scholarly journals Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

2021 ◽  
Vol 12 ◽  
Author(s):  
Sèyi Fridaïus Ulrich Vanvanhossou ◽  
Tong Yin ◽  
Carsten Scheper ◽  
Ruedi Fries ◽  
Luc Hippolyte Dossa ◽  
...  
Keyword(s):  
Production Systems ◽  
Principal Component ◽  
West African ◽  
Economic Traits ◽  
Selection Signatures ◽  
Extended Haplotype ◽  
Indigenous Cattle ◽  
Environmental Pressures ◽  
Inbreeding Coefficients ◽  
Recent Selection

The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.

scholarly journals Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3469
Author(s):  
Jun Ma ◽  
Xue Gao ◽  
Junya Li ◽  
Huijiang Gao ◽  
Zezhao Wang ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Muscle Growth ◽  
Snp Array ◽  
Cattle Breed ◽  
Principal Component ◽  
Composite Likelihood ◽  
Mechanism Analysis ◽  
Economic Traits ◽  
Selection Signatures ◽  
Genetic Features

Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.

scholarly journals Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Diercles Francisco Cardoso ◽  
Gerardo Alves Fernandes Júnior ◽  
Daiane Cristina Becker Scalez ◽  
Anderson Antonio Carvalho Alves ◽  
Ana Fabrícia Braga Magalhães ◽  
...  
Keyword(s):  
Growth Traits ◽  
Genomic Analysis ◽  
Principal Component ◽  
Divergent Selection ◽  
Genomic Diversity ◽  
Population Subdivision ◽  
Selection Signatures ◽  
Inbreeding Coefficients ◽  
Angus Cattle ◽  
Genomic Regions

Abstract Highlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N = 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via FST and varLD tests. The principal component analysis revealed a sub-structure with a close connection between the two subpopulations. The averages of genomic relationships, inbreeding coefficients, and linkage disequilibrium at varying genomic distances were rather similar across them, suggesting non-accentuated differences in overall genomic diversity. Autozygosity islands revealed selection signatures common to both subpopulations at chromosomes 13 (63.77–65.25 Mb) and 14 (22.81–23.57 Mb), which are notably known regions affecting growth traits. Nevertheless, further autozygosity islands along with FST and varLD tests unravel particular sites with accentuated population subdivision at BTAs 7 and 18 overlapping with known QTL and candidate genes of reproductive performance, thermoregulation, and resistance to infectious diseases. Our findings indicate overall genomic similarity between Angus subpopulations, with noticeable signals of divergent selection in genomic regions associated with the adaptation in different environments.

scholarly journals Shared Ancestry and Signatures of Recent Selection in Gotland Sheep

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 433
Author(s):  
Seyed Mohammad Ghoreishifar ◽  
Christina Marie Rochus ◽  
Sima Moghaddaszadeh-Ahrabi ◽  
Pourya Davoudi ◽  
Siavash Salek Ardestani ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth Traits ◽  
Significant Snps ◽  
P Value ◽  
Economic Traits ◽  
Selection Signatures ◽  
Shared Ancestry ◽  
The Baltic ◽  
Genomic Regions ◽  
Recent Selection

Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (~50%), Karakul (~30%), Romanov (~20%), and Fjällnäs (~10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation FST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the FST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep.

Genetic Evaluation and Bi-plot Analysis in Okra Hybrids for Yield, Quality Components and YVMV Resistance

2018 ◽  
Vol 5 (04) ◽  
Author(s):  
SS SOLANKEY ◽  
ANIL K SINGH
Keyword(s):  
Genetic Divergence ◽  
Principal Component ◽  
F1 Hybrids ◽  
Genetic Advance ◽  
Economic Traits ◽  
Cross Combination ◽  
Plot Analysis ◽  
Eigen Value ◽  
Coefficient Of Variability ◽  
Yield Quality

