869 research outputs found
Genetic variation and expression changes associated with molybdate resistance from a glutathione producing wine strain of Saccharomyces cerevisiae
No full textGlutathione (GSH) production during wine fermentation is a desirable trait as it can limit must and wine oxidation and protect various aromatic compounds. UMCC 2581 is a Saccharomyces cerevisiae wine strain with enhanced GSH content at the end of wine fermentation. This strain was previously derived by selection for molybdate resistance following a sexual cycle of UMCC 855 using an evolution-based strategy. In this study, we examined genetic and gene expression changes associated with the derivation of UMCC 2581. For genetic analysis we sporulated the diploid UMCC 855 parental strain and found four phenotype classes of segregants related to molybdate resistance, demonstrating the presence of segregating variation from the parental strain. Using bulk segregant analysis we mapped molybdate traits to two loci. By sequencing both the parental and evolved strain genomes we identified candidate mutations within the two regions as well as an extra copy of chromosome 1 in UMCC 2581. Combining the mapped loci with gene expression profiles of the evolved and parental strains we identified a number of candidate genes with genetic and/or gene expression changes that could underlie molybdate resistance and increased GSH levels. Our results provide insight into the genetic basis of GSH production relevant to winemaking and highlight the value of enhancing wine strains using existing variation present in wine strains
A multi-phase approach to select new wine yeast strains with enhanced fermentative fitness and glutathione production
No full textThe genetic improvement of winemaking yeasts is a virtually infinite process, as the design of new strains must always cope with varied and ever-evolving production contexts. Good wine yeasts must feature both good primary traits, which are related to the overall fermentative fitness of the strain, and secondary traits, which provide accessory features augmenting its technological value. In this context, the superiority of “blind,” genetic improvement techniques, as those based on the direct selection of the desired phenotype without prior knowledge of the genotype, was widely proven. Blind techniques such as adaptive evolution strategies were implemented for the enhancement of many traits of interest in the winemaking field. However, these strategies usually focus on single traits: this possibly leads to genetic tradeoff phenomena, where the selection of enhanced secondary traits might lead to sub-optimal primary fermentation traits. To circumvent this phenomenon, we applied a multi-step and strongly directed genetic improvement strategy aimed at combining a strong fermentative aptitude (primary trait) with an enhanced production of glutathione (secondary trait). We exploited the random genetic recombination associated to a library of 69 monosporic clones of strain UMCC 855 (Saccharomyces cerevisiae) to search for new candidates possessing both traits. This was achieved by consecutively applying three directional selective criteria: molybdate resistance (1), fermentative aptitude (2), and glutathione production (3). The strategy brought to the selection of strain 21T2-D58, which produces a high concentration of glutathione, comparable to that of other glutathione high-producers, still with a much greater fermentative aptitude
Supplemental Material for Riles and Fay, 2018
No full textData availability statement: All strains and constructs
are available upon request to the corresponding author. Supplemental Table 1: Strains used in this study. Supplemental
Table 2: Recombinant strain barcode indices, sequencing and phenotypes used for
QTL mapping. Supplemental Table 3: Primers used in this study. Supplemental
Table 4: Summary of candidate genes tested for two QTL regions. Supplemental
Table 5: Genes tested for complementation using a MoBY and/or a hemizygosity
test. Supplemental Table 6: Colony size measurements using ImageJ for HN6 X KO
Hemizygotes on Chromosome 14. Supplementary Figure 1: Ethanol and heat
sensitivity of control strains. Supplementary Figure 2: Logarithm of the odds
ratio (LOD) of a quantitative trait locus for heat and ethanol tolerance at
high temperature across the genome. Supplementary Figure 3: Protein alignment
of HN6, Oak and S288c for SEC24 and PSD1. Supplementary Figure 4: Phenotypes of resistant wild yeast
strains, Oak, Wine and S288c, containing high copy Oak allele plasmids grown at
40o. Data File S1. Genotypes and phenotypes of recombinant strains
used for QTL mapping. The raw data used to call genotypes for QTL mapping has
been deposited into NCBI's SRA under BioProject: PRJNA480857.</p
Comparative genomics approaches accurately predict deleterious variants in plants
