scholarly journals Inbred or Outbred? Genetic diversity in laboratory rodent colonies

2017 ◽  
Author(s):  
Thomas D. Brekke ◽  
Katherine A. Steele ◽  
John F. Mulley
Keyword(s):  
Genetic Diversity ◽  
Genetic Divergence ◽  
Genetic Basis ◽  
High Throughput Sequencing ◽  
Meriones Unguiculatus ◽  
Biological Research ◽  
Deer Mice ◽  
Replication Crisis ◽  
Genetic Crossing ◽  
Very High

ABSTRACTNon-model rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift and so may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants. Here we use high throughput sequencing to demonstrate genetic divergence in three isolated colonies of Mongolian gerbil (Meriones unguiculatus) even though they were all established recently from the same source. We also show that genetic diversity in allegedly ‘outbred’ colonies of non-model rodents (gerbils, hamsters, house mice, and deer mice) varies considerably from nearly no segregating diversity, to very high levels of polymorphism. We conclude that genetic divergence in isolated colonies may play an important role in the ‘replication crisis’. In a more positive light, divergent rodent colonies represent an opportunity to leverage genetically distinct individuals in genetic crossing experiments. In sum, awareness of the genetic diversity of an animal colony is paramount as it allows researchers to properly replicate experiments and also to capitalize on other, genetically distinct individuals to explore the genetic basis of a trait.

scholarly journals Genetic diversity of Avena strigosa Schreb. ecotypes on the basis of isoenzyme markers

2009 ◽  
Vol 15 (1) ◽  
pp. 23-28 ◽  
Author(s):  
Katarzyna Kubiak
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Avena Strigosa ◽  
Total Genetic Diversity ◽  
Geographical Regions ◽  
The World ◽  
Total Variability ◽  
The Mean ◽  
Intrapopulation Diversity ◽  
Very High

Genetic diversity ofAvena strigosaSchreb. ecotypes on the basis of isoenzyme markersGenetic diversity was analyzed in 19 ecotypes of the diploid oatA. strigosaoriginating from various geographical regions of the world. Six isoenzyme systems (AAT, ACP, EST, LAP, MDH, PX) were studied and 16 loci were identified. Only two loci (Est4andMdh2) were polymorphic. Ecotypes were characterized by the percentage of polymorphic loci (P=3.3%), the mean number of alleles per locus (A=1.04) and intrapopulation diversity (HS=0.013). Total genetic diversity (HT=0.07) and interpopulation diversity (DST=0.057) were examined as well. The value of the coefficient of gene differentiation (GST=0.821) indicated that diversity among populations was an important contributor to total variability. Genetic similarity betweenA. strigosapopulations was very high (IN=0.94). Cluster analysis did not demonstrate strongly differentiated groups among the ecotypes examined.

PSXII-2 Identification of candidate SNPs associated with high prolificacy in Romanov sheep

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 254-255
Author(s):  
Alexey V Shakhin ◽  
Arsen V Dotsev ◽  
Tatiana E Deniskova ◽  
Gottfried Brem ◽  
Natalia A Zinovieva
Keyword(s):  
Higher Education ◽  
Genetic Basis ◽  
Reference Genome ◽  
Unique Property ◽  
Candidate Snps ◽  
Merino Sheep ◽  
Sheep Breeds ◽  
Important Trait ◽  
Very High ◽  
Selection Of

Abstract Prolificacy is a very important trait in sheep. Romanov sheep, the well-known Russian sheep breed, are characterized by very high prolificacy; however, the genetic basis of this unique property of Romanov sheep is still unknown. It was reported that Ovine BMPR1B gene, located on the OAR6, is associated with prolificacy in several sheep breeds. The aim of our study was to identify candidate SNPs within BMPR1B gene, related to prolificacy. To achieve this goal, using NGS technology, we sequenced ovine BMPR1B gene in Romanov sheep (n = 6), which are characterized by high prolificacy (about 270 lambs per 100 ewes). The sequences of BMPR1B gene of Noire du Velay, Tan, Southdown and Australian Horned Merino sheep breeds as well as Asiatic mouflon (n = 1), which are characterized by significantly lower prolificacy (from 110 to 180 lambs per 100 ewes) were derived from publicly available sources and used for comparison. FST analysis performed in PLINK 1.9 program revealed 10 SNPs with values higher than 0.8. The majority of candidate SNPs under putative selection were localized in the region from 29,382,098 to 29,430,387 on OAR6 of Ovine reference genome (Oar_v3.1 (Ensembl release 98). Thus, we can suggest, that this region of the BMPR1B gene can be considered as the putative region, associated with high prolificacy of Romanov sheep. Additional studies will be needed to confirm the effect of identified candidate SNPs on prolificacy traits. The research results will be useful for artificial selection of sheep with higher prolific capacity, including the introduction of desired alleles in sheep populations using genome editing technologies. This work was supported by the Russian Ministry of Science and Higher Education No. 0445-2019-0024 and RFBR No. 20-516-56002.

