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Contreras‐Ruiz A, Minebois R, Alonso‐del‐Real J, Barrio E, Querol A. Differences in metabolism among Saccharomyces species and their hybrids during wine fermentation. Microb Biotechnol 2024; 17:e14476. [PMID: 38801338 PMCID: PMC11129674 DOI: 10.1111/1751-7915.14476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/11/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
This study aimed to investigate how parental genomes contribute to yeast hybrid metabolism using a metabolomic approach. Previous studies have explored central carbon and nitrogen metabolism in Saccharomyces species during wine fermentation, but this study analyses the metabolomes of Saccharomyces hybrids for the first time. We evaluated the oenological performance and intra- and extracellular metabolomes, and we compared the strains according to nutrient consumption and production of the main fermentative by-products. Surprisingly, no common pattern was observed for hybrid genome influence; each strain behaved differently during wine fermentation. However, this study suggests that the genome of the S. cerevisiae species may play a more relevant role in fermentative metabolism. Variations in biomass/nitrogen ratios were also noted, potentially linked to S. kudriavzevii and S. uvarum genome contributions. These results open up possibilities for further research using different "omics" approaches to comprehend better metabolic regulation in hybrid strains with genomes from different species.
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Affiliation(s)
- Alba Contreras‐Ruiz
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
| | - Romain Minebois
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
| | - Javier Alonso‐del‐Real
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
- Departament de GenèticaUniversitat de ValènciaValènciaSpain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés BiotecnológicoInstituto de Agroquímica y Tecnología de Los Alimentos (IATA)‐CSICValènciaSpain
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Nyirimana P, Kondoh D, Tomiyasu J, Watanabe M, Okada Y, Nishida Y, Goto T. Morphological variation of tail bone among two chicken breeds and their F 1 progeny. J Morphol 2024; 285:e21704. [PMID: 38702980 DOI: 10.1002/jmor.21704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024]
Abstract
Fancy breeds of Japanese indigenous chicken display extensive morphological diversity, particularly in tail feathers. Although marked differences in tail and bone traits have been reported between Tosa-jidori (wild type) and Minohikichabo (rich type) breeds, little is known about the pattern of genetic inheritance in cross experiments. Therefore, this study aimed to investigate the strain and sex effects, and inheritance patterns, in the morphometric variation of pygostyle bones among Tosa-jidori, Minohikichabo, and their F1 hybrids. Five morphological traits, angle of the apex of the pygostyle, pygostyle length, margo cranialis length, tail feather number, and body weight, were evaluated at the adult stage. A significant strain difference was detected in all traits, whereas significant sex differences were observed in only three traits, but not in the angle of the apex of the pygostyle and tail feather number. In F1 hybrids, the angle of the apex of the pygostyle was significantly different to that of Tosa-jidori but not that of Minohikichabo, whereas the pygostyle length and tail number of F1 hybrids were significantly different from those of Minohikichabo but not those of Tosa-jidori. A significant heterosis effect was found in the margo cranialis length and body weight. All five traits showed nonadditive inheritance patterns but varied in each trait between partial dominance (angle of the apex of pygostyle), full dominance (pygostyle length and tail feather number), and over-dominance (margo cranialis length and body weight). Interestingly, different patterns of genetic inheritance in the F1 hybrid were observed at different locations, even within the same pygostyle bone. Using the Japanese indigenous chicken model, these results provide a substantial step toward understanding the genetic architecture of morphology in chickens.
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Affiliation(s)
- Prudence Nyirimana
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Daisuke Kondoh
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Jumpei Tomiyasu
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Momoka Watanabe
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Yume Okada
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Yuma Nishida
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Tatsuhiko Goto
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
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Dai Y, Shi G, Chen M, Chen G, Wu Q. Using Polygenic Risk Scores Related to Complex Traits to Predict Production Performance in Cross-Breeding of Yeast. J Fungi (Basel) 2022; 8:jof8090914. [PMID: 36135639 PMCID: PMC9500933 DOI: 10.3390/jof8090914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The cultivation of hybrids with favorable complex traits is one of the important goals for animal, plant, and microbial breeding practices. A method that can closely predict the production performance of hybrids is of great significance for research and practice. In our study, polygenic risk scores (PRSs) were introduced to estimate the production performance of Saccharomyces cerevisiae. The genetic variation of 971 published isolates and their growth ratios under 35 medium conditions were analyzed by genome-wide association analysis, and the precise p-value threshold for each phenotype was calculated. Risk markers for the above 35 phenotypes were obtained. By estimating the genotype of F1 hybrids according to that of the parents, the PRS of 613 F1 hybrids was predicted. There was a significant linear correlation between the maximum growth rate at 40 °C and PRS in F1 hybrids and their parents (R2 = 0.2582, R2 = 0.2414, respectively), which indicates that PRS can be used to estimate the production performance of individuals and their hybrids. Our method can provide a reference for strain selection and F1 prediction in cross-breeding yeasts, reduce workload, and improve work efficiency.
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Affiliation(s)
- Yi Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Guohui Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengmeng Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Guotao Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence:
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4
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Tutaj H, Pirog A, Tomala K, Korona R. Genome-scale patterns in the loss of heterozygosity incidence in Saccharomyces cerevisiae. Genetics 2022; 221:6536968. [PMID: 35212738 PMCID: PMC9071580 DOI: 10.1093/genetics/iyac032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/17/2022] [Indexed: 02/07/2023] Open
Abstract
Former studies have established that loss of heterozygosity can be a key driver of sequence evolution in unicellular eukaryotes and tissues of metazoans. However, little is known about whether the distribution of loss of heterozygosity events is largely random or forms discernible patterns across genomes. To initiate our experiments, we introduced selectable markers to both arms of all chromosomes of the budding yeast. Subsequent extensive assays, repeated over several genetic backgrounds and environments, provided a wealth of information on the genetic and environmental determinants of loss of heterozygosity. Three findings stand out. First, the number of loss of heterozygosity events per unit time was more than 25 times higher for growing than starving cells. Second, loss of heterozygosity was most frequent when regions of homology around a recombination site were identical, about a half-% sequence divergence was sufficient to reduce its incidence. Finally, the density of loss of heterozygosity events was highly dependent on the genome's physical architecture. It was several-fold higher on short chromosomal arms than on long ones. Comparably large differences were seen within a single arm where regions close to a centromere were visibly less affected than regions close, though usually not strictly adjacent, to a telomere. We suggest that the observed uneven distribution of loss of heterozygosity events could have been caused not only by an uneven density of initial DNA damages. Location-depended differences in the mode of DNA repair, or its effect on fitness, were likely to operate as well.
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Affiliation(s)
- Hanna Tutaj
- Institute of Environmental Sciences, Jagiellonian University, 30-387 Cracow, Poland
| | - Adrian Pirog
- Institute of Environmental Sciences, Jagiellonian University, 30-387 Cracow, Poland
| | - Katarzyna Tomala
- Institute of Environmental Sciences, Jagiellonian University, 30-387 Cracow, Poland
| | - Ryszard Korona
- Institute of Environmental Sciences, Jagiellonian University, 30-387 Cracow, Poland,Corresponding author: Institute of Environmental Sciences, Jagiellonian University, Gronostajowa Street 7, 30-387 Krakow, Poland.
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5
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Bai FY, Han DY, Duan SF, Wang QM. The Ecology and Evolution of the Baker's Yeast Saccharomyces cerevisiae. Genes (Basel) 2022; 13:230. [PMID: 35205274 PMCID: PMC8871604 DOI: 10.3390/genes13020230] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/01/2023] Open
Abstract
The baker's yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an 'out-of-China' origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae.
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Affiliation(s)
- Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
- College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
| | - Da-Yong Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
| | - Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
| | - Qi-Ming Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China;
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Michelotti LA, Sun S, Heitman J, James TY. Clonal evolution in serially passaged Cryptococcus neoformans × deneoformans hybrids reveals a heterogenous landscape of genomic change. Genetics 2022; 220:iyab142. [PMID: 34849836 PMCID: PMC8733418 DOI: 10.1093/genetics/iyab142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/25/2021] [Indexed: 11/14/2022] Open
Abstract
Cryptococcus neoformans × deneoformans hybrids (also known as serotype AD hybrids) are basidiomycete yeasts that are common in a clinical setting. Like many hybrids, the AD hybrids are largely locked at the F1 stage and are mostly unable to undergo normal meiotic reproduction. However, these F1 hybrids, which display a high (∼10%) sequence divergence are known to genetically diversify through mitotic recombination and aneuploidy, and this diversification may be adaptive. In this study, we evolved a single AD hybrid genotype in six diverse environments by serial passaging and then used genome resequencing of evolved clones to determine evolutionary mechanisms of adaptation. The evolved clones generally increased fitness after passaging, accompanied by an average of 3.3 point mutations, 2.9 loss of heterozygosity (LOH) events, and 0.7 trisomic chromosomes per clone. LOH occurred through nondisjunction of chromosomes, crossing over consistent with break-induced replication, and gene conversion, in that order of prevalence. The breakpoints of these recombination events were significantly associated with regions of the genome with lower sequence divergence between the parents and clustered in sub-telomeric regions, notably in regions that had undergone introgression between the two parental species. Parallel evolution was observed, particularly through repeated homozygosity via nondisjunction, yet there was little evidence of environment-specific parallel change for either LOH, aneuploidy, or mutations. These data show that AD hybrids have both a remarkable genomic plasticity and yet are challenged in the ability to recombine through sequence divergence and chromosomal rearrangements, a scenario likely limiting the precision of adaptive evolution to novel environments.
