scholarly journals Applications of ancestry estimation in cattle population genetics

2019 ◽  
Author(s):  
◽  
Tamar Crum
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Population Genetic ◽  
Human Population ◽  
Disease Risk ◽  
Allele Frequencies ◽  
Population Substructure ◽  
Association Analyses ◽  
Genotype Frequencies ◽  
Ancestry Estimation

Accounting for ancestry and cryptic population structure is important in population genetic data analysis. The estimation of ancestry can help elucidate the effects of admixture or stratification on allele and genotype frequencies caused by population substructure. Human population genetics has examined these issues in detail and has developed models which incorporate ancestry effects in the estimation of population susceptibilities to disease risk in association analyses, as well as for the interpretation of genotype disease risks in admixed individuals for use in personalized medicine. In livestock, allele frequencies frequently differ between breeds and these breeds frequently also differ for phenotypes of interest. If these population differences are not accounted for in the analysis, the differences in allele frequencies due to population structure can lead to erroneous associations of loci with phenotypes. The effects of domestication and breed formation in shaping the cattle genome along with the rampant use of crossbreeding to form admixed individuals in the modern beef cattle industry provides an opportunity to evaluate the impacts of breed differences on association analyses of economically relevant traits such as the conversion of feed to weight gain and disease susceptibility. Here, we review the methods used for ancestry estimation and the impacts of ancestry prediction in human population genetic analyses and opportunities for use of these techniques in cattle, and more generally in livestock populations. The incorporation of accurate genomic-based predictions of breed composition could fine-tune the resolution of mapping studies targeting the identification of causal loci for livestock species.

scholarly journals Allele frequencies in loci controlling coat colour in Polish Coldblood horses

2018 ◽  
Vol 63 (No. 11) ◽  
pp. 462-472
Author(s):  
Anna Stachurska ◽  
Antoni Brodacki ◽  
Marta Liss
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Coat Colour ◽  
Allele Frequencies ◽  
Square Root ◽  
Horse Population ◽  
Hardy Weinberg Equilibrium ◽  
Recessive Phenotype

The objective of this study was to estimate the frequencies of alleles which produce coat colour in Polish Coldblood horse population, and to verify the hypothesis that coat colour is not considered in its selection. The analysis included 35 928 horses and their parents having been registered in the studbook over a half-century. Allele frequencies in Agouti (A), Extension (E), Dun (D), Roan (Rn), and Grey (G) loci, in parental and offspring generations, were estimated according to test matings and the square root of recessive phenotype frequency. The population structure is in Hardy–Weinberg equilibrium only at E locus and coat colour is regarded by breeders. Black horses are favoured. Higher E locus homozygosity in blacks than in bays makes it easier to obtain black foals. Dun-diluted, roan and grey coat colours are undesirable and the population has come to consist almost uniformly of basic coat colours. These results show the importance of studies on population genetic structure, which despite no formal criteria for breeding for colour, can considerably change through generations.

scholarly journals Development of microsatellite loci and population genetics in the bumblebee catfish species Pseudopimelodus atricaudus and Pseudopimelodus magnus (Siluriformes: Pseudopimelodidae)

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
José David Rangel-Medrano ◽  
Edna Judith Márquez
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Genetic Differentiation ◽  
River Basin ◽  
Microsatellite Loci ◽  
Population Genetic ◽  
High Genetic Diversity ◽  
The Family ◽  
The Mean

ABSTRACT The Neotropical freshwater catfish Pseudopimelodus atricaudus and Pseudopimelodus magnus are two recently discovered species endemic to the Colombian Magdalena-Cauca River basin. In this study, a set of 13 microsatellite loci were developed by using next generation sequence technology to assess the genetic diversity and population structure in P. atricaudus and test for cross-species amplification in P. magnus. Both species exhibited high genetic diversity (P. atricaudus: Na: 9.000 - 9.769 alleles/locus, Ho: 0.760 - 0.804, HE: 0.804 - 0.840; P. magnus: Na: 12.8 - 5.4 alleles/locus, Ho: 0.638 - 0.683, HE: 0.747 - 0.755) compared to the mean levels of genetic diversity reported for Neotropical Siluriformes, and lack of genetic differentiation among sampling sites within the Cauca River (P. atricaudus: F’ST=0.013 - 0.017, P > 0.05, D’est= -0.004 - 0.023, P > 0.05; P. magnus: F’ST= 0.031, P= 0.055; D’est= 0.045, P= 0.058). This work is the first insight on the diversity and the population genetics of species of the family Pseudopimelodidae and provides a framework to further population genetic and conservation analyses needed in this poorly studied family at the microevolutionary level.

