Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation

Mapping Intimacies ◽

10.1101/233122 ◽

2017 ◽

Author(s):

Jacob L. Steenwyk ◽

Antonis Rokas

Keyword(s):

Genetic Diversity ◽

Copy Number ◽

Molecular Mechanisms ◽

Phenotypic Diversity ◽

Wine Yeast ◽

Nucleotide Polymorphisms ◽

Wide Range ◽

Number Variation ◽

Fungal Populations ◽

Yeast Genetic

AbstractIn recent years, copy number (CN) variation has emerged as a new and significant source of genetic polymorphisms contributing to the phenotypic diversity of populations. CN variants are defined as genetic loci that, due to duplication and deletion, vary in their number of copies across individuals in a population. CN variants range in size from 50 base pairs to whole chromosomes, can influence gene activity, and are associated with a wide range of phenotypes in diverse organisms, including the budding yeastSaccharomyces cerevisiae.In this review, we introduce CN variation, discuss the genetic and molecular mechanisms implicated in its generation, how they can contribute to genetic and phenotypic diversity in fungal populations, and consider how CN variants may influence wine yeast adaptation in fermentation-related processes. In particular, we focus on reviewing recent work investigating the contribution of changes in CN of fermentation-related genes associated with the adaptation and domestication of yeast wine strains and offer notable illustrations of such changes, including the high levels of CN variation among theCUPgenes, which confer resistance to copper, and the preferential deletion and duplication of theMALIandMAL3loci, respectively, which are responsible for metabolizing maltose and sucrose. Based on the available data, we propose that CN variation is a substantial dimension of yeast genetic diversity that occurs largely independent of single nucleotide polymorphisms. As such, CN variation harbors considerable potential for understanding and manipulating yeast strains in the wine fermentation environment and beyond.

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Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation

Frontiers in Microbiology ◽

10.3389/fmicb.2018.00288 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 16

Author(s):

Jacob L. Steenwyk ◽

Antonis Rokas

Keyword(s):

Genetic Diversity ◽

Copy Number Variation ◽

Copy Number ◽

Wine Yeast ◽

Number Variation ◽

Yeast Genetic

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Genetics of Schizophrenia and Bipolar Disorder

10.1093/med/9780190681425.003.0013 ◽

2017 ◽

Author(s):

Alexander Charney ◽

Pamela Sklar

Keyword(s):

Bipolar Disorder ◽

Copy Number ◽

Psychotic Disorders ◽

Copy Number Variants ◽

Nucleotide Polymorphisms ◽

Common Variants ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Number Variation

Schizophrenia and bipolar disorder are the classic psychotic disorders. Both diseases are strongly familial, but have proven recalcitrant to genetic methodologies for identifying the etiology until recently. There is now convincing genetic evidence that indicates a contribution of many DNA changes to the risk of becoming ill. For schizophrenia, there are large contributions of rare copy number variants and common single nucleotide variants, with an overall highly polygenic genetic architecture. For bipolar disorder, the role of copy number variation appears to be much less pronounced. Specific common single nucleotide polymorphisms are associated, and there is evidence for polygenicity. Several surprises have emerged from the genetic data that indicate there is significantly more molecular overlap in copy number variants between autism and schizophrenia, and in common variants between schizophrenia and bipolar disorder.

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Population genetics of immune-related multilocus copy number variation in Native Americans

Journal of The Royal Society Interface ◽

10.1098/rsif.2017.0057 ◽

2017 ◽

Vol 14 (128) ◽

pp. 20170057 ◽

Cited By ~ 3

Author(s):

Luciana W. Zuccherato ◽

Silvana Schneider ◽

Eduardo Tarazona-Santos ◽

Robert J. Hardwick ◽

Douglas E. Berg ◽

...

