scholarly journals Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography

2020 ◽  
Vol 42 (10) ◽  
pp. 1169-1178
Author(s):  
Agraw Amane ◽  
Gurja Belay ◽  
Yao Nasser ◽  
Martina Kyalo ◽  
Tadelle Dessie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
Genetic Research ◽  
Principal Component ◽  
Conservation Strategies ◽  
Genetic Cluster ◽  
Sheep Population ◽  
Indigenous Sheep ◽  
Genome Wide

Abstract Background Ethiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies. Objective The study was aimed to investigate genome-wide genetic diversity and population structure of eight Ethiopian sheep populations. Methods A total of 115 blood samples were collected from four Ethiopian sheep populations that include Washera, Farta and Wollo (short fat-tailed) and Horro (long fat-tailed). DNA was extracted using Quick-DNA™ Miniprep plus kit. All DNA samples were genotyped using Ovine 50 K SNP BeadChip. To infer genetic relationships of Ethiopian sheep at national, continental and global levels, genotype data on four Ethiopian sheep (Adilo, Arsi-Bale, Menz and Black Head Somali) and sheep from east, north, and south Africa, Middle East and Asia were included in the study as reference. Results Mean genetic diversity of Ethiopian sheep populations ranged from 0.352 ± 0.14 for Horro to 0.379 ± 0.14 for Arsi-Bale sheep. Population structure and principal component analyses of the eight Ethiopian indigenous sheep revealed four distinct genetic cluster groups according to their tail phenotype and geographical distribution. The short fat-tailed sheep did not represent one genetic cluster group. Ethiopian fat-rump sheep share a common genetic background with the Kenyan fat-tailed sheep. Conclusion The results of the present study revealed the principal component and population structure follows a clear pattern of tail morphology and phylogeography. There is clear signature of admixture among the study Ethiopian sheep populations

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 Genetic Diversity and Population Structure of Traditional Chinese Herb “Chai-Hu” Resources Using Genome-Wide SNPs Through Genotyping-By-Sequencing

2022 ◽  
Author(s):  
Ming Jiang ◽  
Song Yan ◽  
Weichao Ren ◽  
Nannan Xing ◽  
Hongyuan Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Chinese Herb ◽  
Genetic Research ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Intrapopulation Variation ◽  
Traditional Chinese Herb ◽  
High Quality Snps ◽  
Population Structure Analysis

Abstract Bupleurum (named “Chai-hu”) is an important traditional Chinese medicine resource in China. It has been widely used since ancient times and has antipyretic, analgesic and cholagogic functions, but there is little research on its genetic diversity. In this study, genotyping-by-sequencing (GBS) was used to detect SNP loci in 39 Bupleurum germplasm resources from different regions in China and analyse their genetic diversity. A total of 25.1 Gb of data was obtained by sequencing, with an average of 0.64 Gb per sample. After screening, 83898 high-quality SNPs were obtained. The results of genetic research were obtained by phylogenetic tree, principal component analysis and population structure analysis, and the 39 experimental materials were divided into three groups. The average observed heterozygosity and expected heterozygosity of Bupleurum populations were 0.24 and 0.17, respectively, indicating that Bupleurum populations from five different provinces had a low level of genetic diversity. Population nucleotide diversity analysis and analysis of molecular variance showed that the percentage of intrapopulation variation was 120.88%, while the percentage of interpopulation variation was only 2.46%. There was relative aggregation of Bupleurum samples with the same geographical origin, but the division of population structure was not completely correlated with sample origin. The results showed that the genetic diversity of the materials was low and that the genetic variation was narrow. This provides a good basis for the genetic breeding and protection of species diversity of Bupleurum.

scholarly journals Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10485
Author(s):  
Zhixin Wang ◽  
Yalin Sun ◽  
Xinfang Huang ◽  
Feng Li ◽  
Yuping Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Conservation ◽  
Principal Component ◽  
Snp Markers ◽  
Colocasia Esculenta ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Entire Collection ◽  
Tuber Crop

Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.

scholarly journals Genome-wide diversity of coconut from northern South America uncovers genotypes present in Colombia and strong population structure

2019 ◽  
Author(s):  
Jorge Mario Muñoz-Pérez ◽  
Gloria Patricia Cañas ◽  
Lorena López ◽  
Tatiana Arias
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
South America ◽  
Genetic Relationships ◽  
Cocos Nucifera ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
The Pacific ◽  
Population Structure Analysis ◽  
Northern South America

