High-throughput measurement of fibroblast rhythms reveals genetic heritability of circadian phenotypes in diversity outbred mice and their founder strains

AbstractCircadian variability is driven by genetics and Diversity Outbred (DO) mice is a powerful tool for examining the genetics of complex traits because their high genetic and phenotypic diversity compared to conventional mouse crosses. The DO population combines the genetic diversity of eight founder strains including five common inbred and three wild-derived strains. In DO mice and their founders, we established a high-throughput system to measure cellular rhythms using in vitro preparations of skin fibroblasts. Among the founders, we observed strong heritability for rhythm period, robustness, phase and amplitude. We also found significant sex and strain differences for these rhythms. Extreme differences in period for molecular and behavioral rhythms were found between the inbred A/J strain and the wild-derived CAST/EiJ strain, where A/J had the longest period and CAST/EiJ had the shortest. In addition, we measured cellular rhythms in 329 DO mice, which displayed far greater phenotypic variability than the founders—80% of founders compared to only 25% of DO mice had periods of ~ 24 h. Collectively, our findings demonstrate that genetic diversity contributes to phenotypic variability in circadian rhythms, and high-throughput characterization of fibroblast rhythms in DO mice is a tractable system for examining the genetics of circadian traits.

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High-throughput sequencing analysis reveals the genetic diversity of different regions of the murine norovirus genome during in vitro replication

Archives of Virology ◽

10.1007/s00705-016-3179-y ◽

2016 ◽

Vol 162 (4) ◽

pp. 1019-1023 ◽

Cited By ~ 2

Author(s):

Axel Mauroy ◽

Bernard Taminiau ◽

Carine Nezer ◽

Elsa Ghurburrun ◽

Denis Baurain ◽

...

Keyword(s):

Genetic Diversity ◽

High Throughput ◽

High Throughput Sequencing ◽

Sequencing Analysis ◽

Murine Norovirus ◽

In Vitro Replication

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HUMAN ADENOVIRUS TYPE 4 COMPRISES TWO MAJOR PHYLOGROUPS WITH DISTINCT REPLICATIVE FITNESS AND VIRULENCE PHENOTYPES

10.1101/2020.12.18.365858 ◽

2020 ◽

Author(s):

Camden R Bair ◽

Wei Zhang ◽

Gabriel Gonzalez ◽

Arash Kamali ◽

Daniel Stylos ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Rat Model ◽

Phenotypic Diversity ◽

Human Adenovirus ◽

Adenovirus Type ◽

Polymorphism Analysis ◽

Cotton Rat ◽

Replicative Fitness

Human adenovirus type 4 (HAdV-E4) is the only type (and serotype) classified within species Human mastadenovirus E that has been isolated from a human host to the present. Recent phylogenetic analysis of whole genome sequences of strains representing the spectrum of intratypic genetic diversity described to date identified two major evolutionary lineages designated phylogroups (PG) I, and II, and validated the early clustering of HAdV-E4 genomic variants into two major groups by low resolution restriction fragment length polymorphism analysis. In this study we expanded our original analysis of intra- and inter-PG genetic variability, and used a panel of viruses representative of the spectrum of genetic diversity described for HAdV-E4 to examine the magnitude of inter- and intra-PG phenotypic diversity using an array of cell-based assays and a cotton rat model of HAdV respiratory infection. Our proteotyping of HAdV-E strains using concatenated protein sequences in selected coding regions including E1A, E1B-19K and -55K, DNA polymerase, L4-100K, various E3 proteins, and E4-34K confirmed that the two clades encode distinct variants/proteotypes at most of these loci. Our in vitro and in vivo studies demonstrated that PG I and PG II differ in their growth, spread, and cell killing phenotypes in cell culture and in their pulmonary pathogenic phenotypes. Surprisingly, the differences in replicative fitness documented in vitro between PGs did not correlate with the differences in virulence observed in the cotton rat model. This body of work is the first reporting phenotypic correlates of naturally occurring intratypic genetic variability for HAdV-E4.

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Dissection of Allelic Variation Underlying Floral and Fruit Traits in Flare Tree Peony (Paeonia rockii) Using Association Mapping

Frontiers in Genetics ◽

10.3389/fgene.2021.664814 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xin Guo ◽

Chunyan He ◽

Fangyun Cheng ◽

Yuan Zhong ◽

Xinyun Cheng ◽

...

