scholarly journals Population Genomic Analysis of Two Endemic Schizothoracins Reveals Their Genetic Differences and Underlying Selection Associated with Altitude and Temperature

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 447
Author(s):  
Tianyan Yang ◽  
Wei Meng ◽  
Baocheng Guo
Keyword(s):  
Mixed Model ◽  
Isolation By Distance ◽  
Genomic Analysis ◽  
Principal Component ◽  
Mantel Test ◽  
Tibet Plateau ◽  
Tarim River ◽  
Genome Wide ◽  
Isolation By Environment ◽  
Kaidu River

Schizothoracins are a group of cyprinid fishes distributed throughout the Qinghai–Tibet Plateau, which can be classified in three grades: primitive, specialised and highly specialised according to adaptation ability to plateau environments. As the only specialised schizothoracins in Xinjiang, China, Diptychus maculates and Gymnodiptychus dybowskii are ideal materials for adaptive evolution research. Based on single-nucleotide polymorphism (SNP) loci detected by specific-locus amplified fragment (SLAF) technology, the genome-wide genetic diversities of these two species from nine sites in Xinjiang were evaluated. D.maculates in the Muzat River (BM) and G. dybowskii in the Kaidu River (LKG) presented the lowest genetic diversity levels, whereas D. maculates in the Kumarik River (BK) and G.dybowskii in the Kashi River (LK) were just the opposite. Cluster and principal component analysis demonstrated a distant genetic affinity between D. maculates in the Tashkurgan River (BT) and other populations. Outlier SNP loci were discovered both in D. maculates and G. dybowskii. The coalescent Bayenv and latent factor mixed model (LFMM) methods showed that a total of thirteen and eighteen SNPs in D. maculates were associated with altitude and temperature gradient, respectively. No intersection was revealed in G. dybowskii. The results indicated that D. maculates was subject to much greater divergent selection pressure. A strong signal of isolation-by-distance (IBD) was detected across D. maculates (Mantel test, rs = 0.65; p = 0.05), indicating an evident geographical isolation in the Tarim River. Isolation-by-environment (IBE) analysis implied that temperature and altitude selections were more intensive in D. maculates, with greater environmental variation resulting in weak gene flow.

scholarly journals Genome-wide SNPs of vegetable leafminer, Liriomyza sativae: insights into the recent Australian invasion

2022 ◽  
Author(s):  
Xuefen Xu ◽  
Tom L. Schmidt ◽  
Jiaxin Liang ◽  
Peter M. Ridland ◽  
Jessica Chung ◽  
...  
Keyword(s):  
Isolation By Distance ◽  
Principal Component ◽  
Global Scale ◽  
Invasion History ◽  
Nucleotide Polymorphisms ◽  
Multiple Sources ◽  
Liriomyza Sativae ◽  
Local Spread ◽  
Genome Wide ◽  
Torres Strait

Liriomyza sativae, the vegetable leafminer, is a serious agricultural pest originally from the Americas which has now colonized all continents except Antarctica. In 2015, L. sativae arrived on the Australian mainland and established on the Cape York Peninsula in the northeast of the country. Here, we assessed genetic variation in L. sativae based on genome-wide single nucleotide polymorphisms (SNPs) generated by double-digest restriction-site associated DNA sequencing (ddRAD-seq) to uncover the potential origin(s) of this pest in Australia and contribute to reconstructing its global invasion history. Our principal component analyses (PCA) results suggested that Australian mainland populations were genetically close to populations from the Torres Strait and had connections to Bali and Papua New Guinea (PNG), whereas populations from Asia and Africa were more distantly related. Hawaii was genetically distinct from populations from Asia, Africa and Australia. Co-ancestry analyses pointed to signals of gene flow from the Torres Strait into the Australian mainland, while Indonesia/PNG were the likely sources of the initial invasion into the Torres Strait. Admixture analyses further revealed that L. sativae from the Torres Strait had genetic diversity originating from multiple sources, which has now spread to the Australian mainland. The L. sativae lineages from Asia/Africa appear closely related and may share co-ancestry. Isolation by distance (IBD) was found at a broad global scale, but not within small regions, suggesting human-mediated factors contribute to the local spread of this pest. Overall, our findings highlight the challenges in quarantine measures aimed at restricting the distribution of this global pest.

