Development of retrotransposons insertion polymorphic markers and application in the genetic variation evaluation of Chinese Bama miniature pigs

Retrotransposons are genetic elements that can amplify themselves in a genome and are abundant in many eukaryotic organisms. In this study, we established some new short interspersed nuclear elements (SINE) and endogenous retroviruses (ERV) retrotransposons insertion polymorphism (RTIP) markers based on BLAT alignment tool strategy, and followed by PCR evaluation. We investigated the genetic variations among four subpopulations of Chinese Bama miniature pigs (BM), including BM in national conservation farm (BM-cov), BM inbreeding population (BM-inb) and BM closed Herd (BM-clo) in Guangxi University, and BM in the Experimental pig farm of Yangzhou University (BM-yzu). Genetic distance, polymorphism information content (PIC) and heterozygosity (He) of these markers in four of BM subpopulations were measured. Twelve SINE and twenty-eight ERV polymorphic molecular markers were identified in the four subpopulations. The BM-cov pigs represented the highest He and PIC, which indicated that BM-cov pigs maintain relatively highly genetic diversity. BM-inb pigs represented the lowest He and PIC indicating less variation and a high degree of inbreeding. Microsatellites polymorphism in four BM populations also well supported the results of these RTIP markers. In summary, retrotransposons insertion polymorphic markers could be a useful tool for population genetic variation analysis. Current SINE and ERV variation data may also provide a reference guide for the conservation and utilization of the BM miniature pig resource.

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Retraction: Development of retrotransposon insertion polymorphic markers and application in the genetic variation evaluation of Chinese Bama miniature pigs

Canadian Journal of Animal Science ◽

10.1139/cjas-2020-0039 ◽

2020 ◽

Vol 100 (2) ◽

pp. 389-389

Author(s):

Li Zhang ◽

Xiaoyan Wang ◽

Cai Chen ◽

Wei Wang ◽

Kunlun Yang ◽

...

Keyword(s):

Genetic Variation ◽

Polymorphic Markers ◽

Miniature Pigs ◽

Retrotransposon Insertion

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Long-Term Experimental Evolution in Escherichia coli. VI. Environmental Constraints on Adaptation and Divergence

Genetics ◽

10.1093/genetics/146.2.471 ◽

1997 ◽

Vol 146 (2) ◽

pp. 471-479 ◽

Cited By ~ 2

Author(s):

Michael Travisano

Keyword(s):

Escherichia Coli ◽

Genetic Variation ◽

Experimental Evolution ◽

Population Genetic ◽

Environmental Constraints ◽

Asymmetric Pattern ◽

Nutrient Environment ◽

Mean Fitness ◽

Population Genetic Variation

The effect of environment on adaptation and divergence was examined in two sets of populations of Escherichia coli selected for 1000 generations in either maltose- or glucose-limited media. Twelve replicate populations selected in maltose-limited medium improved in fitness in the selected environment, by an average of 22.5%. Statistically significant among-population genetic variation for fitness was observed during the course of the propagation, but this variation was small relative to the fitness improvement. Mean fitness in a novel nutrient environment, glucose-limited medium, improved to the same extent as in the selected environment, with no statistically significant among-population genetic variation. In contrast, 12 replicate populations previously selected for 1000 generations in glucose-limited medium showed no improvement, as a group, in fitness in maltose-limited medium and substantial genetic variation. This asymmetric pattern of correlated responses suggests that small changes in the environment can have profound effects on adaptation and divergence.

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Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

BMC Ecology and Evolution ◽

10.1186/s12862-020-01739-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Kelly B. Klingler ◽

Joshua P. Jahner ◽

Thomas L. Parchman ◽

Chris Ray ◽

Mary M. Peacock

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Sierra Nevada ◽

Spatial Genetic Structure ◽

Spatial Scales ◽

Thermal Sensitivity ◽

Genomic Variation ◽

Genome Wide ◽

A Genome ◽

American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

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Genetic variation in recombination rate in the pig

Genetics Selection Evolution ◽

10.1186/s12711-021-00643-0 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Martin Johnsson ◽

Andrew Whalen ◽

Roger Ros-Freixedes ◽

Gregor Gorjanc ◽

Ching-Yi Chen ◽

...