Keyword(s):

Genetic Diversity ◽

Association Analysis ◽

Complex Traits ◽

Allelic Variation ◽

Phenotypic Diversity ◽

Woody Species ◽

Fruit Traits ◽

Tree Peony ◽

Single Marker ◽

Paeonia Rockii

Allelic variation in floral quantitative traits, including the elements of flowers and fruits, is caused by extremely complex regulatory processes. In the genetic improvement of flare tree peony (Paeonia rockii), a unique ornamental and edible oil woody species in the genus Paeonia, a better understanding of the genetic composition of these complex traits related to flowers and fruits is needed. Therefore, we investigated the genetic diversity and population structure of 160 P. rockii accessions and conducted single-marker association analysis for 19 quantitative flower and fruit traits using 81 EST-SSR markers. The results showed that the population had a high phenotypic diversity (coefficients of variation, 11.87–110.64%) and a high level of genetic diversity (mean number of alleles, NA = 6.09). These accessions were divided into three subgroups by STRUCTURE analysis and a neighbor-joining tree. Furthermore, we also found a low level of linkage disequilibrium between these EST-SSRs and, by single-marker association analysis, identified 134 significant associations, including four flower traits with 11 EST-SSRs and 10 fruit traits with 32 EST-SSRs. Finally, based on the sequence alignment of the associated markers, P280, PS2, PS12, PS27, PS118, PS131, and PS145 may be considered potential loci to increase the yield of flare tree peony. These results laid the foundation for further analysis of the genetic structure of some key traits in P. rockii and had an obvious potential application value in marker-assisted selection breeding.

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Exploiting High-Throughput Indoor Phenotyping to Characterize the Founders of a Structured B. napus Breeding Population

Frontiers in Plant Science ◽

10.3389/fpls.2021.780250 ◽

2022 ◽

Vol 12 ◽

Author(s):

Jana Ebersbach ◽

Nazifa Azam Khan ◽

Ian McQuillan ◽

Erin E. Higgins ◽

Kyla Horner ◽

...

Keyword(s):

Machine Learning ◽

Image Processing ◽

Drought Stress ◽

High Throughput ◽

Complex Traits ◽

Phenotypic Diversity ◽

Crop Improvement ◽

Breeding Population ◽

Supervised Machine Learning ◽

Oilseed Crop

Phenotyping is considered a significant bottleneck impeding fast and efficient crop improvement. Similar to many crops, Brassica napus, an internationally important oilseed crop, suffers from low genetic diversity, and will require exploitation of diverse genetic resources to develop locally adapted, high yielding and stress resistant cultivars. A pilot study was completed to assess the feasibility of using indoor high-throughput phenotyping (HTP), semi-automated image processing, and machine learning to capture the phenotypic diversity of agronomically important traits in a diverse B. napus breeding population, SKBnNAM, introduced here for the first time. The experiment comprised 50 spring-type B. napus lines, grown and phenotyped in six replicates under two treatment conditions (control and drought) over 38 days in a LemnaTec Scanalyzer 3D facility. Growth traits including plant height, width, projected leaf area, and estimated biovolume were extracted and derived through processing of RGB and NIR images. Anthesis was automatically and accurately scored (97% accuracy) and the number of flowers per plant and day was approximated alongside relevant canopy traits (width, angle). Further, supervised machine learning was used to predict the total number of raceme branches from flower attributes with 91% accuracy (linear regression and Huber regression algorithms) and to identify mild drought stress, a complex trait which typically has to be empirically scored (0.85 area under the receiver operating characteristic curve, random forest classifier algorithm). The study demonstrates the potential of HTP, image processing and computer vision for effective characterization of agronomic trait diversity in B. napus, although limitations of the platform did create significant variation that limited the utility of the data. However, the results underscore the value of machine learning for phenotyping studies, particularly for complex traits such as drought stress resistance.