scholarly journals Genes involved in immune, gene translation and chromatin organization pathways associated with Mycoplasma ovipneumoniae presence in nasal secretions of domestic sheep

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0247209
Author(s):  
Michelle R. Mousel ◽  
Stephen N. White ◽  
Maria K. Herndon ◽  
David R. Herndon ◽  
J. Bret Taylor ◽  
...  
Keyword(s):  
Copy Number ◽  
Mixed Model ◽  
Principal Component ◽  
Chromatin Organization ◽  
Production Cycle ◽  
Domestic Sheep ◽  
Immune Gene ◽  
Dna Copy Number ◽  
Genome Wide ◽  
Mycoplasma Ovipneumoniae

Mycoplasma ovipneumoniae contributes to polymicrobial pneumonia in domestic sheep. Elucidation of host genetic influences of M. ovipneumoniae nasal detection has the potential to reduce the incidence of polymicrobial pneumonia in sheep through implementation of selective breeding strategies. Nasal mucosal secretions were collected from 647 sheep from a large US sheep flock. Ewes of three breeds (Polypay n = 222, Rambouillet n = 321, and Suffolk n = 104) ranging in age from one to seven years, were sampled at three different times in the production cycle (February, April, and September/October) over four years (2015 to 2018). The presence and DNA copy number of M. ovipneumoniae was determined using a newly developed species-specific qPCR. Breed (P<0.001), age (P<0.024), sampling time (P<0.001), and year (P<0.001) of collection affected log10 transformed M. ovipneumoniae DNA copy number, where Rambouillet had the lowest (P<0.0001) compared with both Polypay and Suffolk demonstrating a possible genetic component to detection. Samples from yearlings, April, and 2018 had the highest (P<0.046) detected DNA copy number mean. Sheep genomic DNA was genotyped with the Illumina OvineHD BeadChip. Principal component analysis identified most of the variation in the dataset was associated with breed. Therefore, genome wide association analysis was conducted with a mixed model (EMMAX), with principal components 1 to 6 as fixed and a kinship matrix as random effects. Genome-wide significant (P<9x10-8) SNPs were identified on chromosomes 6 and 7 in the all-breed analysis. Individual breed analysis had genome-wide significant (P<9x10-8) SNPs on chromosomes 3, 4, 7, 9, 10, 15, 17, and 22. Annotated genes near these SNPs are part of immune (ANAPC7, CUL5, TMEM229B, PTPN13), gene translation (PIWIL4), and chromatin organization (KDM2B) pathways. Immune genes are expected to have increased expression when leukocytes encounter M. ovipneumoniae which would lead to chromatin reorganization. Work is underway to narrow the range of these associated regions to identify the underlying causal mutations.

scholarly journals Genomic regions associated with Mycoplasma ovipneumoniae presence in nasal secretions of domestic sheep

2021 ◽  
Author(s):  
Michelle R. Mousel ◽  
Stephen N. White ◽  
Maria K. Herndon ◽  
David R. Herndon ◽  
J. Bret Taylor ◽  
...  
Keyword(s):  
Copy Number ◽  
Mixed Model ◽  
Principal Component ◽  
Production Cycle ◽  
Domestic Sheep ◽  
Dna Copy Number ◽  
Immune Genes ◽  
Genetic Components ◽  
Genome Wide ◽  
Mycoplasma Ovipneumoniae