Keyword(s):

Population Genetics ◽

Population Structure ◽

Native American ◽

Native Americans ◽

Copy Number Variation ◽

Copy Number ◽

Genomic Variation ◽

Population Subdivision ◽

Nucleotide Polymorphisms ◽

Number Variation

While multiallelic copy number variation (mCNV) loci are a major component of genomic variation, quantifying the individual copy number of a locus and defining genotypes is challenging. Few methods exist to study how mCNV genetic diversity is apportioned within and between populations (i.e. to define the population genetic structure of mCNV). These inferences are critical in populations with a small effective size, such as Amerindians, that may not fit the Hardy–Weinberg model due to inbreeding, assortative mating, population subdivision, natural selection or a combination of these evolutionary factors. We propose a likelihood-based method that simultaneously infers mCNV allele frequencies and the population structure parameter f , which quantifies the departure of homozygosity from the Hardy–Weinberg expectation. This method is implemented in the freely available software CNVice, which also infers individual genotypes using information from both the population and from trios, if available. We studied the population genetics of five immune-related mCNV loci associated with complex diseases (beta-defensins, CCL3L1/CCL4L1 , FCGR3A , FCGR3B and FCGR2C ) in 12 traditional Native American populations and found that the population structure parameters inferred for these mCNVs are comparable to but lower than those for single nucleotide polymorphisms studied in the same populations.

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Agro-morphological traits-based genetic diversity assessment in Ethiopian barley (Hordeum vulgare L.) landrace collections from Bale highlands, Southeast Ethiopia

Agriculture & Food Security ◽

10.1186/s40066-021-00335-4 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Fekadu Gadissa ◽

Meskerem Abebe ◽

Tesfaye Bekele

Keyword(s):

Genetic Diversity ◽

Hordeum Vulgare ◽

Phenotypic Diversity ◽

Genetic Erosion ◽

Morphometric Traits ◽

Lattice Design ◽

Diversity Assessment ◽

Wide Range ◽

Days To Maturity ◽

Cultivated Barley

Abstract Background Cultivated barley (Hordeum vulgare L.) is one of the world’s important cereal crops. Ethiopia is claimed to be the centre of origin due to its high phenotypic diversity and flavonoid patterns. It is widely cultivated on subsistence bases and important in supporting the livelihood of local poor. However, the local landraces are currently under threat of severing genetic erosion. Hence, assessing the extents of its genetic diversity is timely in improvement and conservation. Methodology 120 representative cultivated barley landraces have been collected from Bale highlands, Ethiopia, and tested at two locations using alpha lattice design. Data were collected on 21 agro-morphometric traits and analysed using MINITAB 19, SAS 9.4 and FigTree v1.4.3. Results Most morphotypes in each of the qualitative traits considered and mean performance values in most of the quantitative traits revealed wide range of variations suggesting existence of phenotypic diversity among the landraces. Analysis of variance also showed significant variations among the landraces. All the traits, except days to maturity and plant height showed a significant variation for location and treatment-location interactions revealing the high impact of environmental conditions on the variations. Estimates of the variance components also revealed a wider range of variations in most of the traits considered with eventual medium to low genotypic (GCV), phenotypic (PCV) and genotype–environment coefficients of variation (GECV). Estimates of heritability in broad sense (H2) is low (< 40%) in all the traits except in days to maturity. Grouping of the landraces showed poor geographic areas of collection-based pattern suggesting extensive gene flow among the areas. Conclusion The landraces evaluated in the present study showed high morphological diversity. However, the effect of environment factor is pronounced and thus, multiple locations and years with large number of samples must be considered to exploit the available genetic-based variations for breeding and conservation of the crop.

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Training for genes - how to design it?

Medicinski pregled ◽

10.2298/mpns1708227p ◽

2017 ◽

Vol 70 (7-8) ◽

pp. 227-233

Author(s):

Jelena Popadic-Gacesa

Keyword(s):