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Genetic and phenotypic analysis of Tunisian Theileria annulata clones

Parasitology ◽

10.1017/s0031182002002810 ◽

2003 ◽

Vol 126 (3) ◽

pp. 241-252 ◽

Cited By ~ 9

Author(s):

L. H. TAYLOR ◽

F. KATZER ◽

B. R. SHIELS ◽

S. C. WELBURN

Keyword(s):

Genetic Diversity ◽

Growth Rates ◽

Parasite Species ◽

Phenotypic Diversity ◽

Theileria Annulata ◽

Raw Material ◽

Phenotypic Traits ◽

Phenotypic Analysis ◽

Host Interactions

Many parasite species are known to show high levels of genetic diversity, yet the consequences of this diversity for host–parasite interactions are not well understood. Variation in phenotypic traits such as growth rates and the ability to form transmission stages are raw material for natural and artificial selection to act upon with consequences for the evolution of the parasite species and disease control. In order to study genetic and phenotypic diversity amongst Theileria annulata parasites, a collection of 52 parasite clones was generated from cattle isolates and tick material recently collected in Tunisia. Genetic diversity was assessed using PCR-RFLP and monoclonal antibody markers, and genetically distinct clones selected for further study. Clones varied significantly in their growth rates in culture at 37 °C, their viability after a period of culture at 41 °C and their differentiation rates into transmission stages after culturing at 41 °C. The viability of a clone after culturing at 41 °C could not be predicted from its growth rate at 37 °C, but across clones, differentiation rates were positively correlated with growth rates at 37 °C. All 3 in vitro measures are likely to have relevance to parasite–host interactions in animals with clinical theileriosis, and should be acted on by within-host and between-host selection.

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Aggressiveness and Fungicide Sensitivity of Alternaria dauci from Cultivated Carrot

Plant Disease ◽

10.1094/pdis-94-4-0405 ◽

2010 ◽

Vol 94 (4) ◽

pp. 405-412 ◽

Cited By ~ 11

Author(s):

P. M. Rogers ◽

W. R. Stevenson

Keyword(s):

Genetic Diversity ◽

Disease Susceptibility ◽

Phenotypic Diversity ◽

Fungicide Sensitivity ◽

Northeastern North America ◽

Alternaria Leaf Blight ◽

Leaf Chlorosis ◽

Alternaria Dauci ◽

In Vitro Response

Isolates of Alternaria dauci causing Alternaria leaf blight (ALB) were collected from commercial carrot (Daucus carota var. sativus) fields in northeastern North America during 2004. Twenty-two isolates representing a range of genetic diversity were analyzed for their aggressiveness on three commercial carrot varieties (Bolero, Enterprise, and Heritage) varying in disease susceptibility as well as their in vitro response to three fungicides (azoxystrobin, chlorothalonil, and boscalid) commonly used for ALB control. Severity of leaf and petiole blight and leaf chlorosis varied among isolates and carrot varieties in each of three experiments. Visible differences in disease severity, which ranged from 10.9 to 45.1% of the leaf area affected, were apparent 16 days after inoculation. Intensity of chlorosis correlated strongly with blight severity among all isolates. Significant differences were noted among carrot varieties in response to ALB. These varieties may prove useful as differentials capable of distinguishing isolates because variety by isolate interactions were detected. Inhibition of conidial germination ranged from 0.01 to 0.37 μg/ml for azoxystrobin, 0.009 to 0.08 μg/ml for chlorothalonil, and 0.09 to 0.59 μg/ml for boscalid. On average, isolates were more sensitive to chlorothalonil than to azoxystrobin and boscalid. No significant correlation was noted between fungicide sensitivity and aggressiveness. These data provide evidence for phenotypic diversity among A. dauci isolates collected from areas of commercial carrot production.

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Genomic and Phenotypic Diversity among Ten Laboratory Isolates ofPseudomonas aeruginosaPAO1

Journal of Bacteriology ◽

10.1128/jb.00595-18 ◽

2018 ◽

Vol 201 (5) ◽

Cited By ~ 14

Author(s):

Courtney E. Chandler ◽

Alexander M. Horspool ◽

Preston J. Hill ◽

Daniel J. Wozniak ◽

Jeffrey W. Schertzer ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Phenotypic Diversity ◽