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Affiliation(s)
- Lucas A Michelotti
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Solieri L, Cassanelli S, Huff F, Barroso L, Branduardi P, Louis EJ, Morrissey JP. Insights on life cycle and cell identity regulatory circuits for unlocking genetic improvement in Zygosaccharomyces and Kluyveromyces yeasts. FEMS Yeast Res 2021; 21:foab058. [PMID: 34791177 PMCID: PMC8673824 DOI: 10.1093/femsyr/foab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/14/2021] [Indexed: 11/14/2022] Open
Abstract
Evolution has provided a vast diversity of yeasts that play fundamental roles in nature and society. This diversity is not limited to genotypically homogeneous species with natural interspecies hybrids and allodiploids that blur species boundaries frequently isolated. Thus, life cycle and the nature of breeding systems have profound effects on genome variation, shaping heterozygosity, genotype diversity and ploidy level. The apparent enrichment of hybrids in industry-related environments suggests that hybridization provides an adaptive route against stressors and creates interest in developing new hybrids for biotechnological uses. For example, in the Saccharomyces genus where regulatory circuits controlling cell identity, mating competence and meiosis commitment have been extensively studied, this body of knowledge is being used to combine interesting traits into synthetic F1 hybrids, to bypass F1 hybrid sterility and to dissect complex phenotypes by bulk segregant analysis. Although these aspects are less known in other industrially promising yeasts, advances in whole-genome sequencing and analysis are changing this and new insights are being gained, especially in the food-associated genera Zygosaccharomyces and Kluyveromyces. We discuss this new knowledge and highlight how deciphering cell identity circuits in these lineages will contribute significantly to identify the genetic determinants underpinning complex phenotypes and open new avenues for breeding programmes.
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Affiliation(s)
- Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Stefano Cassanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Franziska Huff
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Liliane Barroso
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Edward J Louis
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John P Morrissey
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
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Brice C, Zhang Z, Bendixsen D, Stelkens R. Hybridization Outcomes Have Strong Genomic and Environmental Contingencies. Am Nat 2021; 198:E53-E67. [PMID: 34403309 DOI: 10.1086/715356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractExtreme F2 phenotypes known as transgressive segregants can cause increased or decreased fitness in hybrids beyond the ranges seen in parental populations. Despite the usefulness of transgression for plant and animal breeding and its potential role in hybrid speciation, the genetic mechanisms and predictors of transgressive segregation remain largely untested. We generated seven hybrid crosses between five widely divergent Saccharomyces yeast species and measured the fitness of the parents and their viable F1 and F2 hybrids in seven stressful environments. We found that on average 16.6% of all replicate F2 hybrids had higher fitness than both parents. Against our predictions, transgression frequency was not a function of parental genetic and phenotypic distances across test environments. Within environments, some relationships were significant, but not in the predicted direction; for example, genetic distance was negatively related to transgression in ethanol and hydrogen peroxide. Significant effects of hybrid cross, test environment, and cross × environment interactions suggest that the amount of transgression produced in a hybrid cross is highly context specific and that outcomes of hybridization differ even among crosses made from the same two parents. If the goal is to reliably predict hybrid fitness and forecast the evolutionary potential of admixed populations, we need more efforts to identify patterns beyond the idiosyncrasies caused by specific genomic or environmental contexts.
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Song L, Shi JY, Duan SF, Han DY, Li K, Zhang RP, He PY, Han PJ, Wang QM, Bai FY. Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature. Genome Res 2021; 31:622-634. [PMID: 33722936 PMCID: PMC8015850 DOI: 10.1101/gr.262055.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 02/12/2021] [Indexed: 11/25/2022]
Abstract
Heterosis or hybrid vigor is a common phenomenon in plants and animals; however, the molecular mechanisms underlying heterosis remain elusive, despite extensive studies on the phenomenon for more than a century. Here we constructed a large collection of F1 hybrids of Saccharomyces cerevisiae by spore-to-spore mating between homozygous wild strains of the species with different genetic distances and compared growth performance of the F1 hybrids with their parents. We found that heterosis was prevalent in the F1 hybrids at 40°C. A hump-shaped relationship between heterosis and parental genetic distance was observed. We then analyzed transcriptomes of selected heterotic and depressed F1 hybrids and their parents growing at 40°C and found that genes associated with one-carbon metabolism and related pathways were generally up-regulated in the heterotic F1 hybrids, leading to improved cellular redox homeostasis at high temperature. Consistently, genes related with DNA repair, stress responses, and ion homeostasis were generally down-regulated in the heterotic F1 hybrids. Furthermore, genes associated with protein quality control systems were also generally down-regulated in the heterotic F1 hybrids, suggesting a lower level of protein turnover and thus higher energy use efficiency in these strains. In contrast, the depressed F1 hybrids, which were limited in number and mostly shared a common aneuploid parental strain, showed a largely opposite gene expression pattern to the heterotic F1 hybrids. We provide new insights into molecular mechanisms underlying heterosis and thermotolerance of yeast and new clues for a better understanding of the molecular basis of heterosis in plants and animals.
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Affiliation(s)
- Liang Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun-Yan Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Da-Yong Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ri-Peng Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Yu He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pei-Jie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi-Ming Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Abstract
The genus Saccharomyces is an evolutionary paradox. On the one hand, it is composed of at least eight clearly phylogenetically delineated species; these species are reproductively isolated from each other, and hybrids usually cannot complete their sexual life cycles. On the other hand, Saccharomyces species have a long evolutionary history of hybridization, which has phenotypic consequences for adaptation and domestication. A variety of cellular, ecological, and evolutionary mechanisms are responsible for this partial reproductive isolation among Saccharomyces species. These mechanisms have caused the evolution of diverse Saccharomyces species and hybrids, which occupy a variety of wild and domesticated habitats. In this article, we introduce readers to the mechanisms isolating Saccharomyces species, the circumstances in which reproductive isolation mechanisms are effective and ineffective, and the evolutionary consequences of partial reproductive isolation. We discuss both the evolutionary history of the genus Saccharomyces and the human history of taxonomists and biologists struggling with species concepts in this fascinating genus.
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Affiliation(s)
- Jasmine Ono
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
| | - Duncan Greig
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
| | - Primrose J Boynton
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
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K. Srivastava R, Bollam S, Pujarula V, Pusuluri M, Singh RB, Potupureddi G, Gupta R. Exploitation of Heterosis in Pearl Millet: A Review. PLANTS (BASEL, SWITZERLAND) 2020; 9:E807. [PMID: 32605134 PMCID: PMC7412370 DOI: 10.3390/plants9070807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 01/06/2023]
Abstract
The phenomenon of heterosis has fascinated plant breeders ever since it was first described by Charles Darwin in 1876 in the vegetable kingdom and later elaborated by George H Shull and Edward M East in maize during 1908. Heterosis is the phenotypic and functional superiority manifested in the F1 crosses over the parents. Various classical complementation mechanisms gave way to the study of the underlying potential cellular and molecular mechanisms responsible for heterosis. In cereals, such as maize, heterosis has been exploited very well, with the development of many single-cross hybrids that revolutionized the yield and productivity enhancements. Pearl millet (Pennisetum glaucum (L.) R. Br.) is one of the important cereal crops with nutritious grains and lower water and energy footprints in addition to the capability of growing in some of the harshest and most marginal environments of the world. In this highly cross-pollinating crop, heterosis was exploited by the development of a commercially viable cytoplasmic male-sterility (CMS) system involving a three-lines breeding system (A-, B- and R-lines). The first set of male-sterile lines, i.e., Tift 23A and Tift18A, were developed in the early 1960s in Tifton, Georgia, USA. These provided a breakthrough in the development of hybrids worldwide, e.g., Tift 23A was extensively used by Punjab Agricultural University (PAU), Ludhiana, India, for the development of the first single-cross pearl millet hybrid, named Hybrid Bajra 1 (HB 1), in 1965. Over the past five decades, the pearl millet community has shown tremendous improvement in terms of cytoplasmic and nuclear diversification of the hybrid parental lines, which led to a progressive increase in the yield and adaptability of the hybrids that were developed, resulting in significant genetic gains. Lately, the whole genome sequencing of Tift 23D2B1 and re-sequencing of circa 1000 genomes by a consortium led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) has been a significant milestone in the development of cutting-edge genetic and genomic resources in pearl millet. Recently, the application of genomics and molecular technologies has provided better insights into genetic architecture and patterns of heterotic gene pools. Development of whole-genome prediction models incorporating heterotic gene pool models, mapped traits and markers have the potential to take heterosis breeding to a new level in pearl millet. This review discusses advances and prospects in various fronts of heterosis for pearl millet.
