aa-tRNAs, providing a functional probe to distinguish between these two classes. Deletion of the accessory elongation factor eEF1Bgamma promoted increased misreading of near-cognate, but hyperaccurate reading of non-cognate codons, suggesting that this factor also has a role in tRNA discrimination. A mutant of eEF1Balpha, the nucleotide exchange factor for eEF1A, promoted a general increase in fidelity, suggesting that the decreased rates of elongation may provide more time for discrimination between aa-tRNAs. A mutant form of ribosomal protein L5 promoted hyperaccurate decoding of both types of codons, even though it is topologically distant from the decoding center.Conclusions/significanceIt is important to distinguish between near-cognate and non-cognate mRNA:tRNA interactions, because such a definition may be important for informing therapeutic strategies for suppressing these two different categories of mutations underlying many human diseases. This study suggests that the defining feature of near-cognate aa-tRNAs is their potential to form mini-helical structures with A-site codons in the ribosomal decoding center. An aminoglycoside and a ribosomal factor can be used to distinguish between near-cognate and non-cognate interactions.

Dataset Information

Rapid Identification of Major QTLS Associated With Near- Freezing Temperature Tolerance in Saccharomyces cerevisiae.

Publications

Rapid Identification of Major QTL<sub>S</sub> Associated With Near- Freezing Temperature Tolerance in <i>Saccharomyces cerevisiae</i>.

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