Keyword(s):

Genetic Variation ◽

Recombination Rate ◽

Large Scale ◽

Genome Wide Association Study ◽

Genetic Material ◽

A Genome ◽

Pig Genome ◽

Genetic Length ◽

Trait Locus ◽

Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

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A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Nature Communications ◽

10.1038/s41467-021-25158-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Omid Oftadeh ◽

Pierre Salvy ◽

Maria Masid ◽

Maxime Curvat ◽

Ljubisa Miskovic ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Expression System ◽

Biomass Composition ◽

Industrial Biotechnology ◽

Overflow Metabolism ◽

Cellular Expression ◽

A Genome ◽

Wide Range ◽

Eukaryotic Organisms ◽

Genome Scale

AbstractEukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of multiple biological networks into a single model for cell analysis and engineering. One of the most accurate models of biological systems include Expression and Thermodynamics FLux (ETFL), which efficiently integrates RNA and protein synthesis with traditional genome-scale metabolic models. However, ETFL is so far only applicable for E. coli. To adapt this model for Saccharomyces cerevisiae, we developed yETFL, in which we augmented the original formulation with additional considerations for biomass composition, the compartmentalized cellular expression system, and the energetic costs of biological processes. We demonstrated the ability of yETFL to predict maximum growth rate, essential genes, and the phenotype of overflow metabolism. We envision that the presented formulation can be extended to a wide range of eukaryotic organisms to the benefit of academic and industrial research.

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Quantitative Trait Loci for the Monoamine-Related Traits Heart Rate and Headless Behavior inDrosophila melanogaster

Genetics ◽

10.1093/genetics/157.1.283 ◽

2001 ◽

Vol 157 (1) ◽

pp. 283-294 ◽

Cited By ~ 2

Author(s):

Kristie Ashton ◽

Ana Patricia Wagoner ◽

Roland Carrillo ◽

Greg Gibson

Keyword(s):

Heart Rate ◽

Genetic Variation ◽

Recombinant Inbred Lines ◽

Model Organism ◽

Interval Mapping ◽

Activity Levels ◽

Environmental Variance ◽

Genome Wide ◽

A Genome ◽

Monoamine Receptors

AbstractDrosophila melanogaster appears to be well suited as a model organism for quantitative pharmacogenetic analysis. A genome-wide deficiency screen for haploinsufficient effects on prepupal heart rate identified nine regions of the genome that significantly reduce (five deficiencies) or increase (four deficiencies) heart rate across a range of genetic backgrounds. Candidate genes include several neurotransmitter receptor loci, particularly monoamine receptors, consistent with results of prior pharmacological manipulations of heart rate, as well as genes associated with paralytic phenotypes. Significant genetic variation is also shown to exist for a suite of four autonomic behaviors that are exhibited spontaneously upon decapitation, namely, grooming, grasping, righting, and quivering. Overall activity levels are increased by application of particular concentrations of the drugs octopamine and nicotine, but due to high environmental variance both within and among replicate vials, the significance of genetic variation among wild-type lines for response to the drugs is difficult to establish. An interval mapping design was also used to map two or three QTL for each behavioral trait in a set of recombinant inbred lines derived from the laboratory stocks Oregon-R and 2b.

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Genetic variation rs10484761 on 6p21.1 derived from a genome-wide association study is associated with gastric cancer survival in a Chinese population

Gene ◽

10.1016/j.gene.2013.11.087 ◽

2014 ◽

Vol 536 (1) ◽

pp. 59-64 ◽

Cited By ~ 10

Author(s):

Meiyun Kang ◽

Xiaojie Ding ◽

Ming Xu ◽

Haixia Zhu ◽

Sang Liu ◽

...

Keyword(s):

Gastric Cancer ◽

Genetic Variation ◽

Association Study ◽

Chinese Population ◽

Genome Wide Association Study ◽

Cancer Survival ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

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The genomics of adaptation

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2012.2322 ◽

2012 ◽

Vol 279 (1749) ◽

pp. 5024-5028 ◽

Cited By ~ 35

Author(s):

Jacek Radwan ◽

Wiesław Babik

Keyword(s):

Genetic Variation ◽

Natural Selection ◽

Royal Society ◽

Genetic Basis ◽

Genomic Data ◽

Evolutionary Change ◽

Introductory Article ◽

Technological Advances ◽

A Genome ◽

Genome Level

The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

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