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Affiliation(s)
- Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad TS 502324, India; (S.B.); (V.P.); (M.P.); (R.B.S.); (G.P.)
| | | | | | | | | | | | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad TS 502324, India; (S.B.); (V.P.); (M.P.); (R.B.S.); (G.P.)
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12
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Gorter de Vries AR, Pronk JT, Daran JMG. Lager-brewing yeasts in the era of modern genetics. FEMS Yeast Res 2020; 19:5573808. [PMID: 31553794 PMCID: PMC6790113 DOI: 10.1093/femsyr/foz063] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022] Open
Abstract
The yeast Saccharomyces pastorianus is responsible for the annual worldwide production of almost 200 billion liters of lager-type beer. S. pastorianus is a hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus that has been studied for well over a century. Scientific interest in S. pastorianus intensified upon the discovery, in 2011, of its S. eubayanus ancestor. Moreover, advances in whole-genome sequencing and genome editing now enable deeper exploration of the complex hybrid and aneuploid genome architectures of S. pastorianus strains. These developments not only provide novel insights into the emergence and domestication of S. pastorianus but also generate new opportunities for its industrial application. This review paper combines historical, technical and socioeconomic perspectives to analyze the evolutionary origin and genetics of S. pastorianus. In addition, it provides an overview of available methods for industrial strain improvement and an outlook on future industrial application of lager-brewing yeasts. Particular attention is given to the ongoing debate on whether current S. pastorianus originates from a single or multiple hybridization events and to the potential role of genome editing in developing industrial brewing yeast strains.
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Affiliation(s)
- Arthur R Gorter de Vries
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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13
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Zhang Z, Bendixsen DP, Janzen T, Nolte AW, Greig D, Stelkens R. Recombining Your Way Out of Trouble: The Genetic Architecture of Hybrid Fitness under Environmental Stress. Mol Biol Evol 2020; 37:167-182. [PMID: 31518427 PMCID: PMC6984367 DOI: 10.1093/molbev/msz211] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hybridization between species can either promote or impede adaptation. But we know very little about the genetic basis of hybrid fitness, especially in nondomesticated organisms, and when populations are facing environmental stress. We made genetically variable F2 hybrid populations from two divergent Saccharomyces yeast species. We exposed populations to ten toxins and sequenced the most resilient hybrids on low coverage using ddRADseq to investigate four aspects of their genomes: 1) hybridity, 2) interspecific heterozygosity, 3) epistasis (positive or negative associations between nonhomologous chromosomes), and 4) ploidy. We used linear mixed-effect models and simulations to measure to which extent hybrid genome composition was contingent on the environment. Genomes grown in different environments varied in every aspect of hybridness measured, revealing strong genotype–environment interactions. We also found selection against heterozygosity or directional selection for one of the parental alleles, with larger fitness of genomes carrying more homozygous allelic combinations in an otherwise hybrid genomic background. In addition, individual chromosomes and chromosomal interactions showed significant species biases and pervasive aneuploidies. Against our expectations, we observed multiple beneficial, opposite-species chromosome associations, confirmed by epistasis- and selection-free computer simulations, which is surprising given the large divergence of parental genomes (∼15%). Together, these results suggest that successful, stress-resilient hybrid genomes can be assembled from the best features of both parents without paying high costs of negative epistasis. This illustrates the importance of measuring genetic trait architecture in an environmental context when determining the evolutionary potential of genetically diverse hybrid populations.
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Affiliation(s)
- Zebin Zhang
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Devin P Bendixsen
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Thijs Janzen
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Arne W Nolte
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Duncan Greig
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Max Planck Institute for Evolutionary Biology, Plön, Germany
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14
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Origone AC, González Flores M, Rodríguez ME, Querol A, Lopes CA. Inheritance of winemaking stress factors tolerance in Saccharomyces uvarum/S. eubayanus × S. cerevisiae artificial hybrids. Int J Food Microbiol 2020; 320:108500. [PMID: 32007764 DOI: 10.1016/j.ijfoodmicro.2019.108500] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/30/2019] [Accepted: 12/26/2019] [Indexed: 10/25/2022]
Abstract
Stress has been defined as any environmental factor that impairs the growth of a living organism. High concentrations of ethanol, sugars and SO2 as well as temperature variations occurring during winemaking processes are some recognized stress factors that yeasts must overcome in order to avoid stuck or sluggish fermentations. At least two of these factors -sugar and ethanol concentrations- are strongly influenced by the global warming, which become them a worry for the future years in the winemaking industry. One of the most interesting strategies to face this complex situation is the generation of hybrids possessing, in a single yeast strain, a broader range of stress factors tolerance than their parents. In the present study, we evaluated four artificial hybrids generated with S. cerevisiae, S. uvarum and S. eubayanus using a non-GMO-generating method, in their tolerance to a set of winemaking stress factors. Their capacity to overcome specific artificial winemaking situations associated with global warming was also analyzed. All four hybrids were able to grow in a wider temperature range (8-37 °C) than their parents. Hybrids showed intermediate tolerance to higher ethanol, sugar and sulphite concentrations than their parents. Additionally, the hybrids showed an excellent fermentative behaviour in musts containing high fructose concentrations at low temperature as well as under a condition mimicking a stuck fermentation.
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Affiliation(s)
- Andrea Cecilia Origone
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN), Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén, Argentina; Facultad de Ciencias Agrarias, Universidad Nacional del Comahue, Argentina
| | - Melisa González Flores
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN), Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén, Argentina; Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Argentina
| | - María Eugenia Rodríguez
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN), Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén, Argentina; Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Argentina
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA, CSIC. Agustín Escardino Benlloch, 7, 46980 Paterna, Spain
| | - Christian Ariel Lopes
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN), Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén, Argentina; Facultad de Ciencias Agrarias, Universidad Nacional del Comahue, Argentina.
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15
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Dakal TC, Dhabhai B. Current status of genetic & metabolic engineering and novel QTL mapping-based strategic approach in bioethanol production. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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Korhola M, Naumova ES, Partti E, Aittamaa M, Turakainen H, Naumov GI. Exploiting heterozygosity in industrial yeasts to create new and improved baker's yeasts. Yeast 2019; 36:571-587. [PMID: 31243797 DOI: 10.1002/yea.3428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/31/2019] [Accepted: 06/11/2019] [Indexed: 01/24/2023] Open
Abstract
The main aim of the work was to utilize heterozygosity of industrial yeast strains to construct new baker's yeast strains. Commercial baker's yeast strain ALKO 743, its more ethanol tolerant descendant ALKO 554 selected initially for growth over 300 generations in increasing ethanol concentrations in a glucose medium, and ALKO 3460 from an old domestic sour dough starter were used as starting strains. Isolated meiotic segregants of the strains were characterized genetically for sporulation ability and mating type, and the ploidy was determined physically. Heterozygosity of the segregant strains was estimated by a variety of molecular characterizations and fermentation and growth assays. The results showed wide heterozygosity and that the segregants were clustered into subgroups. This clustering was used for choosing distantly or closely related partners for strain construction crosses. Intrastrain hybrids made with segregants of ALKO 743 showed 16-24% hybrid vigour or heterosis. Interstrain hybrids with segregants of ALKO 743 and ALKO 3460 showed a wide variety of characteristics but also clear heterosis of 27-31% effects as assayed by lean and sugar dough raising. Distiller's yeast ALKO 554 turned out to be a diploid genetic segregant and not just a more ethanol tolerant mutant of the tetraploid parent strain ALKO 743.