AbstractMycoplasma ovipneumoniae contributes to polymicrobial pneumonia in domestic sheep. Elucidation of host genetic components to M. ovipneumoniae nasal detection would have the potential to reduce the incidence of pneumonia. Nasal mucosal secretions were collected from 647 sheep from a large US sheep flock. Ewes of three breeds (Polypay n=222, Rambouillet n=321, and Suffolk n=104) ranging in age from one to seven years, were sampled at three different times of the production cycle (February, April, and September/October) over four years (2015 to 2018). The presence and quantity of M. ovipneumoniae was determined using a species-specific qPCR with 3 to 10 sampling times per sheep. Breed (P<0.001), age (P<0.024), sampling time (P<0.001), and year (P<0.001) of collection affected log10 transformed M. ovipneumoniae DNA copy number, where Rambouillet had the lowest (P<0.0001) compared with both Polypay and Suffolk demonstrating a possible genetic component to detection. Samples from yearlings, April, and 2018 had the highest (P<0.046) detected DNA copy number mean. Sheep genomic DNA was genotyped with the Illumina OvineHD BeadChip. Principal component analysis identified most of the variation in the dataset was associated with breed. Therefore, genome wide association analysis was conducted with a mixed model (EMMAX), with principle components 1 to 6 as fixed and a kinship matrix as random effects. Genome-wide significant (P<9×10−8) SNPs were identified on chromosomes 6 and 7 in the all-breed analysis. Individual breed analysis had genome-wide significant (P<9×10−8) SNPs on chromosomes 3, 4, 7, 9, 10, 15, 17, and 22. Annotated genes near these SNPs are part of immune (ANAPC7, CUL5, TMEM229B, PTPN13), gene translation (PIWIL4), and chromatin organization (KDM2B) pathways. Immune genes are expected to have increased expression when leukocytes encounter M. ovipneumoniae which would lead to chromatin reorganization. Work is underway to narrow the range of these associated regions to identify the underlying causal mutations.

scholarly journals First genome-wide analysis of an endangered lichen reveals isolation by distance and strong population structure

2017 ◽  
Author(s):  
Jessica L. Allen ◽  
Sean K. McKenzie ◽  
Robin S. Sleith ◽  
S. Elizabeth Alter
Keyword(s):  
Genetic Diversity ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Distribution Models ◽  
Extrinsic Factors ◽  
Biogeographic Patterns ◽  
Ecological Requirements ◽  
Genome Wide ◽  
Isolation By Environment

AbstractLichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes driving diversification and genetic differentiation in these lineages. Though few studies have examined population genetic patterns in lichens, their geographic distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, while their reproductive structures are observable, the lack of information about recombination mechanisms and rates can make inferences about reproductive strategies difficult. Here we investigate the population genomics ofCetradonia linearis, an endangered lichen narrowly endemic to the southern Appalachians of eastern North America, to test the relative contributions of environmental factors and geographic distance in shaping genetic structure, and to gain insights into the demography and reproductive biology of range restricted fungi. Analysis of genome-wide SNP data indicated strong evidence for both low rates of recombination and for strong isolation by distance, but did not support isolation by environment. Hindcast species distribution models and the spatial distribution of genetic diversity also suggested thatC. linearishad a larger range during the last glacial maximum, especially in the southern portion of its current extent, consistent with previous findings in other southern Appalachian taxa. These results contribute to our understanding of intrinsic and extrinsic factors shaping genetic diversity and biogeographic patterns inC. linearis, and more broadly, in rare and endangered fungi.

scholarly journals Genome-Wide Association Analyses of Fertility Traits in Beef Heifers

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 217
Author(s):  
Morgan R. Stegemiller ◽  
Gordon K. Murdoch ◽  
Troy N. Rowan ◽  
Kimberly M. Davenport ◽  
Gabrielle M. Becker ◽  
...  
Keyword(s):  
Mixed Model ◽  
Association Studies ◽  
Principal Component ◽  
Genome Wide Association ◽  
Trend Test ◽  
Future Research ◽  
Genome Wide Association Studies ◽  
Chromosome 2 ◽  
Beef Heifers ◽  
Genome Wide

