scholarly journals Assessing accuracy of imputation in Gyr breed using different SNP panels

Genome ◽  
2021 ◽  
Author(s):  
Alejandra Maria Toro Ospina ◽  
Ignacio Aguilar ◽  
Matheus Henrique Vargas de Oliveira ◽  
Luiz eduardo Cruz dos Santos Correia ◽  
Anibal Eugenio Vercesi Filho ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Bos Taurus ◽  
Imputation Accuracy ◽  
Bos Indicus ◽  
Principal Component ◽  
Reference Population ◽  
Medium Density ◽  
Genomic Relationship ◽  
Snp Panels ◽  
Two Populations

The objective of this study was to evaluate the accuracy of imputation in a Gyr population using two medium density panels (Bos taurus - Bos indicus) and to test whether the inclusion of the Nellore breed increases the imputation accuracy in the Gyr population. The database consisted of 289 Gyr females from Brazil genotyped with the GGP Bovine LDv4 chip containing 30,000 SNPs and 158 Gyr females from Colombia genotyped with the GGP indicus chip containing 35,000 SNPs. A customized chip was created that contained the information of 9,109 SNPs (9K) to test the imputation accuracy in Gyr populations; 604 Nellore animals with information of LD SNPs tested in the scenarios were included in the reference population. Four scenarios were tested: LD9K_30KGIR, LD9K_35INDGIR, LD9K_30KGIR_NEL and LD9K_35INDGIR_NEL. Principal component analysis (PCA) was computed for the genomic matrix and sample-specific imputation accuracies were calculated using Pearson’s correlation (CS) and the concordance rate (CR) for imputed genotypes. The results of PCA of the Colombian and Brazilian Gyr populations demonstrated the genomic relationship between the two populations. The CS and CR ranged from 0.88 to 0.94 and from 0.93 to 0.96, respectively. Among the scenarios tested, the highest CS (0.94) was observed for the LD9K_30KGIR scenario.However, the variation in SNPs may reduce the imputation accuracy even when the chip of the Bos indicus subspecies is used

RELATIONSHIPS BETWEEN SOME PROPERTIES OF ORGANIC SOILS FROM THE SOUTHERN CANADIAN SHIELD

1990 ◽  
Vol 70 (3) ◽  
pp. 363-377 ◽  
Author(s):  
D. ANN BROWN ◽  
S. P. MATHUR ◽  
ANTON BROWN ◽  
D. J. KUSHNER
Keyword(s):  
Principal Component Analysis ◽  
Acid Leaching ◽  
Principal Component ◽  
Organic Soil ◽  
Component Analysis ◽  
Soil Types ◽  
Organic Soils ◽  
Mining Districts ◽  
Two Populations ◽  
Inorganic Components

Different numerical methods used to distinguish between organic soil types are evaluated. The research was initiated by the suggestion that acid leaching from mining wastes could be prevented by capping the tailings with a self-renewing methane-producing muskeg bog, in order to prevent the penetration of oxygen to the wastes. Thirty organic soils from bogs in the mining districts of Elliot Lake, Sudbury, and Timmins, Ontario, and Noranda, Quebec, were sampled and 28 soil characteristics were measured. These characteristics, whose values are normally or lognormally distributed, were analyzed by several different statistical methods. Some characteristics indicate the existence of two populations, and others are bivariantly correlated. Canonical discriminant analysis was more successful than cluster analysis in separating the bogs into well-defined geographical groups. However, principal component analysis proved best at grouping the organic soils according to their organic and inorganic components, and we suggest that this is a suitable method for the general discrimination of organic soil types. Methane was present in all the 17 bogs tested for it, and in two very wet bogs more than 2 mmol of methane per liter were extracted. Key words: Muskeg bog, organic soils, soil characterization, principal component analysis

scholarly journals The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
N. Z. Gebrehiwot ◽  
E. M. Strucken ◽  
H. Aliloo ◽  
K. Marshall ◽  
J. P. Gibson
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Large Population ◽  
Bos Indicus ◽  
Principal Component ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
African Cattle ◽  
Snp Data

Abstract Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

scholarly journals Comparative analysis of shell occupation by two southern populations of the hermit crab Loxopagurus loxochelis (Decapoda, Diogenidae)