Phenotypic Variability ◽

Membrane Vesicle ◽

Genomic Analysis ◽

Extracellular Dna ◽

Content Type ◽

Phenotypic Differences

ABSTRACTPseudomonas aeruginosais an opportunistic pathogen found ubiquitously in the environment and commonly associated with airway infection in patients with cystic fibrosis.P. aeruginosastrain PAO1 is one of the most commonly used laboratory-adapted research strains and is a standard laboratory-adapted strain in multiple laboratories and strain banks worldwide. Due to potential isolate-to-isolate variability, we investigated the genomic and phenotypic diversity among 10 PAO1 strains (henceforth called sublines) obtained from multiple research laboratories and commercial sources. Genomic analysis predicted a total of 5,682 genes, with 5,434 (95.63%) being identical across all 10 strains. Phenotypic analyses revealed comparable growth phenotypes in rich media and biofilm formation profiles. Limited differences were observed in antibiotic susceptibility profiles and immunostimulatory potential, measured using heat-killed whole-cell preparations in four immortalized cell lines followed by quantification of interleukin-6 (IL-6) and IL-1β secretion. However, variability was observed in the profiles of secreted molecular products, most notably, in rhamnolipid, pyoverdine, pyocyanin,Pseudomonasquinolone signal (PQS), extracellular DNA, exopolysaccharide, and outer membrane vesicle production. Many of the observed phenotypic differences did not correlate with subline-specific genetic changes, suggesting alterations in transcriptional and translational regulation. Taken together, these results suggest that individually maintained sublines of PAO1, even when acquired from the same parent subline, are continuously undergoing microevolution during culture and storage that results in alterations in phenotype, potentially affecting the outcomes ofin vitrophenotypic analyses andin vivopathogenesis studies.IMPORTANCELaboratory-adapted strains of bacteria are used throughout the world for microbiology research. These prototype strains help keep research data consistent and comparable between laboratories. However, we have observed phenotypic variability when using different strains ofPseudomonas aeruginosaPAO1, one of the major laboratory-adopted research strains. Here, we describe the genomic and phenotypic differences among 10 PAO1 strains acquired from independent sources over 15 years to understand how individual maintenance affects strain characteristics. We observed limited genomic changes but variable phenotypic changes, which may have consequences for cross-comparison of data generated using different PAO1 strains. Our research highlights the importance of limiting practices that may promote the microevolution of model strains and calls for researchers to specify the strain origin to ensure reproducibility.

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High-throughput sleep phenotyping produces robust and heritable traits in Diversity Outbred mice and their founder strains

SLEEP ◽

10.1093/sleep/zsz278 ◽

2020 ◽

Vol 43 (5) ◽

Cited By ~ 2

Author(s):

Brendan T Keenan ◽

Raymond J Galante ◽

Jie Lian ◽

Petr Simecek ◽

Daniel M Gatti ◽

...

Keyword(s):

High Throughput ◽

Genetic Factors ◽

Wheel Running ◽

Sleep Latency ◽

Phenotypic Variability ◽

Genetic Effects ◽

Broad Sense ◽

Broad Sense Heritability ◽

Diversity Outbred ◽

High Throughput Phenotyping

Abstract Study Objectives This study describes high-throughput phenotyping strategies for sleep and circadian behavior in mice, including examinations of robustness, reliability, and heritability among Diversity Outbred (DO) mice and their eight founder strains. Methods We performed high-throughput sleep and circadian phenotyping in male mice from the DO population (n = 338) and their eight founder strains: A/J (n = 6), C57BL/6J (n = 14), 129S1/SvlmJ (n = 6), NOD/LtJ (n = 6), NZO/H1LtJ (n = 6), CAST/EiJ (n = 8), PWK/PhJ (n = 8), and WSB/EiJ (n = 6). Using infrared beam break systems, we defined sleep as at least 40 s of continuous inactivity and quantified sleep–wake amounts and bout characteristics. We developed assays to measure sleep latency in a new environment and during a modified Murine Multiple Sleep Latency Test, and estimated circadian period from wheel-running experiments. For each trait, broad-sense heritability (proportion of variability explained by all genetic factors) was derived in founder strains, while narrow-sense heritability (proportion of variability explained by additive genetic effects) was calculated in DO mice. Results Phenotypes were robust to different inactivity durations to define sleep. Differences across founder strains and moderate/high broad-sense heritability were observed for most traits. There was large phenotypic variability among DO mice, and phenotypes were reliable, although estimates of heritability were lower than in founder mice. This likely reflects important nonadditive genetic effects. Conclusions A high-throughput phenotyping strategy in mice, based primarily on monitoring of activity patterns, provides reliable and heritable estimates of sleep and circadian traits. This approach is suitable for discovery analyses in DO mice, where genetic factors explain some proportion of phenotypic variation.

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