scholarly journals TEMPORAL AND MICROGEOGRAPHIC VARIATION IN ALLOZYME FREQUENCIES IN A NATURAL POPULATION OF DROSOPHILA BUZZATII

Genetics ◽  
1986 ◽  
Vol 112 (3) ◽  
pp. 577-611
Author(s):  
J S F Barker ◽  
P D East ◽  
B S Weir
Keyword(s):  
Population Structure ◽  
Environmental Variables ◽  
Allele Frequencies ◽  
Significant Heterogeneity ◽  
Linkage Disequilibria ◽  
Drosophila Buzzatii ◽  
Genotype Frequencies ◽  
Microgeographic Variation ◽  
Significant Linkage ◽  
Over Time

ABSTRACT Temporal variation in allozyme frequencies at six loci was studied by making monthly collections over 4 yr in one population of the cactophilic species Drosophila buzzatii. Ten sites were defined within the study locality, and for all temporal samples, separate collections were made at each of these sites. Population structure over microgeographic space and changes in population structure over time were analyzed using F-statistic estimators, and multivariate analyses of allele and genotype frequencies with environmental variables were carried out.—Allele frequencies showed significant variation over time, although there were no clear cyclical or seasonal patterns. A biplot analysis of allele frequencies over seasons within years and over years showed clear discrimination among years by alleles at four loci. During the 4 yr, three alleles showed directional changes which were associated with directional changes in environmental variables. Significant associations with one or more environmental variables were found for allele frequencies at every locus and for both expected and observed heterozygosities (except those for Est-1 and Est-2). Thus, variation in allele frequencies over time cannot be attributed solely to drift. Significant linkage disequilibria were detected among three loci (Est-2, Hex and Aldox), but there was no evidence for spatial or temporal patterns.—The F-statistic analyses showed significant differentiation among months within years for all loci, but the statistic used (coancestry) was heterogeneous among loci. Estimates of F (inbreeding) for all loci were significantly different from zero, with the loci in four groups, Adh-1 (negative), Pgm (small positive), Est-2 and Hex (intermediate) and Est-1 and Aldox (high positive). The correlation of genes within individuals within populations (f) for each locus in each month by site sample differed among loci, as did the patterns of change in f over time (seasons). Heterogeneity in the F-statistic estimates indicates that natural selection is directly or indirectly affecting allele and genotype frequencies at some loci. However, the F-statistic analyses showed essentially no microgeographic structure (i.e., among sites), although there was significant heterogeneity in allele frequencies among flies emerging from individual rots.—Thus, microspatial heterogeneity probably is most important at the level of individual rots, and coupled with habitat selection, it could be a major factor promoting diversifying selection and the maintenance of polymorphism. Resolution of the nature of this selection and of the apparent inbreeding detected at all loci except Adh-1 will require detailed study of the breeding structure of the population at the microhabitat level (individual rots) and of gene flow within the population.

scholarly journals Population genetic considerations for using biobanks as international resources in the pandemic era and beyond

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hannah Carress ◽  
Daniel John Lawson ◽  
Eran Elhaik
Keyword(s):  
Population Genetic ◽  
Disease Risk ◽  
Meta Analysis ◽  
Association Analyses ◽  
Privacy Concerns ◽  
The Past ◽  
Genomic Tools ◽  
Genomic Studies ◽  
Health And Disease ◽  
Global Understanding

AbstractThe past years have seen the rise of genomic biobanks and mega-scale meta-analysis of genomic data, which promises to reveal the genetic underpinnings of health and disease. However, the over-representation of Europeans in genomic studies not only limits the global understanding of disease risk but also inhibits viable research into the genomic differences between carriers and patients. Whilst the community has agreed that more diverse samples are required, it is not enough to blindly increase diversity; the diversity must be quantified, compared and annotated to lead to insight. Genetic annotations from separate biobanks need to be comparable and computable and to operate without access to raw data due to privacy concerns. Comparability is key both for regular research and to allow international comparison in response to pandemics. Here, we evaluate the appropriateness of the most common genomic tools used to depict population structure in a standardized and comparable manner. The end goal is to reduce the effects of confounding and learn from genuine variation in genetic effects on phenotypes across populations, which will improve the value of biobanks (locally and internationally), increase the accuracy of association analyses and inform developmental efforts.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

Allozyme variation and an estimate of the inbreeding coefficient in the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

1995 ◽  
Vol 85 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Philippe Borsa ◽  
D. Pierre Gingerich
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
New Caledonia ◽  
Allozyme Variation ◽  
Inbreeding Coefficient ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Biological Features ◽  
High Degree