2012 ◽  
Vol 60 (3) ◽  
pp. 299-310 ◽  
Author(s):  
Luciane Ayres-Peres ◽  
Aline Ferreira Quadros ◽  
Fernando L. Mantelatto
Keyword(s):  
Principal Component Analysis ◽  
Comparative Analysis ◽  
Hermit Crab ◽  
Regression Tree ◽  
Principal Component ◽  
Hermit Crabs ◽  
Pca Analysis ◽  
Internal Volume ◽  
The Relationship ◽  
Two Populations

The present study aimed to comparatively verify the relation between the hermit crabs and the shells they use in two populations of Loxopagurus loxochelis. Samples were collected monthly from July 2002 to June 2003, at Caraguatatuba and Ubatuba Bay, São Paulo, Brazil. The animals sampled had their sex identified, were weighed and measured; their shells were identified, measured and weighed, and their internal volume determined. To relate the hermit crab's characteristics and the shells' variables, principal component analysis (PCA) and a regression tree were used. According to the PCA analysis, the three gastropod shells most frequently used by L. loxochelis varied in size. The regression tree successfully explained the relationship between the hermit crab's characteristics and the internal volume of the inhabited shell. It can be inferred that the relationship between the morphometry of an individual hermit crab and its shell is not straightforward and it is impossible to explain only on the basis of direct correlations between the body's and the shell's attributes. Several factors (such as the morphometry and the availability of the shell, environmental conditions and inter- and intraspecific competition) interact and seem to be taken into consideration by the hermit crabs when they choose a shell, resulting in the diversified pattern of shell occupancy shown here and elsewhere.

scholarly journals SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Netsanet Z. Gebrehiwot ◽  
Eva M. Strucken ◽  
Karen Marshall ◽  
Hassan Aliloo ◽  
John P. Gibson
Keyword(s):  
Allele Frequency ◽  
Bos Taurus ◽  
Low Cost ◽  
Bos Indicus ◽  
High Density ◽  
Indigenous Populations ◽  
Genetic Admixture ◽  
Genotype Data ◽  
Parentage Assignment ◽  
Snp Panels

Abstract Background Understanding the relationship between genetic admixture and phenotypic performance is crucial for the optimization of crossbreeding programs. The use of small sets of informative ancestry markers can be a cost-effective option for the estimation of breed composition and for parentage assignment in situations where pedigree recording is difficult. The objectives of this study were to develop small single nucleotide polymorphism (SNP) panels that can accurately estimate the total dairy proportion and assign parentage in both West and East African crossbred dairy cows. Methods Medium- and high-density SNP genotype data (Illumina BovineSNP50 and BovineHD Beadchip) for 4231 animals sampled from African crossbreds, African Bos taurus, European Bos taurus, Bos indicus, and African indigenous populations were used. For estimating breed composition, the absolute differences in allele frequency were calculated between pure ancestral breeds to identify SNPs with the highest discriminating power, and different combinations of SNPs weighted by ancestral origin were tested against estimates based on all available SNPs. For parentage assignment, informative SNPs were selected based on the highest minor allele frequency (MAF) in African crossbred populations assuming two Scenarios: (1) parents were selected among all the animals with known genotypes, and (2) parents were selected only among the animals known to be a parent of at least one progeny. Results For the medium-density genotype data, SNPs selected for the largest differences in allele frequency between West African indigenous and European Bos taurus breeds performed best for most African crossbred populations and achieved a prediction accuracy (r2) for breed composition of 0.926 to 0.961 with 200 SNPs. For the high-density dataset, a panel with 70% of the SNPs selected on their largest difference in allele frequency between African and European Bos taurus performed best or very near best across all crossbred populations with r2 ranging from 0.978 to 0.984 with 200 SNPs. In all African crossbred populations, unambiguous parentage assignment was possible with ≥ 300 SNPs for the majority of the panels for Scenario 1 and ≥ 200 SNPs for Scenario 2. Conclusions The identified low-cost SNP assays could overcome incomplete or inaccurate pedigree records in African smallholder systems and allow effective breeding decisions to produce progeny of desired breed composition.