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Affiliation(s)
- Matti Korhola
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Elena S Naumova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Edvard Partti
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Marja Aittamaa
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Hilkka Turakainen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Gennadi I Naumov
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
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17
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Vacher M, Small I. Simulation of heterosis in a genome-scale metabolic network provides mechanistic explanations for increased biomass production rates in hybrid plants. NPJ Syst Biol Appl 2019; 5:24. [PMID: 31341636 PMCID: PMC6639380 DOI: 10.1038/s41540-019-0101-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 06/28/2019] [Indexed: 01/13/2023] Open
Abstract
Heterosis, or hybrid vigour, is said to occur when F1 individuals exhibit increased performance for a number of traits compared to their parental lines. Improved traits can include increased size, better yield, faster development and a higher tolerance to pathogens or adverse conditions. The molecular basis for the phenomenon remains disputed, despite many decades of theorising and experimentation. In this study, we add a genetics layer to a constraint-based model of plant (Arabidopsis) primary metabolism and show that we can realistically reproduce and quantify heterosis in a highly complex trait (the rate of biomass production). The results demonstrate that additive effects coupled to the complex patterns of epistasis generated by a large metabolic network are sufficient to explain most or all the heterosis seen in typical F1 hybrids. Such models provide a simple approach to exploring and understanding heterosis and should assist in designing breeding strategies to exploit this phenomenon in the future.
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Affiliation(s)
- Michael Vacher
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009 Australia
- Present Address: Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation, Floreat, WA 6014 Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009 Australia
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18
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Aroma production and fermentation performance of S. cerevisiae × S. kudriavzevii natural hybrids under cold oenological conditions. Int J Food Microbiol 2019; 297:51-59. [DOI: 10.1016/j.ijfoodmicro.2019.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 02/04/2019] [Accepted: 03/10/2019] [Indexed: 12/30/2022]
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19
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Multiple interacting QTLs affect disease challenge survival in common carp (Cyprinus carpio). Heredity (Edinb) 2019; 123:565-578. [PMID: 31036952 DOI: 10.1038/s41437-019-0224-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 03/20/2019] [Accepted: 04/12/2019] [Indexed: 11/08/2022] Open
Abstract
With the steady growth of the human population, food security becomes a prime challenge. Aquaculture is the fastest growing sector providing proteins from an animal source, but outbreaks of infectious diseases repeatedly hamper the production and further development of this sector. Breeding of disease-resistant strains is a desired sustainable solution to this problem. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus damaging production of common carp, an important food and ornamental fish. Previously, we have demonstrated successful introgression of CyHV-3 resistance from a feral strain to commercial strains. Here, we used genotyping by sequencing to identify two novel quantitative trait loci (QTLs) for disease survival that map to different linkage groups than two other QTLs that we previously identified. Effects of these four QTLs were validated and further studied in 14 families with various levels of disease resistance. CyHV-3 survival was found to be a quantitative trait conditioned by mild additive QTL effects and by intricate dominant allelic and epistatic QTL-QTL interactions. Both rare feral alleles and alleles common to feral and cultured strains contributed to survival. This and other advantages of feral alleles introgression were demonstrated. These QTLs, which affected survival of individuals within families, had no significant effect on variation in cumulative family % survival, suggesting that more between family variation remains to be explored. Unraveling the underlying genetics of survival is important for enhancing the breeding of resistant strains and our knowledge of disease resistance mechanisms.
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20
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Gorter de Vries AR, Koster CC, Weening SM, Luttik MAH, Kuijpers NGA, Geertman JMA, Pronk JT, Daran JMG. Phenotype-Independent Isolation of Interspecies Saccharomyces Hybrids by Dual-Dye Fluorescent Staining and Fluorescence-Activated Cell Sorting. Front Microbiol 2019; 10:871. [PMID: 31105669 PMCID: PMC6498416 DOI: 10.3389/fmicb.2019.00871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/04/2019] [Indexed: 11/13/2022] Open
Abstract
Interspecies hybrids of Saccharomyces species are found in a variety of industrial environments and often outperform their parental strains in industrial fermentation processes. Interspecies hybridization is therefore increasingly considered as an approach for improvement and diversification of yeast strains for industrial application. However, current hybridization methods are limited by their reliance on pre-existing or introduced selectable phenotypes. This study presents a high-throughput phenotype-independent method for isolation of interspecies Saccharomyces hybrids based on dual dye-staining and subsequent mating of two strains, followed by enrichment of double-stained hybrid cells from a mating population by fluorescence-activated cell sorting (FACS). Pilot experiments on intra-species mating of heterothallic haploid S. cerevisiae strains showed that 80% of sorted double-stained cells were hybrids. The protocol was further optimized by mating an S. cerevisiae haploid with homothallic S. eubayanus spores with complementary selectable phenotypes. In crosses without selectable phenotype, using S. cerevisiae and S. eubayanus haploids derived from laboratory as well as industrial strains, 10 to 15% of double-stained cells isolated by FACS were hybrids. When applied to rare mating, sorting of double-stained cells consistently resulted in about 600-fold enrichment of hybrid cells. Mating of dual-stained cells and FACS-based selection allows efficient enrichment of interspecies Saccharomyces hybrids within a matter of days and without requiring selectable hybrid phenotypes, both for homothallic and heterothallic strains. This strategy should accelerate the isolation of laboratory-made hybrids, facilitate research into hybrid heterosis and offer new opportunities for non-GM industrial strain improvement and diversification.
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Affiliation(s)
| | - Charlotte C Koster
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Susan M Weening
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Niels G A Kuijpers
- Global Innovation and Research, HEINEKEN Supply Chain B.V., Zoeterwoude, Netherlands
| | | | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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21
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Vasseur F, Fouqueau L, de Vienne D, Nidelet T, Violle C, Weigel D. Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana. PLoS Biol 2019; 17:e3000214. [PMID: 31017902 PMCID: PMC6481775 DOI: 10.1371/journal.pbio.3000214] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 03/21/2019] [Indexed: 12/22/2022] Open
Abstract
Heterosis describes the phenotypic superiority of hybrids over their parents in traits related to agronomic performance and fitness. Understanding and predicting nonadditive inheritance such as heterosis is crucial for evolutionary biology as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we examined a model of physiological dominance initially proposed by Sewall Wright to explain the nonadditive inheritance of traits like metabolic fluxes at the cellular level. We evaluated Wright's model for two fitness-related traits at the whole-plant level, growth rate and fruit number, using 450 hybrids derived from crosses among natural accessions of A. thaliana. We found that allometric relationships between traits constrain phenotypic variation in a nonlinear and similar manner in hybrids and accessions. These allometric relationships behave predictably, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wright's model of physiological dominance and suggest that the emergence of heterosis on plant performance is an intrinsic property of nonlinear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of phenotypic relationships for predicting heterosis of major components of crop productivity and yield.
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Affiliation(s)
- François Vasseur
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, UMR759, Montpellier, France
| | - Louise Fouqueau
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
| | - Dominique de Vienne
- GQE–Le Moulon, INRA, Univ Paris-Sud, CNRS, AgroParisTech, Univ Paris-Saclay, Gif-sur-Yvette, France
| | - Thibault Nidelet
- SPO, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Cyrille Violle
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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22
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Clergeot PH, Rode NO, Glémin S, Brandström Durling M, Ihrmark K, Olson Å. Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle: A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum. Genetics 2019; 211:963-976. [PMID: 30598467 PMCID: PMC6404244 DOI: 10.1534/genetics.118.301855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/22/2018] [Indexed: 11/18/2022] Open
Abstract
Many eukaryote species, including taxa such as fungi or algae, have a lifecycle with substantial haploid and diploid phases. A recent theoretical model predicts that such haploid-diploid lifecycles are stable over long evolutionary time scales when segregating deleterious mutations have stronger effects in homozygous diploids than in haploids and when they are partially recessive in heterozygous diploids. The model predicts that effective dominance-a measure that accounts for these two effects-should be close to 0.5 in these species. It also predicts that diploids should have higher fitness than haploids on average. However, an appropriate statistical framework to conjointly investigate these predictions is currently lacking. In this study, we derive a new quantitative genetic model to test these predictions using fitness data of two haploid parents and their diploid offspring, and genome-wide genetic distance between haploid parents. We apply this model to the root-rot basidiomycete fungus Heterobasidion parviporum-a species where the heterokaryotic (equivalent to the diploid) phase is longer than the homokaryotic (haploid) phase. We measured two fitness-related traits (mycelium growth rate and the ability to degrade wood) in both homokaryons and heterokaryons, and we used whole-genome sequencing to estimate nuclear genetic distance between parents. Possibly due to a lack of power, we did not find that deleterious mutations were recessive or more deleterious when expressed during the heterokaryotic phase. Using this model to compare effective dominance among haploid-diploid species where the relative importance of the two phases varies should help better understand the evolution of haploid-diploid life cycles.