scholarly journals GENETIC DIVERGENCE AND MORPHO-AGRONOMIC PERFORMANCE OF JATROPHA CURCAS L. CLONES FOR SELECTION OF CLONAL VARIETIES

2016 ◽  
Vol 29 (4) ◽  
pp. 841-849
Author(s):  
ADRIANA QUEIROZ DE ALMEIDA ◽  
SIMONE ALVES SILVA ◽  
VANESSA DE OLIVEIRA ALMEIDA ◽  
DEOCLIDES RICARDO DE SOUZA ◽  
GILMARA DE MELO ARAÚJO
Keyword(s):  
Genetic Diversity ◽  
Multivariate Analysis ◽  
Plant Height ◽  
Genetic Divergence ◽  
Morphological Characterization ◽  
Stem Diameter ◽  
Agronomic Performance ◽  
And Performance ◽  
Lower Contribution ◽  
Selection Of

ABSTRACT The knowledge about genetic diversity of jatropha crop is important for genetic conservation resources and breeding of this species. The aim of this study was to evaluate the genetic diversity and performance of jatropha clones through morphological characterization to selection of clonal varieties for biofuels production. The clones were obtained through shoot cuttings from previous selection in a population of half-sibs progenies. The morphoagronomic analyses of clones was carried out at 180 days after transplantation and were evaluated plant height, stem diameter, number of primary branches and number of secondary branches, number of bunches and number of fruits per plant. Evaluating clones performance, significant results were found for the number of secondary branches. About analysis of genetic diversity, the measures of dissimilarity genetic varied from 0.62 to 13.11, this way, the UFRBPR14 and UFRBPR15 clones were more divergent. The Tocher method was efficient to verify formation of four groups. The characteristics that most contributed to the divergence among clones were branches number, height and number of bunches, and, stem diameter had lower contribution. The jatropha clones differed only in the secondary branches number and multivariate analysis showed divergence among the jatropha clones with formation of four groups. Also, branches number, plant height and number of bunches were characteristic that contributed to genetic divergence.

scholarly journals Hypertriglyceridemia, a common dyslipidemia of complex definition

2013 ◽  
pp. 220-226
Author(s):  
Chiara Trenti ◽  
Emanuele A. Negri ◽  
Ido Iori ◽  
Davide Favali
Keyword(s):  
Cardiovascular Disease ◽  
Acute Pancreatitis ◽  
Genetic Basis ◽  
Hepatic Function ◽  
Biochemical Finding ◽  
Cholesterol Levels ◽  
Severe Hypertriglyceridemia ◽  
Increased Risk ◽  
Very High ◽  
Regular Physical Exercise

Background: Hypertriglyceridemia is a common biochemical finding. Depending on the triglyceride levels it can be associated with increased risk of acute pancreatitis and of cardiovascular disease. The most severe forms have a genetic basis. Clinical case: We report a case of a 60-year-old woman with very high triglycerides (800- 3,000 mg/dL) and normal cholesterol levels. The patient is a non smoker, on hypolipemic diet, non alcoholic consumer, and on regular physical exercise. Her blood pressure is normal, BMI is 20, waist circumference is 78 cm. Thyroid, renal and hepatic function are normal. She has never had acute pancreatitis or cardiovascular disease. Discussion: The diagnostic and therapeutic management of this case is discussed. Causes of primary (genetic) and secondary hypertriglyceridemia are also reviewed, together with clinical features and management on every day practice. We focused on severe hypertriglyceridemia.

scholarly journals GENETIC DIVERSITY IN NON-OILSEED SUNFLOWER (Helianthus annuus L.) GENOTYPES / DIVERSIDAD GENETICA DE GENOTIPOS NO OLEAGINOSOS DEL GIRASOL (Helianthus annuus L.) / DIVERSITÉ GÉNÉTIQUE DANS LES GÉNOTYPES DE TOURNESOL NON-OLÉAGINEUX (Helianthus annuus L.)