Development and evaluation of a low-density single-nucleotide polymorphism chip specific to Bos indicus cattle

2020 ◽  
Vol 60 (15) ◽  
pp. 1769
Author(s):  
J. B. S. Ferraz ◽  
X. -L. Wu ◽  
H. Li ◽  
J. Xu ◽  
R. Ferretti ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genomic Selection ◽  
Bos Taurus ◽  
Imputation Accuracy ◽  
Bos Indicus ◽  
Zebu Cattle ◽  
Low Density ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Chip

Context Genomic selection has been of increasing interest in the genetic improvement of Zebu cattle, particularly for quantitative traits that are difficult or expensive to measure, such as carcass traits and meat tenderness. The success of genomic selection depends on several factors, and at its core is the availability of single-nucleotide polymorphism (SNP) chips that are appropriately designed for Bos indicus cattle. However, the currently available commercial bovine SNP chips are mostly designed for Bos taurus cattle. There are two commercial Bos indicus SNP chips; namely, GeneSeek genomic profiler high-density Bos indicus (GGP-HDi) SNP chip and a low-density (LD) Bos indicus SNP chip (Z chip), but these two Bos indicus SNP chips were built with mixed contents of SNPs for Bos indicus and Bos taurus cattle, due to limited availability of genotype data from Bos indicus cattle. Aims To develop a new GGP indicus 35000 SNP chip specifically for Bos indicus cattle, which has a low cost, but high accuracy of imputation to Illumina BovineHD chips. Methods The design of the chip consisted of 34000 optimally selected SNPs, plus 1000 SNPs pre-reserved for those on the Y chromosome, ‘causative’ mutations for a variety of economically relevant traits, genetic health conditions and International Society for Animal Genetics globally recognised parentage markers for those breeds of cattle. Key results The present results showed that this new indicus LD SNP chip had considerably increased minor allele frequencies in indicus breeds than the previous Z-chip. It demonstrated with high imputation accuracy to HD SNP genotypes in five indicus breeds, and with considerable predictability on 14 growth and reproduction traits in Nellore cattle. Conclusions This new indicus LD chip represented a successful effort to leverage existing knowledge and genotype resources towards the public release of a cost-effective LD SNP chip specifically for Bos indicus cattle, which is expected to replace the previous GGP indicus LD chip and to supplement the existing GGP-HDi 80000 SNP chip. Implications A new SNP chip specifically designed for Bos indicus, with high power of imputation to Illumina BovineHD technology and with excellent coverage of the whole genome, is now available on the market for Bos indicus cattle, and Bos indicus and Bos taurus crosses.

scholarly journals Inference of Ancestries and Heterozygosity Proportion and Genotype Imputation in West African Cattle Populations

2021 ◽  
Vol 12 ◽  
Author(s):  
Netsanet Z. Gebrehiwot ◽  
Hassan Aliloo ◽  
Eva M. Strucken ◽  
Karen Marshall ◽  
Mohammad Al Kalaldeh ◽  
...  
Keyword(s):  
Reference Data ◽  
Bos Taurus ◽  
Imputation Accuracy ◽  
West African ◽  
High Density ◽  
Genotype Imputation ◽  
Indigenous Populations ◽  
Medium Density ◽  
Crossbred Cattle ◽  
Ancestral Origin

Several studies have evaluated computational methods that infer the haplotypes from population genotype data in European cattle populations. However, little is known about how well they perform in African indigenous and crossbred populations. This study investigates: (1) global and local ancestry inference; (2) heterozygosity proportion estimation; and (3) genotype imputation in West African indigenous and crossbred cattle populations. Principal component analysis (PCA), ADMIXTURE, and LAMP-LD were used to analyse a medium-density single nucleotide polymorphism (SNP) dataset from Senegalese crossbred cattle. Reference SNP data of East and West African indigenous and crossbred cattle populations were used to investigate the accuracy of imputation from low to medium-density and from medium to high-density SNP datasets using Minimac v3. The first two principal components differentiated Bos indicus from European Bos taurus and African Bos taurus from other breeds. Irrespective of assuming two or three ancestral breeds for the Senegalese crossbreds, breed proportion estimates from ADMIXTURE and LAMP-LD showed a high correlation (r ≥ 0.981). The observed ancestral origin heterozygosity proportion in putative F1 crosses was close to the expected value of 1.0, and clearly differentiated F1 from all other crosses. The imputation accuracies (estimated as correlation) between imputed and the real data in crossbred animals ranged from 0.142 to 0.717 when imputing from low to medium-density, and from 0.478 to 0.899 for imputation from medium to high-density. The imputation accuracy was generally higher when the reference data came from the same geographical region as the target population, and when crossbred reference data was used to impute crossbred genotypes. The lowest imputation accuracies were observed for indigenous breed genotypes. This study shows that ancestral origin heterozygosity can be estimated with high accuracy and will be far superior to the use of observed individual heterozygosity for estimating heterosis in African crossbred populations. It was not possible to achieve high imputation accuracy in West African crossbred or indigenous populations based on reference data sets from East Africa, and population-specific genotyping with high-density SNP assays is required to improve imputation.