The ability of livestock to reproduce efficiently is critical to the sustainability of animal agriculture. Antral follicle count (AFC) and reproductive tract scores (RTS) can be used to estimate fertility in beef heifers, but the genetic mechanisms influencing variation in these measures are not well understood. Two genome-wide association studies (GWAS) were conducted to identify the significant loci associated with these traits. In total, 293 crossbred beef heifers were genotyped on the Bovine GGP 50K chip and genotypes were imputed to 836,121 markers. A GWAS was performed with the AFC phenotype for 217 heifers with a multi-locus mixed model, conducted using the year, age at time of sampling and principal component analysis groupings as the covariates. The RTS GWAS was performed with 289 heifers using an additive correlation/trend test comparing prepubertal to pubertal heifers. The loci on chromosomes 2, 3 and 23 were significant in the AFC GWAS and the loci on chromosomes 2, 8, 10 and 11 were significant in the RTS GWAS. The significant region on chromosome 2 was similar between both analyses. These regions contained genes associated with cell proliferation, transcription, apoptosis and development. This study proposes candidate genes for beef cattle fertility, although future research is needed to elucidate the precise mechanisms.

scholarly journals Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations

2015 ◽  
Author(s):  
Jason Munshi-South ◽  
Christine P Zolnik ◽  
Stephen E Harris
Keyword(s):  
Population Genomics ◽  
Isolation By Distance ◽  
Impervious Surface ◽  
Snp Markers ◽  
Environment Modeling ◽  
Evolutionary Potential ◽  
Animal Populations ◽  
Genome Wide ◽  
Isolation By Environment ◽  
White Footed Mouse

Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genome-wide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genome-wide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genome-wide variation was estimated as a proxy for evolutionary potential using more than 10,000 SNP markers generated by ddRAD-Seq. We found that genome-wide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genome-wide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genome-wide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns.

scholarly journals Genetic variability and genome-wide association analysis of flavor and texture in cooked beans (Phaseolus vulgaris L.)

2021 ◽  
Author(s):  
Amber Bassett ◽  
Kelvin Kamfwa ◽  
Daniel Ambachew ◽  
Karen Cichy
Keyword(s):  
Genetic Variability ◽  
Seed Coat ◽  
Principal Component ◽  
Breeding Programs ◽  
Flavor Intensity ◽  
Genome Wide ◽  
White Bean ◽  
The Usa ◽  
New Varieties ◽  
End Use

Abstract Key message Cooked bean flavor and texture vary within and across 20 Andean seed types; SNPs are significantly associated with total flavor, beany, earthy, starchy, bitter, seed-coat perception, and cotyledon texture. Abstract Common dry beans are a nutritious food recognized as a staple globally, but their consumption is low in the USA. Improving bean flavor and texture through breeding has the potential to improve consumer acceptance and suitability for new end-use products. Little is known about genetic variability and inheritance of bean sensory characteristics. A total of 430 genotypes of the Andean Diversity Panel representing twenty seed types were grown in three locations, and cooked seeds were evaluated by a trained sensory panel for flavor and texture attribute intensities, including total flavor, beany, vegetative, earthy, starchy, sweet, bitter, seed-coat perception, and cotyledon texture. Extensive variation in sensory attributes was found across and within seed types. A set of genotypes was identified that exhibit extreme attribute intensities generally stable across all three environments. seed-coat perception and total flavor intensity had the highest broad-sense heritability (0.39 and 0.38, respectively), while earthy and vegetative intensities exhibited the lowest (0.14 and 0.15, respectively). Starchy and sweet flavors were positively correlated and highest in white bean genotypes according to principal component analysis. SNPs associated with total flavor intensity (six SNPs across three chromosomes), beany (five SNPs across four chromosomes), earthy (three SNPs across two chromosomes), starchy (one SNP), bitter (one SNP), seed-coat perception (three SNPs across two chromosomes), and cotyledon texture (two SNPs across two chromosomes) were detected. These findings lay a foundation for incorporating flavor and texture in breeding programs for the development of new varieties that entice growers, consumers, and product developers alike.