Athletic Training ◽

Molecular Mechanisms ◽

Ethical Issues ◽

Short Review ◽

Nucleotide Polymorphisms ◽

Training Design ◽

Muscle Adaptation ◽

Genetic Traits ◽

Genetic Profiling ◽

Wide Range

Introduction. The aim of this short review was not to be just another systematic report, but to highlight further research hypotheses regarding the challenges in performance genomics by focusing on three papers published in 2016, which offer innovative and promising approach that would be a breakthrough in more exact application of genetic data in practical work of sports experts and training design. Genes for sports. More than 200 single nucleotide polymorphisms and genetic traits associated with fitness performance have been reported in numerous studies, but genes for angiotensin converting enzyme and alpha-actinin-3 are most frequently associated with enhanced physical performance. Perspectives of epigenetics. Genotype-phenotype interactions include a wide range of molecular mechanisms with complex effects and interconnections. Gene adjusted training protocols. Using genetic profiling to match individual genotype with appropriate training modality may be a powerful tool providing personalized athletic training in the future. Conclusion. When applying genetic profiling prior to and during training programs, special consideration should be made to avoid athlete selection; it should be only used for inclusion, not for exclusion. Also, attention must be paid to social and ethical issues. Wider approach should include training interventional studies and non-athletic population in discovering new molecular pathways of muscle adaptation to exercise through genotype-phenotype interactions.

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Phenotypic and Genotypic Diversity for Drought Tolerance among and within Perennial Ryegrass Accessions

HortScience ◽

10.21273/hortsci.50.8.1148 ◽

2015 ◽

Vol 50 (8) ◽

pp. 1148-1154 ◽

Cited By ~ 5

Author(s):

Yu Cui ◽

Jinsheng Wang ◽

Xingchun Wang ◽

Yiwei Jiang

Keyword(s):

Genetic Diversity ◽

Drought Stress ◽

Drought Tolerance ◽

Genetic Distance ◽

Perennial Ryegrass ◽

Molecular Mechanisms ◽

Phenotypic Diversity ◽

Gene Diversity ◽

Leaf Water Content ◽

Drought Response

Perennial ryegrass (Lolium perenne L.) is a popular cool-season forage and turfgrass in temperate regions. Due to its self-incompatible and out-crossing nature, perennial ryegrass may show a high degree of heterozygosity. Perennial ryegrass generally is susceptible to drought stress, but variations of drought response of individual genotypes within a particular accession or cultivar are not well understood. The objective of this study was to characterize phenotypic diversity of drought tolerance within and among accessions in relation to genetic diversity in perennial ryegrass. Five individual genotypes from each of six accessions varying in origin and growth habits were subjected to drought stress in a greenhouse. Leaf wilting, plant height, chlorophyll fluorescence (Fv/Fm) and leaf water content (LWC) differed significantly among accessions as well as among genotypes within each accession under well-watered control and drought stress conditions. Fv/Fm was highly correlated with LWC under drought stress. Genetic diversity among and within accessions were identified by using previously characterized 23 simple sequence repeat markers. Across accessions, the mean major allele frequency, gene diversity, and heterozygosity values were 0.66, 0.43, and 0.66, respectively. Accessions with closer genetic distance generally had similar drought responses, while accessions with greater genetic distance showed distinct drought tolerance. Significant differences in drought tolerance among and within accessions, especially for individual genotypes within one accession, indicated that variations of drought response could be used for enhancing breeding programs and studying molecular mechanisms of stress tolerance in perennial ryegrass.

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Extensive Copy Number Variation in Fermentation-Related Genes amongSaccharomyces cerevisiaeWine Strains

10.1101/105502 ◽

2017 ◽

Author(s):

Jacob Steenwyk ◽

Antonis Rokas

Keyword(s):

Genetic Diversity ◽

Copy Number ◽

Wine Yeast ◽

Gene Families ◽

Genomic Variation ◽

Genomic Diversity ◽

Major Type ◽

Diauxic Shift ◽

Variable Regions ◽

Yeast Strains

AbstractDue to the importance ofSaccharomyces cerevisiaein wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences ofS. cerevisiaewine strains. We found an average of 97.8 CN variable regions (CNVRs) affecting ~4% of the genome per strain. Using two different measures of CN diversity, we found that gene families involved in fermentation-related processes such as copper resistance (CUP), flocculation (FLO), and glucose metabolism (HXT), as well as theSNOgene family whose members are expressed before or during the diauxic shift showed substantial CN diversity across the 132 strains examined. Importantly, these same gene families have been shown, through comparative transcriptomic and functional assays, to be associated with adaptation to the wine fermentation environment. Our results suggest that CN variation is a substantial contributor to the genomic diversity of wine yeast strains and identify several candidate loci whose levels of CN variation may affect the adaptation and performance of wine yeast strains during fermentation.

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