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Affiliation(s)
- Pierre-Henri Clergeot
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Nicolas O Rode
- Centre de Biologie pour la Gestion des Populations (CBGP), Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut de Recherche pour le Développement (IRD), Montpellier SupAgro, Univ Montpellier, 34988 France
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 752 36 Sweden
- CNRS, Univ Rennes, ECOBIO (Ecosystèmes, biodiversité, évolution) - UMR 6553, F-35000 Rennes, France
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
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23
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Eberlein C, Hénault M, Fijarczyk A, Charron G, Bouvier M, Kohn LM, Anderson JB, Landry CR. Hybridization is a recurrent evolutionary stimulus in wild yeast speciation. Nat Commun 2019; 10:923. [PMID: 30804385 PMCID: PMC6389940 DOI: 10.1038/s41467-019-08809-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/31/2019] [Indexed: 01/30/2023] Open
Abstract
Hybridization can result in reproductively isolated and phenotypically distinct lineages that evolve as independent hybrid species. How frequently hybridization leads to speciation remains largely unknown. Here we examine the potential recurrence of hybrid speciation in the wild yeast Saccharomyces paradoxus in North America, which comprises two endemic lineages SpB and SpC, and an incipient hybrid species, SpC*. Using whole-genome sequences from more than 300 strains, we uncover the hybrid origin of another group, SpD, that emerged from hybridization between SpC* and one of its parental species, the widespread SpB. We show that SpD has the potential to evolve as a novel hybrid species, because it displays phenotypic novelties that include an intermediate transcriptome profile, and partial reproductive isolation with its most abundant sympatric parental species, SpB. Our findings show that repetitive cycles of divergence and hybridization quickly generate diversity and reproductive isolation, providing the raw material for speciation by hybridization. Hybridization can contribute to diversity from the genomic to the species level. Here, Eberlein, Hénault et al. investigate genomic, transcriptomic and phenotypic variation among wild lineages of the yeast Saccharomyces paradoxus and suggest that an incipient species has formed by recurrent hybridization.
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Affiliation(s)
- Chris Eberlein
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada. .,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada. .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada. .,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.
| | - Mathieu Hénault
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Anna Fijarczyk
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Guillaume Charron
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Matteo Bouvier
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Linda M Kohn
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - James B Anderson
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - Christian R Landry
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada. .,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada. .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada. .,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada. .,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC, G1V 0A6, Canada.
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24
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Fiévet JB, Nidelet T, Dillmann C, de Vienne D. Heterosis Is a Systemic Property Emerging From Non-linear Genotype-Phenotype Relationships: Evidence From in Vitro Genetics and Computer Simulations. Front Genet 2018; 9:159. [PMID: 29868111 PMCID: PMC5968397 DOI: 10.3389/fgene.2018.00159] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/17/2018] [Indexed: 11/13/2022] Open
Abstract
Heterosis, the superiority of hybrids over their parents for quantitative traits, represents a crucial issue in plant and animal breeding as well as evolutionary biology. Heterosis has given rise to countless genetic, genomic and molecular studies, but has rarely been investigated from the point of view of systems biology. We hypothesized that heterosis is an emergent property of living systems resulting from frequent concave relationships between genotypic variables and phenotypes, or between different phenotypic levels. We chose the enzyme-flux relationship as a model of the concave genotype-phenotype (GP) relationship, and showed that heterosis can be easily created in the laboratory. First, we reconstituted in vitro the upper part of glycolysis. We simulated genetic variability of enzyme activity by varying enzyme concentrations in test tubes. Mixing the content of "parental" tubes resulted in "hybrids," whose fluxes were compared to the parental fluxes. Frequent heterotic fluxes were observed, under conditions that were determined analytically and confirmed by computer simulation. Second, to test this model in a more realistic situation, we modeled the glycolysis/fermentation network in yeast by considering one input flux, glucose, and two output fluxes, glycerol and acetaldehyde. We simulated genetic variability by randomly drawing parental enzyme concentrations under various conditions, and computed the parental and hybrid fluxes using a system of differential equations. Again we found that a majority of hybrids exhibited positive heterosis for metabolic fluxes. Cases of negative heterosis were due to local convexity between certain enzyme concentrations and fluxes. In both approaches, heterosis was maximized when the parents were phenotypically close and when the distributions of parental enzyme concentrations were contrasted and constrained. These conclusions are not restricted to metabolic systems: they only depend on the concavity of the GP relationship, which is commonly observed at various levels of the phenotypic hierarchy, and could account for the pervasiveness of heterosis.
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Affiliation(s)
- Julie B Fiévet
- GQE-Le Moulon, INRA, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Sud, Gif-sur-Yvette, France
| | - Thibault Nidelet
- Sciences Pour l'Œnologie, INRA, Université de Montpellier, Montpellier, France
| | - Christine Dillmann
- GQE-Le Moulon, INRA, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Sud, Gif-sur-Yvette, France
| | - Dominique de Vienne
- GQE-Le Moulon, INRA, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Sud, Gif-sur-Yvette, France
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25
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Bar-Zvi D, Lupo O, Levy AA, Barkai N. Hybrid vigor: The best of both parents, or a genomic clash? ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Charron G, Landry CR. No evidence for extrinsic post-zygotic isolation in a wild Saccharomyces yeast system. Biol Lett 2017; 13:rsbl.2017.0197. [PMID: 28592521 DOI: 10.1098/rsbl.2017.0197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/12/2017] [Indexed: 12/12/2022] Open
Abstract
Although microorganisms account for the largest fraction of Earth's biodiversity, we know little about how their reproductive barriers evolve. Sexual microorganisms such as Saccharomyces yeasts rapidly develop strong intrinsic post-zygotic isolation, but the role of extrinsic isolation in the early speciation process remains to be investigated. We measured the growth of F1 hybrids between two incipient species of Saccharomyces paradoxus to assess the presence of extrinsic post-zygotic isolation across 32 environments. More than 80% of hybrids showed either partial dominance of the best parent or over-dominance for growth, revealing no fitness defects in F1 hybrids. Extrinsic reproductive isolation therefore likely plays little role in limiting gene flow between incipient yeast species and is not a requirement for speciation.
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Affiliation(s)
- Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, 1030 avenue de la Médecine - Université Laval, Québec, Canada G1 V 0A6
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, 1030 avenue de la Médecine - Université Laval, Québec, Canada G1 V 0A6
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27
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Swindell WR. Meta-Analysis of 29 Experiments Evaluating the Effects of Rapamycin on Life Span in the Laboratory Mouse. J Gerontol A Biol Sci Med Sci 2017; 72:1024-1032. [PMID: 27519886 DOI: 10.1093/gerona/glw153] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/12/2016] [Indexed: 12/16/2022] Open
Abstract
Rapamycin has favorable effects on aging in mice and may eventually be applied to encourage "healthy aging" in humans. This study analyzed raw data from 29 survival studies of rapamycin- and control-treated mice, with the goals of estimating summary statistics and identifying factors associated with effect size heterogeneity. Meta-analysis demonstrated significant heterogeneity across studies, with hazard ratio (HR) estimates ranging from 0.22 (95% confidence interval [CI]: 0.06-0.82) to 0.92 (95% CI: 0.65-1.28). Sex was the major factor accounting for effect size variation, and mortality was decreased more in females (HR = 0.41; 95% CI: 0.35-0.48) as compared with males (HR = 0.63; 95% CI: 0.55-0.71). Rapamycin effects were also genotype dependent, however, with stronger survivorship increases in hybrid mice (14.4%; 95% CI: 12.5-16.3%) relative to pure inbred strains (8.8%; 95% CI: 6.2-11.6%). Number needed to treat was applied as an effect size metric, which consistently identified early senescence as the age of peak treatment benefit. These results provide synthesis of existing data to support the potential translation of findings from mouse to primate species. Because rapamycin's effect on survival depends on sex and genotype, further work is justified to understand how these factors shape treatment response.
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28
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Yang J, Mezmouk S, Baumgarten A, Buckler ES, Guill KE, McMullen MD, Mumm RH, Ross-Ibarra J. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS Genet 2017; 13:e1007019. [PMID: 28953891 PMCID: PMC5633198 DOI: 10.1371/journal.pgen.1007019] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 10/09/2017] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
Deleterious 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.