scholarly journals Quantifying the Variability of Forest Ecosystem Vulnerability in the Largest Water Tower Region Globally

2021 ◽  
Vol 18 (14) ◽  
pp. 7529
Author(s):  
Siqi Sun ◽  
Yihe Lü ◽  
Da Lü ◽  
Cong Wang
Keyword(s):  
Forest Ecosystems ◽  
Human Impacts ◽  
Regional Scale ◽  
Principal Component ◽  
Tibet Plateau ◽  
Slope Aspect ◽  
Environmental Disturbances ◽  
Restoration Planning ◽  
Development Goals ◽  
Qinghai Tibet Plateau

Forests are critical ecosystems for environmental regulation and ecological security maintenance, especially at high altitudes that exhibit sensitivity to climate change and human activities. The Qinghai-Tibet Plateau—the world’s largest water tower region—has been breeding many large rivers in Asia where forests play important roles in water regulation and water quality improvement. However, the vulnerability of these forest ecosystems at the regional scale is still largely unknown. Therefore, the aim of this research is to quantitatively assess the temporal–spatial variability of forest vulnerability on the Qinghai-Tibet Plateau to illustrate the capacity of forests to withstand disturbances. Geographic information system (GIS) and the spatial principal component analysis (SPCA) were used to develop a forest vulnerable index (FVI) to assess the vulnerability of forest ecosystems. This research incorporates 15 factors covering the natural context, environmental disturbances, and socioeconomic impact. Results indicate that the measure of vulnerability was unevenly distributed spatially across the study area, and the whole trend has intensified since 2000. The three factors that contribute the most to the vulnerability of natural contexts, environmental disturbances, and human impacts are slope aspect, landslides, and the distance to the farmland, respectively. The vulnerability is higher in forest areas with lower altitudes, steeper slopes, and southerly directions. These evaluation results can be helpful for forest management in high altitude water tower regions in the forms of forest conservation or restoration planning and implementation towards sustainable development goals.

scholarly journals Genome-Wide Expression and Alternative Splicing in Domesticated Sunflowers (Helianthus annuus L.) under Flooding Stress

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 92
Author(s):  
Joon Seon Lee ◽  
Lexuan Gao ◽  
Laura Melissa Guzman ◽  
Loren H. Rieseberg
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Mixed Model ◽  
Agricultural Land ◽  
Alcohol Fermentation ◽  
Expression Levels ◽  
Flooding Stress ◽  
Genome Wide ◽  
And Control ◽  
Gene Expression Levels

Approximately 10% of agricultural land is subject to periodic flooding, which reduces the growth, survivorship, and yield of most crops, reinforcing the need to understand and enhance flooding resistance in our crops. Here, we generated RNA-Seq data from leaf and root tissue of domesticated sunflower to explore differences in gene expression and alternative splicing (AS) between a resistant and susceptible cultivar under both flooding and control conditions and at three time points. Using a combination of mixed model and gene co-expression analyses, we were able to separate general responses of sunflower to flooding stress from those that contribute to the greater tolerance of the resistant line. Both cultivars responded to flooding stress by upregulating expression levels of known submergence responsive genes, such as alcohol dehydrogenases, and slowing metabolism-related activities. Differential AS reinforced expression differences, with reduced AS frequencies typically observed for genes with upregulated expression. Significant differences were found between the genotypes, including earlier and stronger upregulation of the alcohol fermentation pathway and a more rapid return to pre-flooding gene expression levels in the resistant genotype. Our results show how changes in the timing of gene expression following both the induction of flooding and release from flooding stress contribute to increased flooding tolerance.

scholarly journals Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 832
Author(s):  
Nina Moravčíková ◽  
Radovan Kasarda ◽  
Radoslav Židek ◽  
Luboš Vostrý ◽  
Hana Vostrá-Vydrová ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Structure ◽  
Principal Component ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
German Shepherd ◽  
German Shepherd Dog ◽  
Genome Wide ◽  
Scale Population ◽  
History Effect

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.

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