Helia ◽  
2001 ◽  
Vol 24 (34) ◽  
pp. 17-24
Author(s):  
K. Manjula ◽  
H.L. Nadaf ◽  
K. Giriraj
Keyword(s):  
Genetic Diversity ◽  
Protein Content ◽  
Helianthus Annuus ◽  
Plant Height ◽  
Genetic Divergence ◽  
Oil Content ◽  
Diversité Génétique ◽  
Helianthus Annuus L ◽  
Volume Weight ◽  
Seed Characteristics

SUMMARYGenetic diversity was assessed in 46 non-oilseed sunflower genotypes for 14 characters by adopting D2 analysis. Oil content and plant height exhibited maximum contributions towards genetic divergence. The genotypes were grouped into 11 clusters. The inter-cluster D2 values ranged from 288.17 to 3972.34. The contribution of oil content towards genetic divergence in the 46 genotypes was confirmed when D2 analysis was performed for seed characteristics such as test weight, volume weight, hull content, kernel recovery, oil and protein content.

scholarly journals Genome Resources for the Ex-type of Phytophthora citricola, and well-authenticated isolates of P. hibernalis, P. nicotianae and P. syringae

2021 ◽  
Author(s):  
Subodh K. Srivastava ◽  
Leandra M. Knight ◽  
Mark K. Nakhla ◽  
Z. Gloria Abad
Keyword(s):  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Economic Losses ◽  
Biological Research ◽  
Type Specimens ◽  
High Coverage ◽  
Oxford Nanopore ◽  
Long Read ◽  
Basic And Applied Research ◽  
Diagnostic Applications

Phytophthora is one of the most important genera of plant pathogens with many members causing high economic losses world-wide. To build robust molecular identification systems, it is very important to have information from well-authenticated specimens and in preference the ex-type specimens. The reference genomes of well-authenticated specimens form a critical foundation for genetics, biological research, and diagnostic applications. In this study, we describe four draft Phytophthora genomes resources for the Ex-type of P. citricola BL34 (P0716 WPC) (118 contigs for 50 Mb), and well-authenticated specimens of P. syringae BL57G (P10330 WPC) (591 contigs for 75 Mb), P. hibernalis BL41G (P3822 WPC) (404 contigs for 84 Mb), and P. nicotianae BL162 (P6303 WPC) (3984 contigs for 108 Mb) generated with MinION long-read High-Throughput Sequencing (HTS) technology (Oxford Nanopore Technologies, ONT). Using the quality reads we assembled high coverage genomes of P. citricola with 291X coverage and 16,662 annotated genes; P. nicotianae with 205X coverage and 29,271 annotated genes; P. syringae with 76X coverage and 23,331 annotated genes, and P. hibernalis with 42X coverage and 21,762 annotated genes. With the availability of genomes sequences and its annotations, we predict that these draft genomes will be accommodating for various basic and applied research including diagnostics to protect global agriculture.

Distribution and genetic diversity of Coguvirus eburi in South African citrus and the development of a real-time RT-PCR assay for citrus-infecting coguviruses

Plant Disease ◽  
2022 ◽  
Author(s):  
Rochelle de Bruyn ◽  
Rachelle Bester ◽  
Glynnis Cook ◽  
Chanel Steyn ◽  
Johannes Hendrik Jacobus Breytenbach ◽  
...  
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Real Time ◽  
South African ◽  
High Throughput Sequencing ◽  
Rna Virus ◽  
Citrus Paradisi ◽  
Virus Elimination ◽  
Shoot Tip Grafting ◽  
Citrus Production

Citrus virus A (CiVA), a novel negative-sense single-stranded RNA virus assigned to the species Coguvirus eburi in the genus Coguvirus, was detected in South Africa with the use of high-throughput sequencing (HTS) after its initial discovery in Italy. CiVA is closely related to citrus concave gum-associated virus (CCGaV), recently assigned to the species Citrus coguvirus. Disease association with CiVA is however incomplete. CiVA was detected in grapefruit (Citrus paradisi Macf.), sweet orange (C. sinensis (L.) Osb.) and clementine (C. reticulata Blanco) in South Africa and a survey to determine the distribution, symptom association and genetic diversity was conducted in three provinces and seven citrus production regions. The virus was detected in ‘Delta’ Valencia trees in six citrus production regions and a fruit rind symptom was often observed on CiVA-positive trees. Additionally, grapefruit showing symptoms of citrus impietratura disease were positive for CiVA. This virus was primarily detected in older orchards that were established prior to the application of shoot tip grafting for virus elimination in the South African Citrus Improvement Scheme. The three viral encoded genes of CiVA isolates from each cultivar and region were sequenced to investigate sequence diversity. Genetic differences were detected between the ‘Delta’ Valencia, grapefruit and clementine samples, with greater sequence variation observed with the nucleocapsid protein (NP) compared to the RNA-dependent RNA polymerase (RdRp) and the movement protein (MP). A real-time detection assay, targeting the RdRp, was developed to simultaneously detect citrus infecting coguviruses, CiVA and CCGaV, using a dual priming reverse primer to improve PCR specificity.