No full textThe genes and mutations information in this table were downloaded from UniProt/Swiss-Prot database (http://www.uniprot.org/) and http://www.arabidopsis.org. Single nucleotide polymorphisms (SNPs) without any known phenotype were obtained from a set of 80 sequenced A. thaliana strains (Ensembl, version 81, “Cao_SNPs”, Cao, et al., 2011). We used six approaches: LRT, PolyPhen2, SIFT 4G, Provean, MAPP, Gerp++ to predict deleterious varaints. The details can be avaible in Kono, et al., 2017 (http://www.biorxiv.org/content/early/2017/02/27/112318)Recent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but they are nearly always judged based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910 Arabidopsis thaliana mutants with known phenotypes. We evaluated seven approaches and found that while all performed well, the single best-performing approach was a likelihood ratio test applied to homologs identified in 42 plant genomes. Although the approaches did not always agree, we found only slight differences in performance when comparing mutations with gross versus biochemical phenotypes, duplicated versus single copy genes, and when using a single approach versus ensemble predictions. We conclude that deleterious mutations can be reliably predicted in A. thaliana and likely other plant species, but that the relative performance of various approaches can depend on the organism to which they are applied.US National Science Foundation Plant Genome Program grant (DBI-1339393 to JCF and PLM)US Department of Agriculture Biotechnology Risk Assessment Research Grants Program (BRAG) (USDA BRAG 2015-06504 to PLM)University of Minnesota Doctoral Dissertation Fellowship (to TJYK)Kono, Thomas John Y; Lei, Li; Shih, Ching-Hua; Hoffman, Paul J; Morrell, Peter L; Fay, Justin C. (2018). Comparative genomics approaches accurately predict deleterious variants in plants. Retrieved from the University Digital Conservancy, https://doi.org/10.13020/D6N69S
Development and leadership in computer-mediated collaborative groups
No full textComputer-mediated collaboration is an important feature of modern organisational and educational settings. Despite its ever increasing popularity, it is still commonly compared unfavourably with face-to-face collaboration because non-verbal and paralinguistic cues are minimal. Although research on face-to-face group collaboration is well documented, less is known about computer-mediated collaboration.
The initial focus of this thesis was an in-depth analysis of a case study of a computer-mediated collaborative group. The case study was a large international group of volunteer researchers who collaborated on a two-year research project using asynchronous communication (email). This case study was a window on collaborative dialogue in the early 1990s (1992-94) at a time when information and communication technologies were at an early stage of development.
After identifying the issues emerging from this early case study, another case study using technologies and virtual environments developed over the past decade, was designed to further understand how groups work together on a collaborative activity. The second case study was a small group of students enrolled in a unit of study at Murdoch University who collaborated on a series of nine online workshops using synchronous communication (chat room). This case study was a window on collaborative dialogue in the year 2000 when information and communication technologies had developed at a rate which few people envisioned in the early 90s.
The primary aim of the research described in this thesis was to gain a better understanding of how computer-mediated collaborative communities develop and grow. In particular, the thesis addresses questions related to the developmental and leadership characteristics of collaborative groups.
Internet research requires a set of assumptions relating to ontology, epistemology, human nature and methodological approach that differs from traditional research assumptions. A research framework for Internet research - Complementary Explorative Data Analysis (CEDA) - was therefore developed and applied to the two case studies.
The results of the two case studies using the CEDA methodology indicate that computer-mediated collaborative groups are highly adaptive to the aim of the collaborative task to be completed, and the medium in which they collaborate. In the organisational setting, it has been found that virtual teams can devise and complete a collaborative task entirely online. It may be an advantage, but it is certainly not mandatory to have preliminary face-to-face discussions. What is more important is to ensure that time is allowed for an initial period of structuration which involves social interaction to develop a social presence and eventually cohesiveness. In the educational setting, a collaborative community increases pedagogical effectiveness. Providing collaborative projects and interdependent tasks promotes constructivist learning and a strong foundation for understanding how to collaborate in the global workplace. Again, this research has demonstrated that students can collaborate entirely online, although more pedagogical scaffolding may be required than in the organisational setting. The importance of initial social interaction to foster a sense of presence and community in a mediated environment has also been highlighted.
This research also provided greater understanding of emergent leadership in computer-mediated collaborative groups. It was found that sheer volume of words does not make a leader but frequent messages with topic-related content does contribute to leadership qualities.