Fifty one okra F1 hybrids (using 17 lines as female and 3 testers as male parent) were evaluated in RCBD design during two different consecutive seasons (summer and rainy). Phenotypic coefficient of variability (PCV) was higher than genotypic coefficient of variability (GCV) for all studied character exhibiting environmental effects on the expression of characters. Heritability (h2b) along with genetic advance per cent of mean was found highest for character YVMV (86.95% and 150.61%). All the 51 okra hybrids were grouped into 4 distinct clusters in which Cluster II was the largest cluster having 28 F1s (54.90% of total F1s) followed by Cluster I with 14 F1s (27.45% of total F1s). Out of the major 6 PCs, 4 principal components (PC1, PC2, PC3 and PC4) accounted with proportionate values of 22.61, 17.22, 11.87 and 10.63%, respectively and contributed 62.33 % of the cumulative variation having Eigen value more than one. Moreover, based on PCs and genetic divergence in Cluster I and Cluster IV for plant height, YVMV and number of fruit per plant is important to identify the best cross combination (Arka Abhay × Arka Anamika) in okra. Therefore, the best cross combinations for improvement in various economic traits can be recommended on the basis of genetic divergence and principal component analysis in okra.

Identification of cavitation in centrifugal pump by artificial immune network

2021 ◽  
pp. 095440892110284
Author(s):  
Seyed M Matloobi ◽  
Mohammad Riahi
Keyword(s):  
Immune System ◽  
Production Systems ◽  
Principal Component ◽  
Immune Network ◽  
Centrifugal Pumps ◽  
Artificial Immune ◽  
Human Immune System ◽  
Time Frequency ◽  
Artificial Immune Network ◽  
Damage Condition

Reducing the cost of unscheduled shutdowns and enhancing the reliability of production systems is an important goal for various industries; this could be achieved by condition monitoring and artificial intelligence. Cavitation is a common undesired phenomenon in centrifugal pumps, which causes damage and its detection in the preliminary stage is very important. In this paper, cavitation is identified by use of vibration and current signal and artificial immune network that is modeled on the base of the human immune system. For this purpose, first data collection were done by a laboratory setup in health and five stages damage condition; then various features in time, frequency, and time–frequency were extracted from vibration and current signals in addition to pressure and flow rate; next feature selection and dimensions reduction were done by artificial immune method to use for classification; finally, they were used by artificial immune network and some other methods to identify the system condition and classification. The results of this study showed that this method is more accurate in the detection of cavitation in the initial stage compared to methods such as non-linear supportive vector machine, multi-layer artificial neural network, K-means and fuzzy C-means with the same data. Also, selected features with artificial immune system were better than principal component analysis results.

ESTIMATION OF GENETIC DIVERGENCE IN CHILLI PEPPER (CAPSICUM ANNUUM L.) GENOTYPES FOR MORPHOLOGICAL AND FRUIT TRAITS UNDER HOT CLIMATE OF UMERKOT, SINDH

2021 ◽  
Vol 37 (1) ◽  
pp. 21-28
Author(s):  
A. Memon ◽  
R. Ahmad ◽  
M. S. Depar ◽  
A. K. Pathan ◽  
D. Ibrar
Keyword(s):  
Cluster Analysis ◽  
Genetic Divergence ◽  
Agricultural Research ◽  
Arid Zone ◽  
Principal Component ◽  
Fruit Weight ◽  
Economic Traits ◽  
Chilli Pepper ◽  
Hot Climate ◽  
Improvement Programs

Thirty-two genotypes of chilli from three different sources (local dandicuts, AVRDC and PGRI PARC) were evaluated for the presence of genetic divergence among them for different agro-economic traits i.e., plant height, stem girth, fruit length, fruit girth, number of fruits per plant, number of seed per fruit, fresh fruit weight and dry fruit weight at Arid Zone Agricultural Research Institute, Umerkot, Sindh during 2018. All these genotypes were found to be significantly different from each other for all the studied traits. For further diversity analysis, multivariate analyses like principal component analysis (PCA) and Cluster analysis were also performed to figure out the traits responsible for maximum variability and grouping of genotypes according to their similarities and differences for their future utilization in chilli breeding programs. PCA analysis showed that first four PCs exhibited 82.79% of the total variability among these 32 chilli genotypes. Cluster analysis showed four different sub-clusters and the genotypes from every single source merge in each sub-cluster, thus showing that chilli genotypes are from different geographical backgrounds. Based on these results, the chilli genotypes can be further utilized in future chilli improvement programs in Pakistan.  Genotypes AZRI-DS-14, AZRI-DS-01 and AVPP-9804 showed better performance.