scholarly journals Orthohantaviruses, Emerging Zoonotic Pathogens

Pathogens ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 775
Author(s):  
Emmanuel Kabwe ◽  
Yuriy Davidyuk ◽  
Anton Shamsutdinov ◽  
Ekaterina Garanina ◽  
Ekaterina Martynova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Point Mutations ◽  
Geographical Location ◽  
Hemorrhagic Fever ◽  
Current Data ◽  
Emerging Infections ◽  
Natural Hosts ◽  
And Migration ◽  
High Level ◽  
Very High

Orthohantaviruses give rise to the emerging infections such as of hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS) in Eurasia and the Americas, respectively. In this review we will provide a comprehensive analysis of orthohantaviruses distribution and circulation in Eurasia and address the genetic diversity and evolution of Puumala orthohantavirus (PUUV), which causes HFRS in this region. Current data indicate that the geographical location and migration of the natural hosts can lead to the orthohantaviruses genetic diversity as the rodents adapt to the new environmental conditions. The data shows that a high level of diversity characterizes the genome of orthohantaviruses, and the PUUV genome is the most divergent. The reasons for the high genome diversity are mainly caused by point mutations and reassortment, which occur in the genome segments. However, it still remains unclear whether this diversity is linked to the disease’s severity. We anticipate that the information provided in this review will be useful for optimizing and developing preventive strategies of HFRS, an emerging zoonosis with potentially very high mortality rates.

scholarly journals The genetics of morphological and behavioural island traits in deer mice

2019 ◽  
Vol 286 (1914) ◽  
pp. 20191697 ◽  
Author(s):  
Felix Baier ◽  
Hopi E. Hoekstra
Keyword(s):  
Genetic Basis ◽  
Genetic Effect ◽  
Deer Mice ◽  
Plastic Response ◽  
Common Environment ◽  
Environmental Extremes ◽  
Laboratory Colonies ◽  
Island Syndrome ◽  
Heritable Change ◽  
Plastic Responses

Animals on islands often exhibit dramatic differences in morphology and behaviour compared with mainland individuals, a phenomenon known as the ‘island syndrome’. These differences are thought to be adaptations to island environments, but the extent to which they have a genetic basis or instead represent plastic responses to environmental extremes is often unknown. Here, we revisit a classic case of island syndrome in deer mice ( Peromyscus maniculatus ) from British Columbia. We first show that Saturna Island mice and those from neighbouring islands are approximately 35% (approx. 5 g) heavier than mainland mice and diverged approximately 10 000 years ago. We then establish laboratory colonies and find that Saturna Island mice are heavier both because they are longer and have disproportionately more lean mass. These trait differences are maintained in second-generation captive-born mice raised in a common environment. In addition, island–mainland hybrids reveal a maternal genetic effect on body weight. Using behavioural testing in the laboratory, we also find that wild-caught island mice are less aggressive than mainland mice; however, laboratory-raised mice born to these founders do not differ in aggression. Together, our results reveal that these mice have different responses to the environmental conditions on islands—a heritable change in a morphological trait and a plastic response in a behavioural trait.

Genetic structure and variability in Pinusstrobus in Quebec

1994 ◽  
Vol 24 (8) ◽  
pp. 1726-1733 ◽  
Author(s):  
J. Beaulieu ◽  
J.-P. Simon
Keyword(s):  
Genetic Diversity ◽  
Statistical Tests ◽  
Natural Populations ◽  
Genetic Distances ◽  
White Pine ◽  
Eastern White Pine ◽  
Improvement Program ◽  
Bonferroni Procedure ◽  
Natural Range ◽  
Very High

The level of genetic diversity of natural populations of eastern white pine (Pinusstrobus L.) from Quebec was estimated from allozyme variants of 18 loci coding 12 enzyme systems. On average, a white pine population was polymorphic at 50.6% of loci, had 1.96 alleles and 1.22 effective alleles per locus, and observed and expected heterozygosities of 0.176 and 0.180, respectively. The level of genetic diversity was lower in the populations of the St. Lawrence lowlands than in those of western Quebec. This observation will help in guiding the selection program of the eastern white pine improvement program under way in Quebec. Genetic differentiation among sampled populations was weak and accounted for only 2% of the total diversity. The estimate of gene flow was very high, resulting in low values for genetic distances among populations. Only one locus showed a heterogeneity of allelic frequencies among populations after the Bonferroni procedure was applied for simultaneous statistical tests. A cluster analysis based on genetic distances among populations revealed that the Anticosti and Abitibi populations, located at the limit of the natural range of white pine, were similar to populations from regions that were geographically the most distant.

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