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Affiliation(s)
- Jinliang Yang
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Sofiane Mezmouk
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | | | - Edward S. Buckler
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
- Institute for Genomic Diversity, Ithaca, New York, United States of America
- US Department of Agriculture–Agricultural Research Service, Ithaca, New York, United States of America
| | - Katherine E. Guill
- US Department of Agriculture, Agricultural Research Service, Columbia, Missouri, United States of America
| | - Michael D. McMullen
- US Department of Agriculture, Agricultural Research Service, Columbia, Missouri, United States of America
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Rita H. Mumm
- Department of Crop Sciences and the Illinois Plant Breeding Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Center for Population Biology and Genome Center, University of California, Davis, California, United States of America
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29
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Herbst RH, Bar-Zvi D, Reikhav S, Soifer I, Breker M, Jona G, Shimoni E, Schuldiner M, Levy AA, Barkai N. Heterosis as a consequence of regulatory incompatibility. BMC Biol 2017; 15:38. [PMID: 28494792 PMCID: PMC5426048 DOI: 10.1186/s12915-017-0373-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/11/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The merging of genomes in inter-specific hybrids can result in novel phenotypes, including increased growth rate and biomass yield, a phenomenon known as heterosis. Heterosis is typically viewed as the opposite of hybrid incompatibility. In this view, the superior performance of the hybrid is attributed to heterozygote combinations that compensate for deleterious mutations accumulating in each individual genome, or lead to new, over-dominating interactions with improved performance. Still, only fragmented knowledge is available on genes and processes contributing to heterosis. RESULTS We describe a budding yeast hybrid that grows faster than both its parents under different environments. Phenotypically, the hybrid progresses more rapidly through cell cycle checkpoints, relieves the repression of respiration in fast growing conditions, does not slow down its growth when presented with ethanol stress, and shows increased signs of DNA damage. A systematic genetic screen identified hundreds of S. cerevisiae alleles whose deletion reduced growth of the hybrid. These growth-affecting alleles were condition-dependent, and differed greatly from alleles that reduced the growth of the S. cerevisiae parent. CONCLUSIONS Our results define a budding yeast hybrid that is perturbed in multiple regulatory processes but still shows a clear growth heterosis. We propose that heterosis results from incompatibilities that perturb regulatory mechanisms, which evolved to protect cells against damage or prepare them for future challenges by limiting cell growth.
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Affiliation(s)
- Rebecca H Herbst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02114, USA
| | - Dana Bar-Zvi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sharon Reikhav
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ilya Soifer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Current affiliation: Calico Labs, South San Francisco, CA, 94080, USA
| | - Michal Breker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ghil Jona
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Avraham A Levy
- Plant and Environmental Sciences Department, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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30
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Martí-Raga M, Peltier E, Mas A, Beltran G, Marullo P. Genetic Causes of Phenotypic Adaptation to the Second Fermentation of Sparkling Wines in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2017; 7:399-412. [PMID: 27903630 PMCID: PMC5295589 DOI: 10.1534/g3.116.037283] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/14/2016] [Indexed: 01/12/2023]
Abstract
Hybridization is known to improve complex traits due to heterosis and phenotypic robustness. However, these phenomena have been rarely explained at the molecular level. Here, the genetic determinism of Saccharomyces cerevisiae fermentation performance was investigated using a QTL mapping approach on an F1-progeny population. Three main QTL were detected, with positive alleles coming from both parental strains. The heterosis effect found in the hybrid was partially explained by three loci showing pseudooverdominance and dominance effects. The molecular dissection of those QTL revealed that the adaptation to second fermentation is related to pH, lipid, or osmotic regulation. Our results suggest that the stressful conditions of second fermentation have driven the selection of rare genetic variants adapted to maintain yeast cell homeostasis and, in particular, to low pH conditions.
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Affiliation(s)
- Maria Martí-Raga
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- Unité de recherche OEnologie, EA 4577, ISVV, Université Bordeaux, 33882 Villenave d'Ornon, France
| | - Emilien Peltier
- Unité de recherche OEnologie, EA 4577, ISVV, Université Bordeaux, 33882 Villenave d'Ornon, France
- Biolaffort, 33100 Bordeaux, France
| | - Albert Mas
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Gemma Beltran
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Philippe Marullo
- Unité de recherche OEnologie, EA 4577, ISVV, Université Bordeaux, 33882 Villenave d'Ornon, France
- Biolaffort, 33100 Bordeaux, France
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31
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Bernardes JP, Stelkens RB, Greig D. Heterosis in hybrids within and between yeast species. J Evol Biol 2017; 30:538-548. [PMID: 27933674 DOI: 10.1111/jeb.13023] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/14/2016] [Accepted: 11/28/2016] [Indexed: 12/28/2022]
Abstract
The performance of hybrids relative to their parents is an important factor in speciation research. We measured the growth of 46 Saccharomyces yeast F1 interspecific and intraspecific hybrids, relative to the growth of each of their parents, in pairwise competition assays. We found that the growth of a hybrid relative to the average of its parents, a measure of mid-parent heterosis, correlated with the difference in parental growth relative to their hybrid, a measure of phenotypic divergence, which is consistent with simple complementation of low fitness alleles in one parent by high fitness alleles in the other. Interspecific hybrids showed stronger heterosis than intraspecific hybrids. To manipulate parental phenotypic divergence independently of genotype, we also measured the competitive growth of a single interspecific hybrid relative to its parents in 12 different environments. In these assays, we not only identified a strong relationship between parental phenotypic divergence and mid-parent heterosis as before, but, more tentatively, a weak relationship between phenotypic divergence and best-parent heterosis, suggesting that complementation of deleterious mutations was not the sole cause of interspecific heterosis. Our results show that mating between different species can be beneficial, and demonstrate that competition assays between parents and offspring are a useful way to study the evolutionary consequences of hybridization.
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Affiliation(s)
- J P Bernardes
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - R B Stelkens
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - D Greig
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,The Galton Laboratory, Department of Genetics, Evolution, and Environment, University College London, London, UK
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32
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Yeast Population Genomics Goes Wild: The Case of Saccharomyces paradoxus. POPULATION GENOMICS: MICROORGANISMS 2017. [DOI: 10.1007/13836_2017_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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33
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Krogerus K, Magalhães F, Vidgren V, Gibson B. Novel brewing yeast hybrids: creation and application. Appl Microbiol Biotechnol 2016; 101:65-78. [PMID: 27885413 PMCID: PMC5203825 DOI: 10.1007/s00253-016-8007-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 11/29/2022]
Abstract
The natural interspecies Saccharomyces cerevisiae × Saccharomyces eubayanus hybrid yeast is responsible for global lager beer production and is one of the most important industrial microorganisms. Its success in the lager brewing environment is due to a combination of traits not commonly found in pure yeast species, principally low-temperature tolerance, and maltotriose utilization. Parental transgression is typical of hybrid organisms and has been exploited previously for, e.g., the production of wine yeast with beneficial properties. The parental strain S. eubayanus has only been discovered recently and newly created lager yeast strains have not yet been applied industrially. A number of reports attest to the feasibility of this approach and artificially created hybrids are likely to have a significant impact on the future of lager brewing. De novo S. cerevisiae × S. eubayanus hybrids outperform their parent strains in a number of respects, including, but not restricted to, fermentation rate, sugar utilization, stress tolerance, and aroma formation. Hybrid genome function and stability, as well as different techniques for generating hybrids and their relative merits are discussed. Hybridization not only offers the possibility of generating novel non-GM brewing yeast strains with unique properties, but is expected to aid in unraveling the complex evolutionary history of industrial lager yeast.
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Affiliation(s)
- Kristoffer Krogerus
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, 02044, Espoo, Finland. .,Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, Aalto, P.O. Box 16100, Espoo, 00076, Finland.
| | - Frederico Magalhães
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, 02044, Espoo, Finland.,Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, Aalto, P.O. Box 16100, Espoo, 00076, Finland
| | - Virve Vidgren
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, 02044, Espoo, Finland
| | - Brian Gibson
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, 02044, Espoo, Finland
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34
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Hallin J, Märtens K, Young AI, Zackrisson M, Salinas F, Parts L, Warringer J, Liti G. Powerful decomposition of complex traits in a diploid model. Nat Commun 2016; 7:13311. [PMID: 27804950 PMCID: PMC5097135 DOI: 10.1038/ncomms13311] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 09/21/2016] [Indexed: 01/20/2023] Open
Abstract
Explaining trait differences between individuals is a core and challenging aim of life sciences. Here, we introduce a powerful framework for complete decomposition of trait variation into its underlying genetic causes in diploid model organisms. We sequence and systematically pair the recombinant gametes of two intercrossed natural genomes into an array of diploid hybrids with fully assembled and phased genomes, termed Phased Outbred Lines (POLs). We demonstrate the capacity of this approach by partitioning fitness traits of 6,642 Saccharomyces cerevisiae POLs across many environments, achieving near complete trait heritability and precisely estimating additive (73%), dominance (10%), second (7%) and third (1.7%) order epistasis components. We map quantitative trait loci (QTLs) and find nonadditive QTLs to outnumber (3:1) additive loci, dominant contributions to heterosis to outnumber overdominant, and extensive pleiotropy. The POL framework offers the most complete decomposition of diploid traits to date and can be adapted to most model organisms.