The results described in this thesis have practical implications for managers of virtual teams and educators in e-learning
Variants from "The role of deleterious substitutions in crop genomes"
No full textThere are two gzipped VCF (variant call format) files with variant calls for barley and soybean. A total of 652,797 SNPs were identified in the barley lines, which consisted of 13 cultivars and 2 wild accessions. For soybean, 7 cultivars and 1 wild accession were used, and 586,102 SNPs were called. Whether a variant is deleterious or not was determined using SIFT (http://sift.jcvi.org/), PolyPhen2 (http://genetics.bwh.harvard.edu/pph2/), and a likelihood ratio test of sequence conservation. Raw reads are available through the SRA accession numbers in Table S1 of Kono et al. 2016. The code used for this research, BAD_Mutations, is open source and freely available at https://github.com/MorrellLAB/BAD_Mutations.SNP calls in protein coding regions were obtained from 15 barley and 8 soybean lines. Non synonymous SNPs were predicted to be deleterious or not using three approaches.USDA NIFA National Needs Fellowship (Appropriation No. 5430-21000-006-00D)MnDrive 2014 Food Security FellowshipMinnesota Agricultural Experiment Station Variety Development fundUnited Soybean BoardU.S. NSF Plant Genome Program (BDI-1339393)Kono, Thomas J Y; Fu, Fengli; Mohammadi, Mohsen; Hoffman, Paul J; Liu, Chaochih; Stupar, Robert M; Smith, Kevin P; Tiffin, Peter; Fay, Justin C; Morrell, Peter L. (2016). Variants from "The role of deleterious substitutions in crop genomes". Retrieved from the University Digital Conservancy, http://doi.org/10.13020/D65C7D
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Joint effects of genes underlying a temperature specialization tradeoff in yeast
No full textA central goal of evolutionary genetics is to understand, at the molecular level, how organisms adapt to their environments. For a given trait, the answer often involves the acquisition of variants at unlinked sites across the genome. Genomic methods have achieved landmark successes in pinpointing adaptive loci. To figure out how a suite of adaptive alleles work together, and to what extent they can reconstitute the phenotype of interest, requires their transfer into an exogenous background. We studied the joint effect of adaptive, gain-of-function thermotolerance alleles at eight unlinked genes from Saccharomyces cerevisiae, when introduced into a thermosensitive sister species, S. paradoxus. Although the loci damped each other's beneficial impact (that is, they were subject to negative epistasis), most boosted high-temperature growth alone and in combination, and none was deleterious. The complete set of eight genes was sufficient to confer ~15% of the S. cerevisiae phenotype in the S. paradoxus background. The same loci also contributed to a heretofore unknown advantage in cold growth by S. paradoxus. Together, our data establish temperature resistance in yeasts as a model case of a genetically complex evolutionary tradeoff, which can be partly reconstituted from the sequential assembly of unlinked underlying loci.Funding provided by: National Institutes of HealthCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000002Award Number: R01 GM120430Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: GRFP DGE 175281
Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize.
No full textDeleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD) analysis and perform genomic prediction analyses in which we weigh blocks on the basis of complementation for segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding
Genetic architecture of a reinforced, postmating, reproductive isolation barrier between Neurospora species indicates evolution via natural selection.
No full textA role for natural selection in reinforcing premating barriers is recognized, but selection for reinforcement of postmating barriers remains controversial. Organisms lacking evolvable premating barriers can theoretically reinforce postmating isolation, but only under restrictive conditions: parental investment in hybrid progeny must inhibit subsequent reproduction, and selected postmating barriers must restore parents' capacity to reproduce successfully. We show that reinforced postmating isolation markedly increases maternal fitness in the fungus Neurospora crassa, and we detect the evolutionary genetic signature of natural selection by quantitative trait locus (QTL) analysis of the reinforced barrier. Hybrid progeny of N. crassa and N. intermedia are highly inviable. Fertilization by local N. intermedia results in early abortion of hybrid fruitbodies, and we show that abortion is adaptive because only aborted maternal colonies remain fully receptive to future reproduction. In the first QTL analysis of postmating reinforcement in microbial eukaryotes, we identify 11 loci for abortive hybrid fruitbody development, including three major QTLs that together explain 30% of trait variance. One of the major QTLs and six QTLs of lesser effect are found on the mating-type determining chromosome of Neurospora. Several reinforcement QTLs are flanked by genetic markers showing either segregation distortion or non-random associations with alleles at other loci in a cross between N. crassa of different clades, suggesting that the loci also are associated with local effects on same-species reproduction. Statistical analysis of the allelic effects distribution for abortive hybrid fruitbody development indicates its evolution occurred under positive selection. Our results strongly support a role for natural selection in the evolution of reinforced postmating isolation in N. crassa
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