scholarly journals Detection and evaluation of selection signatures in sheep

2018 ◽  
Vol 53 (5) ◽  
pp. 527-539 ◽  
Author(s):  
Tiago do Prado Paim ◽  
Patrícia Ianella ◽  
Samuel Rezende Paiva ◽  
Alexandre Rodrigues Caetano ◽  
Concepta Margaret McManus Pimentel
Keyword(s):  
Statistical Methods ◽  
Phenotypic Diversity ◽  
Selection Process ◽  
Genomic Data ◽  
Research Field ◽  
Economic Traits ◽  
Selection Signatures ◽  
Important Species ◽  
Challenges And Opportunities ◽  
Genomic Regions

Abstract: The recent development of genome-wide single nucleotide polymorphism (SNP) arrays made it possible to carry out several studies with different species. The selection process can increase or reduce allelic (or genic) frequencies at specific loci in the genome, besides dragging neighboring alleles in the chromosome. This way, genomic regions with increased frequencies of specific alleles are formed, caracterizing selection signatures or selective sweeps. The detection of these signatures is important to characterize genetic resources, as well as to identify genes or regions involved in the control and expression of important production and economic traits. Sheep are an important species for theses studies as they are dispersed worldwide and have great phenotypic diversity. Due to the large amounts of genomic data generated, specific statistical methods and softwares are necessary for the detection of selection signatures. Therefore, the objectives of this review are to address the main statistical methods and softwares currently used for the analysis of genomic data and the identification of selection signatures; to describe the results of recent works published on selection signatures in sheep; and to discuss some challenges and opportunities in this research field.

scholarly journals Genome-wide genetic diversity, population structure and admixture analysis in Eritrean Indigenous Cattle

2020 ◽  
Vol 49 (6) ◽  
pp. 1083-1092
Author(s):  
S Goitom ◽  
M.G. Gicheha ◽  
F.K. Njonge ◽  
N Kiplangat
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Population Differentiation ◽  
Principal Component ◽  
Vital Role ◽  
Group Method ◽  
Indigenous Cattle ◽  
Ecological Zones ◽  
Genome Wide

Indigenous cattle play a vital role in subsistence and livelihood of pastoral producers in Eritrea. In order to optimally utilize and conserve these valuable indigenous cattle genetic resources, the need to carry out an inventory of their genetic diversity was recognized. This study assessed the genetic variability, population structure and admixture of the indigenous cattle populations (ICPs) of Eritrea using a genotype by sequencing (GBS) approach. The authors genotyped 188 animals, which were sampled from 27 cattle populations in three diverse agro-ecological zones (western lowlands, highlands and eastern lowlands). The genome-wide analysis results from this study revealed genetic diversity, population structure and admixture among the ICPs. Averages of the minor allele frequency (AF), observed heterozygosity (HO), expected heterozygosity (HE), and inbreeding coefficient (FIS) were 0.157, 0.255, 0.218, and -0.089, respectively. Nei’s genetic distance (Ds) between populations ranged from 0.24 to 0.27. Mean population differentiation (FST) ranged from 0.01 to 0.30. Analysis of molecular variance revealed high genetic variation between the populations. Principal component analysis and the distance-based unweighted pair group method and arithmetic mean analyses revealed weak substructure among the populations, separating them into three genetic clusters. However, multi-locus clustering had the lowest cross-validation error when two genetically distinct groups were modelled. This information about genetic diversity and population structure of Eritrean ICPs provided a basis for establishing their conservation and genetic improvement programmes. Keywords: genetic variability, molecular characterization, population differentiation

scholarly journals A spectral theory for Wright’s inbreeding coefficients and related quantities

PLoS Genetics ◽  
2021 ◽  
Vol 17 (7) ◽  
pp. e1009665
Author(s):  
Olivier François ◽  
Clément Gain
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Population Genetic ◽  
Principal Component ◽  
Large Data ◽  
Population Subdivision ◽  
Adaptive Genetic Variation ◽  
Genomic Locus ◽  
Inbreeding Coefficients ◽  
Definition Of

Wright’s inbreeding coefficient, FST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of FST based on the decomposition of the genotype matrix into between and within-population matrices. The average value of Wright’s FST over all loci included in the genotype matrix can be obtained from the PCA of the between-population matrix. Assuming that a separation condition is fulfilled and for reasonably large data sets, this value of FST approximates the proportion of genetic variation explained by the first (K − 1) principal components accurately. The new definition of FST is useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing adaptive genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.

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