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Affiliation(s)
- Johan Hallin
- Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France
| | - Kaspar Märtens
- Institute of Computer Science, University of Tartu, 50090 Tartu, Estonia
| | - Alexander I. Young
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Martin Zackrisson
- Department of Chemistry and Molecular Biology, Gothenburg University, 405 30 Gothenburg, Sweden
| | - Francisco Salinas
- Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France
| | - Leopold Parts
- Institute of Computer Science, University of Tartu, 50090 Tartu, Estonia
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Hinxton, UK
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, Gothenburg University, 405 30 Gothenburg, Sweden
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Gianni Liti
- Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France
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35
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Krogerus K, Arvas M, De Chiara M, Magalhães F, Mattinen L, Oja M, Vidgren V, Yue JX, Liti G, Gibson B. Ploidy influences the functional attributes of de novo lager yeast hybrids. Appl Microbiol Biotechnol 2016; 100:7203-22. [PMID: 27183995 PMCID: PMC4947488 DOI: 10.1007/s00253-016-7588-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/03/2016] [Accepted: 04/24/2016] [Indexed: 12/25/2022]
Abstract
The genomes of hybrid organisms, such as lager yeast (Saccharomyces cerevisiae × Saccharomyces eubayanus), contain orthologous genes, the functionality and effect of which may differ depending on their origin and copy number. How the parental subgenomes in lager yeast contribute to important phenotypic traits such as fermentation performance, aroma production, and stress tolerance remains poorly understood. Here, three de novo lager yeast hybrids with different ploidy levels (allodiploid, allotriploid, and allotetraploid) were generated through hybridization techniques without genetic modification. The hybrids were characterized in fermentations of both high gravity wort (15 °P) and very high gravity wort (25 °P), which were monitored for aroma compound and sugar concentrations. The hybrid strains with higher DNA content performed better during fermentation and produced higher concentrations of flavor-active esters in both worts. The hybrid strains also outperformed both the parent strains. Genome sequencing revealed that several genes related to the formation of flavor-active esters (ATF1, ATF2¸ EHT1, EEB1, and BAT1) were present in higher copy numbers in the higher ploidy hybrid strains. A direct relationship between gene copy number and transcript level was also observed. The measured ester concentrations and transcript levels also suggest that the functionality of the S. cerevisiae- and S. eubayanus-derived gene products differs. The results contribute to our understanding of the complex molecular mechanisms that determine phenotypes in lager yeast hybrids and are expected to facilitate targeted strain development through interspecific hybridization.
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Affiliation(s)
- Kristoffer Krogerus
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland.
- Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, Aalto, P.O. Box 16100, FI-00076, Espoo, Finland.
| | - Mikko Arvas
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
| | - Matteo De Chiara
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, 06107, Nice, France
| | - Frederico Magalhães
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
- Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, Aalto, P.O. Box 16100, FI-00076, Espoo, Finland
| | - Laura Mattinen
- ValiRx Finland Oy, Kiviharjuntie 8, FI-90220, Oulu, Finland
| | - Merja Oja
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
| | - Virve Vidgren
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
| | - Jia-Xing Yue
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, 06107, Nice, France
| | - Gianni Liti
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, 06107, Nice, France
| | - Brian Gibson
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
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36
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Shapira R, David L. Genes with a Combination of Over-Dominant and Epistatic Effects Underlie Heterosis in Growth of Saccharomyces cerevisiae at High Temperature. Front Genet 2016; 7:72. [PMID: 27200081 PMCID: PMC4854886 DOI: 10.3389/fgene.2016.00072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/15/2016] [Indexed: 11/21/2022] Open
Abstract
Heterosis describes a phenotypic phenomenon of hybrid superiority over its homozygous parents. It is a genetically intriguing phenomenon with great importance for food production. Also called hybrid-vigor, heterosis is created by non-additive effects of genes in a heterozygous hybrid made by crossing two distinct homozygous parents. Few models have been proposed to explain how the combination of parental genes creates an exceptional hybrid performance. Over-dominant mode of inheritance is an attractive model since a single gene can potentially create the heterotic effect, but only a few such loci have been identified. To a collection of 120 hybrids, made by crossing 16 divergent Saccharomyces cerevisiae yeast strains, we applied a method for mapping heterozygous loci that non-additively contribute to heterotic growth at 37°. Among 803 candidate loci that were mapped, five were tested for their heterotic effect by analyzing backcrosses and F2 populations in a specific hybrid background. Consistently with the many mapped loci, specific analyses confirmed the minor heterotic effect of the tested candidate loci. Allele-replacement analyses of one gene, AEP3, further supported its heterotic effect. In addition to over-dominant effects, the contribution of epistasis to heterosis was evident from F2 population and allele-replacement analyses. Pairs of over-dominant genes contributed synergistically to heterosis. We show that minor over-dominant effects of multiple genes can combine to condition heterosis, similarly to loci affecting other quantitative traits. Furthermore, by finding of epistatic interactions between loci that each of them individually has an over-dominant effect on heterosis, we demonstrate how hybrid advantage could benefit from a synergistic combination of two interaction types (over-dominant and synergistic epistatic). Thus, by portraying the underlying genetic complexity, these findings advance our understanding of heterosis.
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Affiliation(s)
- Rachel Shapira
- Department of Animal Sciences, R. H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem Rehovot, Israel
| | - Lior David
- Department of Animal Sciences, R. H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem Rehovot, Israel
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Laiba E, Glikaite I, Levy Y, Pasternak Z, Fridman E. Genome scan for nonadditive heterotic trait loci reveals mainly underdominant effects in Saccharomyces cerevisiae. Genome 2016; 59:231-42. [PMID: 26967146 DOI: 10.1139/gen-2015-0127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The overdominant model of heterosis explains the superior phenotype of hybrids by synergistic allelic interaction within heterozygous loci. To map such genetic variation in yeast, we used a population doubling time dataset of Saccharomyces cerevisiae 16 × 16 diallel and searched for major contributing heterotic trait loci (HTL). Heterosis was observed for the majority of hybrids, as they surpassed their best parent growth rate. However, most of the local heterozygous loci identified by genome scan were surprisingly underdominant, i.e., reduced growth. We speculated that in these loci adverse effects on growth resulted from incompatible allelic interactions. To test this assumption, we eliminated these allelic interactions by creating hybrids with local hemizygosity for the underdominant HTLs, as well as for control random loci. Growth of hybrids was indeed elevated for most hemizygous to HTL genes but not for control genes, hence validating the results of our genome scan. Assessing the consequences of local heterozygosity by reciprocal hemizygosity and allele replacement assays revealed the influence of genetic background on the underdominant effects of HTLs. Overall, this genome-wide study on a multi-parental hybrid population provides a strong argument against single gene overdominance as a major contributor to heterosis, and favors the dominance complementation model.
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Affiliation(s)
- Efrat Laiba
- b Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet-Dagan, P.O. Box 6, 50250, Israel
| | - Ilana Glikaite
- a The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Yael Levy
- b Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet-Dagan, P.O. Box 6, 50250, Israel
| | - Zohar Pasternak
- c Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Eyal Fridman
- b Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet-Dagan, P.O. Box 6, 50250, Israel
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Blein-Nicolas M, Albertin W, da Silva T, Valot B, Balliau T, Masneuf-Pomarède I, Bely M, Marullo P, Sicard D, Dillmann C, de Vienne D, Zivy M. A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast. Mol Cell Proteomics 2015; 14:2056-71. [PMID: 25971257 DOI: 10.1074/mcp.m115.048058] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Indexed: 11/06/2022] Open
Abstract
Heterosis is a universal phenomenon that has major implications in evolution and is of tremendous agro-economic value. To study the molecular manifestations of heterosis and to find factors that maximize its strength, we implemented a large-scale proteomic experiment in yeast. We analyzed the inheritance of 1,396 proteins in 55 inter- and intraspecific hybrids obtained from Saccharomyces cerevisiae and S. uvarum that were grown in grape juice at two temperatures. We showed that the proportion of heterotic proteins was highly variable depending on the parental strain and on the temperature considered. For intraspecific hybrids, this proportion was higher at nonoptimal temperature. Unexpectedly, heterosis for protein abundance was strongly biased toward positive values in interspecific hybrids but not in intraspecific hybrids. Computer modeling showed that this observation could be accounted for by assuming concave relationships between protein abundances and their controlling factors, in line with the metabolic model of heterosis. These results point to nonlinear processes that could play a central role in heterosis.