Scanning x-ray fluorescence microscopy and principal component analysis

1992 ◽  
Vol 50 (2) ◽  
pp. 1752-1753
Author(s):  
Brian Cross
Keyword(s):  
Principal Component Analysis ◽  
Fluorescence Microscopy ◽  
Spatial Resolution ◽  
High Speed ◽  
Image Acquisition ◽  
Principal Component ◽  
Fluorescence Microscope ◽  
Acquisition Rate ◽  
X Ray ◽  
Speed Up

A relatively new entry, in the field of microscopy, is the Scanning X-Ray Fluorescence Microscope (SXRFM). Using this type of instrument (e.g. Kevex Omicron X-ray Microprobe), one can obtain multiple elemental x-ray images, from the analysis of materials which show heterogeneity. The SXRFM obtains images by collimating an x-ray beam (e.g. 100 μm diameter), and then scanning the sample with a high-speed x-y stage. To speed up the image acquisition, data is acquired "on-the-fly" by slew-scanning the stage along the x-axis, like a TV or SEM scan. To reduce the overhead from "fly-back," the images can be acquired by bi-directional scanning of the x-axis. This results in very little overhead with the re-positioning of the sample stage. The image acquisition rate is dominated by the x-ray acquisition rate. Therefore, the total x-ray image acquisition rate, using the SXRFM, is very comparable to an SEM. Although the x-ray spatial resolution of the SXRFM is worse than an SEM (say 100 vs. 2 μm), there are several other advantages.

A German version of the Intermittent Claudication Questionnaire (ICQ): cultural adaptation and validation

VASA ◽  
2012 ◽  
Vol 41 (5) ◽  
pp. 333-342 ◽  
Author(s):  
Kirchberger ◽  
Finger ◽  
Müller-Bühl
Keyword(s):  
Principal Component Analysis ◽  
Intermittent Claudication ◽  
Completion Time ◽  
Short Form ◽  
Principal Component ◽  
Component Analysis ◽  
German Version ◽  
Average Completion Time ◽  
Sf 36 ◽  
Related Quality

Background: The Intermittent Claudication Questionnaire (ICQ) is a short questionnaire for the assessment of health-related quality of life (HRQOL) in patients with intermittent claudication (IC). The objective of this study was to translate the ICQ into German and to investigate the psychometric properties of the German ICQ version in patients with IC. Patients and methods: The original English version was translated using a forward-backward method. The resulting German version was reviewed by the author of the original version and an experienced clinician. Finally, it was tested for clarity with 5 German patients with IC. A sample of 81 patients were administered the German ICQ. The sample consisted of 58.0 % male patients with a median age of 71 years and a median IC duration of 36 months. Test of feasibility included completeness of questionnaires, completion time, and ratings of clarity, length and relevance. Reliability was assessed through a retest in 13 patients at 14 days, and analysis of Cronbach’s alpha for internal consistency. Construct validity was investigated using principal component analysis. Concurrent validity was assessed by correlating the ICQ scores with the Short Form 36 Health Survey (SF-36) as well as clinical measures. Results: The ICQ was completely filled in by 73 subjects (90.1 %) with an average completion time of 6.3 minutes. Cronbach’s alpha coefficient reached 0.75. Intra-class correlation for test-retest reliability was r = 0.88. Principal component analysis resulted in a 3 factor solution. The first factor explained 51.5 of the total variation and all items had loadings of at least 0.65 on it. The ICQ was significantly associated with the SF-36 and treadmill-walking distances whereas no association was found for resting ABPI. Conclusions: The German version of the ICQ demonstrated good feasibility, satisfactory reliability and good validity. Responsiveness should be investigated in further validation studies.

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