AbstractSeven presumed Mendelian enzyme loci (Est-2, Est-3, Gpi, Idh-l, Idh-2, Mdh-2 and Mpi) were characterized and tested for polymorphism in coffee berry borers, Hypothenemus hampei (Ferrari), sampled in Côte d′Ivoire, Mexico and New Caledonia. The average genetic diversity was H = 0.080. Two loci, Mdh-2 and Mpi were polymorphic, and thus usable as genetic markers. The population structure of H. hampei was analysed using Weir & Cockerham's estimators of Wright's F-statistics. A high degree of inbreeding (f = 0.298) characterized the elementary geographic sampling unit, the coffee field. The estimate of gene flow between fields within a country was Nm = 10.6 and that between countries was Nm = 2. The population genetic structure in H. hampei could be related to its known population biological features and history.

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals Applicability of human-specific STR systems, GlobalFiler™ PCR Amplification Kit, Investigator 24plex QS Kit, and PowerPlex® Fusion 6C in chimpanzee (Pan troglodytes)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Abhishek Singh ◽  
Vivek Sahajpal ◽  
Mukesh Thakur ◽  
Lalit Kumar Sharma ◽  
Kailash Chandra ◽  
...  
Keyword(s):  
Population Genetics ◽  
Pan Troglodytes ◽  
Human Population ◽  
Pcr Amplification ◽  
Forensic Analysis ◽  
Cross Reactivity ◽  
Allele Size ◽  
Male And Female ◽  
Successful Amplification ◽  
Human Specific

Abstract Objectives Human identification systems based on STRs are widely used in human population genetics and forensic analysis. This study aimed to validate the cross-reactivity of three widely known human-specific STR identification systems i.e. GlobalFiler™ PCR Amplification Kit, Investigator 24plex QS Kit, and PowerPlex® Fusion 6C in chimpanzee. Results The present study revealed the successful amplification of 18 loci using GlobalFiler™ PCR Amplification Kit, 18 loci using Investigator 24plex QS Kit, and 20 loci using PowerPlex® Fusion 6C system. The marker Amelogenin (AMEL) showed differential allele size between male and female revealing the gender identity of chimpanzees and thus validates their application concerning forensic examination, population estimation, and genetic analysis.

scholarly journals Population genetic structure of a major reef-building coral species Acropora downingi in northeastern Arabian Peninsula

Coral Reefs ◽  
2021 ◽  
Author(s):  
Felipe Torquato ◽  
Jessica Bouwmeester ◽  
Pedro Range ◽  
Alyssa Marshell ◽  
Mark A. Priest ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Study ◽  
Persian Gulf ◽  
Population Genetic ◽  
Coral Species ◽  
Arabian Peninsula ◽  
Ecological Speciation ◽  
Population Genetic Study ◽  
Sea Of Oman ◽  
Neutral Markers

AbstractCurrent seawater temperatures around the northeastern Arabian Peninsula resemble future global forecasts as temperatures > 35 °C are commonly observed in summer. To provide a more fundamental aim of understanding the structure of wild populations in extreme environmental conditions, we conducted a population genetic study of a widespread, regional endemic table coral species, Acropora downingi, across the northeastern Arabian Peninsula. A total of 63 samples were collected in the southern Arabian/Persian Gulf (Abu Dhabi and Qatar) and the Sea of Oman (northeastern Oman). Using RAD-seq techniques, we described the population structure of A. downingi across the study area. Pairwise G’st and distance-based analyses using neutral markers displayed two distinct genetic clusters: one represented by Arabian/Persian Gulf individuals, and the other by Sea of Oman individuals. Nevertheless, a model-based method applied to the genetic data suggested a panmictic population encompassing both seas. Hypotheses to explain the distinctiveness of phylogeographic subregions in the northeastern Arabian Peninsula rely on either (1) bottleneck events due to successive mass coral bleaching, (2) recent founder effect, (3) ecological speciation due to the large spatial gradients in physical conditions, or (4) the combination of seascape features, ocean circulation and larval traits. Neutral markers indicated a slightly structured population of A. downingi, which exclude the ecological speciation hypothesis. Future studies across a broader range of organisms are required to furnish evidence for existing hypotheses explaining a population structure observed in the study area. Though this is the most thermally tolerant acroporid species worldwide, A. downingi corals in the Arabian/Persian Gulf have undergone major mortality events over the past three decades. Therefore, the present genetic study has important implications for understanding patterns and processes of differentiation in this group, whose populations may be pushed to extinction as the Arabian/Persian Gulf warms.

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