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Affiliation(s)
- Mélisande Blein-Nicolas
- From the INRA, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France
| | - Warren Albertin
- CNRS, UMR 0320/UMR 8120, Génétique Végétale, F-91190 Gif-sur-Yvette, France; Université Bordeaux, Unité de Recherche Œnologie, EA 4577, ISVV, 210 chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Telma da Silva
- From the INRA, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France; Ariana Pharmaceuticals, 28 rue du Docteur Finlay, 75015 Paris, France
| | - Benoît Valot
- CNRS, Université de Franche-Comté, UMR 6249 Chrono-Environnement, F-25000, Besançon, France
| | - Thierry Balliau
- From the INRA, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France
| | - Isabelle Masneuf-Pomarède
- Université Bordeaux, Unité de Recherche Œnologie, EA 4577, ISVV, 210 chemin de Leysotte, 33140 Villenave d'Ornon, France; Bordeaux Sciences Agro, Gradignan, France
| | - Marina Bely
- Université Bordeaux, Unité de Recherche Œnologie, EA 4577, ISVV, 210 chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Philippe Marullo
- Université Bordeaux, Unité de Recherche Œnologie, EA 4577, ISVV, 210 chemin de Leysotte, 33140 Villenave d'Ornon, France; BIOLAFFORT, F-33034 Bordeaux, France
| | - Delphine Sicard
- Univ Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France; INRA, UMR1083, 2 Place Viala, F-34060 Montpellier, France
| | - Christine Dillmann
- Univ Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France
| | - Dominique de Vienne
- Univ Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France
| | - Michel Zivy
- CNRS, PAPPSO, UMR 0320/UMR 8120 Génétique Végétale, F-91190, Gif-sur-Yvette, France
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da Silva T, Albertin W, Dillmann C, Bely M, la Guerche S, Giraud C, Huet S, Sicard D, Masneuf-Pomarede I, de Vienne D, Marullo P. Hybridization within Saccharomyces Genus Results in Homoeostasis and Phenotypic Novelty in Winemaking Conditions. PLoS One 2015; 10:e0123834. [PMID: 25946464 PMCID: PMC4422614 DOI: 10.1371/journal.pone.0123834] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/21/2015] [Indexed: 11/18/2022] Open
Abstract
Despite its biotechnological interest, hybridization, which can result in hybrid vigor, has not commonly been studied or exploited in the yeast genus. From a diallel design including 55 intra- and interspecific hybrids between Saccharomyces cerevisiae and S. uvarum grown at two temperatures in enological conditions, we analyzed as many as 35 fermentation traits with original statistical and modeling tools. We first showed that, depending on the types of trait--kinetics parameters, life-history traits, enological parameters and aromas -, the sources of variation (strain, temperature and strain * temperature effects) differed in a large extent. Then we compared globally three groups of hybrids and their parents at two growth temperatures: intraspecific hybrids S. cerevisiae * S. cerevisiae, intraspecific hybrids S. uvarum * S. uvarum and interspecific hybrids S. cerevisiae * S. uvarum. We found that hybridization could generate multi-trait phenotypes with improved oenological performances and better homeostasis with respect to temperature. These results could explain why interspecific hybridization is so common in natural and domesticated yeast, and open the way to applications for wine-making.
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Affiliation(s)
- Telma da Silva
- INRA, UMR 0320 / UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
| | - Warren Albertin
- ENSCBP—Bordeaux INP, Pessac, France
- Université de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
| | - Christine Dillmann
- Université Paris-Sud, UMR 0320 / UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
| | - Marina Bely
- Université de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
| | | | | | | | - Delphine Sicard
- Université Paris-Sud, UMR 0320 / UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
| | - Isabelle Masneuf-Pomarede
- Université de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
- Bordeaux Sciences Agro, Gradignan, France
| | - Dominique de Vienne
- Université Paris-Sud, UMR 0320 / UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
| | - Philippe Marullo
- Université de Bordeaux, ISVV, EA 4577, Unité de recherche Œnologie, Villenave d'Ornon, France
- Biolaffort, Bordeaux, France
- * E-mail:
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Snoek T, Picca Nicolino M, Van den Bremt S, Mertens S, Saels V, Verplaetse A, Steensels J, Verstrepen KJ. Large-scale robot-assisted genome shuffling yields industrial Saccharomyces cerevisiae yeasts with increased ethanol tolerance. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:32. [PMID: 25759747 PMCID: PMC4354739 DOI: 10.1186/s13068-015-0216-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 01/29/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND During the final phases of bioethanol fermentation, yeast cells face high ethanol concentrations. This stress results in slower or arrested fermentations and limits ethanol production. Novel Saccharomyces cerevisiae strains with superior ethanol tolerance may therefore allow increased yield and efficiency. Genome shuffling has emerged as a powerful approach to rapidly enhance complex traits including ethanol tolerance, yet previous efforts have mostly relied on a mutagenized pool of a single strain, which can potentially limit the effectiveness. Here, we explore novel robot-assisted strategies that allow to shuffle the genomes of multiple parental yeasts on an unprecedented scale. RESULTS Screening of 318 different yeasts for ethanol accumulation, sporulation efficiency, and genetic relatedness yielded eight heterothallic strains that served as parents for genome shuffling. In a first approach, the parental strains were subjected to multiple consecutive rounds of random genome shuffling with different selection methods, yielding several hybrids that showed increased ethanol tolerance. Interestingly, on average, hybrids from the first generation (F1) showed higher ethanol production than hybrids from the third generation (F3). In a second approach, we applied several successive rounds of robot-assisted targeted genome shuffling, yielding more than 3,000 targeted crosses. Hybrids selected for ethanol tolerance showed increased ethanol tolerance and production as compared to unselected hybrids, and F1 hybrids were on average superior to F3 hybrids. In total, 135 individual F1 and F3 hybrids were tested in small-scale very high gravity fermentations. Eight hybrids demonstrated superior fermentation performance over the commercial biofuel strain Ethanol Red, showing a 2 to 7% increase in maximal ethanol accumulation. In an 8-l pilot-scale test, the best-performing hybrid fermented medium containing 32% (w/v) glucose to dryness, yielding 18.7% (v/v) ethanol with a productivity of 0.90 g ethanol/l/h and a yield of 0.45 g ethanol/g glucose. CONCLUSIONS We report the use of several different large-scale genome shuffling strategies to obtain novel hybrids with increased ethanol tolerance and fermentation capacity. Several of the novel hybrids show best-parent heterosis and outperform the commonly used bioethanol strain Ethanol Red, making them interesting candidate strains for industrial production.
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Affiliation(s)
- Tim Snoek
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Martina Picca Nicolino
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Stefanie Van den Bremt
- />Laboratory of Enzyme, Fermentation and Brewing Technology, KU Leuven technologiecampus Ghent, Gebroeders De Smetstraat 1, 9000 Ghent, Belgium
| | - Stijn Mertens
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Veerle Saels
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Alex Verplaetse
- />Laboratory of Enzyme, Fermentation and Brewing Technology, KU Leuven technologiecampus Ghent, Gebroeders De Smetstraat 1, 9000 Ghent, Belgium
| | - Jan Steensels
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J Verstrepen
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
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Stelkens RB, Brockhurst MA, Hurst GDD, Miller EL, Greig D. The effect of hybrid transgression on environmental tolerance in experimental yeast crosses. J Evol Biol 2014; 27:2507-19. [PMID: 25262771 DOI: 10.1111/jeb.12494] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/22/2014] [Accepted: 09/01/2014] [Indexed: 01/29/2023]
Abstract
Evidence is rapidly accumulating that hybridization generates adaptive variation. Transgressive segregation in hybrids could promote the colonization of new environments. Here, we use an assay to select hybrid genotypes that can proliferate in environmental conditions beyond the conditions tolerated by their parents, and we directly compete them against parental genotypes in habitats across environmental clines. We made 45 different hybrid swarms by crossing yeast strains (both Saccharomyces cerevisiae and S. paradoxus) with different genetic and phenotypic divergence. We compared the ability of hybrids and parents to colonize seven types of increasingly extreme environmental clines, representing both natural and novel challenges (mimicking pollution events). We found that a significant majority of hybrids had greater environmental ranges compared to the average of both their parents' ranges (mid-parent transgression), but only a minority of hybrids had ranges exceeding their best parent (best-parent transgression). Transgression was affected by the specific strains involved in the cross and by the test environment. Genetic and phenotypic crossing distance predicted the extent of transgression in only two of the seven environments. We isolated a set of potentially transgressive hybrids selected at the extreme ends of the clines and found that many could directly outcompete their parents across whole clines and were between 1.5- and 3-fold fitter on average. Saccharomyces yeast is a good model for quantitative and replicable experimental speciation studies, which may be useful in a world where hybridization is becoming increasingly common due to the relocation of plants and animals by humans.
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Affiliation(s)
- R B Stelkens
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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