SummaryCoconut palms (Cocos nucifera) are a combination of wild admixed populations and perennial crops with a worldwide distribution. Here we develop single nucleotide polymorphisms (SNPs) along the coconut genome based on Genotyping by Sequencing (GBS) for at least four different commercially important and widely cultivated coconut varieties and hybrids growing in northern South America. We present a comprehensive catalog of approximately 27K SNPs to conduct genetic diversity, population structure and linkage disequilibrium analysis. A relatively fast LD decay for the Atlantic accessions within ~250Kb was observed in comparison to the Pacific accessions ~ 1500 Kb.The complete SNPs sampling showed a strong population structure at K = 2, separating accessions from the Pacific and Atlantic coasts as it has been found in previous studies. At higher K values, one non-admixed group was observed for the Atlantic while further substructures emerged for the Pacific accessions, where three non-admixed groups were found. Population structure analysis also showed a great degree of admixture between the Atlantic and Pacific populations, and SNPs of the Pacific non-admixed genetic groups were mostly introgressed into the Atlantic individuals but the contrary was rarely observed. The results of principal component analysis and Neighbor-Joining Hierarchical Clustering were consistent with the results from Structure and provided a measure of genetic relationships among individual genotypes. The Pacific group has a lower genetic diversity and a higher rate of inbreeding than the Atlantic group. These results suggest that the Pacific coconuts of Colombia belong to the pre-Columbian population found on the Pacific coast of Panama and Peru. If it had been introduced after Columbus (as in Mexico), genetic diversity would have been higher than on the Atlantic coast.

scholarly journals The Genetic Diversity and Population Structure of Different Geographical Populations of Bottle Gourd (Lagenaria siceraria) Accessions Based on Genotyping-by-Sequencing

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1677
Author(s):  
Rodrigo Contreras-Soto ◽  
Ariel Salvatierra ◽  
Carlos Maldonado ◽  
Jacob Mashilo
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
Genotyping By Sequencing ◽  
Bottle Gourd ◽  
Conservation Strategies ◽  
Lagenaria Siceraria ◽  
Genomic Resources ◽  
Ssr Loci ◽  
Pharmaceutical Industries

Lagenaria siceraria (Molina) Standl is an important horticultural and medicinal crop grown worldwide in the food and pharmaceutical industries. The crop exhibits extensive phenotypic and genetic variation useful for cultivar development targeting economic traits; however, limited genomic resources are available for effective germplasm characterization into breeding and conservation strategies. This study determined the genetic relationships and population structure in a collection of different accessions of bottle gourd derived from Chile, Asia, and South Africa by using single-nucleotide polymorphism (SNP) markers and mining of simple sequence repeat (SSR) loci derived from genotyping-by-sequencing (GBS) data. The GBS resulted in 12,766 SNPs classified as moderate to highly informative, with a mean polymorphic information content of 0.29. The mean gene diversity of 0.16 indicated a low genetic differentiation of the accessions. Analysis of molecular variance revealed less differentiation between (36%) as compared to within (48%) bottle gourd accessions, suggesting that a random mating system dominates inbreeding. Population structure revealed two genetically differentiated groups comprising South African accessions and an admixed group with accessions of Asian and Chilean origin. The results of SSR loci mining from GBS data should be developed and validated before being used in diverse bottle gourd accessions. The SNPs markers developed in the present study are useful genomic resources in bottle gourd breeding programs for assessing the extent of genetic diversity for effective parental selection and breeding.

scholarly journals Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Buweihailiqiemu Ababaikeri ◽  
Yucong Zhang ◽  
Huiying Dai ◽  
Wenjuan Shan
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Tarim Basin ◽  
Principal Component ◽  
Northwest China ◽  
The North ◽  
Genome Wide ◽  
Specific Length

Abstract Background The Yarkand hare (Lepus yarkandensis Günther, 1875) is endemic to oasis and desert areas around the Tarim Basin in the Xinjiang Uyghur Autonomous Region of northwest China; however, genome-wide information for this species remains limited. Moreover, the genetic variation, genetic structure, and phylogenetic relationships of Yarkand hare from the plateau mountain regions have not been reported. Thus, we used specific-length amplified fragment sequencing (SLAF-seq) technology to evaluate the genetic diversity of 76 Yarkand hares from seven geographic populations in the northern and southwestern parts of the Tarim Basin to investigate single-nucleotide polymorphism (SNP) marker-based population differentiation and evolutionary processes. Selective sweep analysis was conducted to identify genetic differences between populations. Results Using SLAF-seq, a total of 1,835,504 SNPs were initially obtained, of which 308,942 high-confidence SNPs were selected for further analysis. Yarkand hares exhibited a relatively high degree of genetic diversity at the SNP level. Based on pairwise FST estimates, the north and southwest groups showed a moderate level of genetic differentiation. Phylogenetic tree and population structure analyses demonstrated evident systematic phylogeographical structure patterns consistent with the geographical distribution of the hares. Hierarchical analysis of molecular variation further indicated that genetic variation was mainly observed within populations. Low to moderate genetic differentiation also occurred among populations despite a common genomic background, likely due to geographical barriers, genetic drift, and differential selection pressure of distinct environments. Nevertheless, the observed lineage-mixing pattern, as indicated by the evolutionary tree, principal component analysis, population structure, and TreeMix analyses, suggests a certain degree of gene flow between the north and southwest groups. This may be related to the migration of hares to high-altitude water sources southwest of the basin during glacial climatic oscillations, as well as river re-diffusion and oasis restoration in the basin following the glacial period. We also identified candidate genes, and their associated gene ontology terms and pathways, related to the adaptation of Yarkand hares to different environmental habitats. Conclusions The identified genome-wide SNPs, genetic diversity, and population structure of Yarkand hares expand our understanding of the genetic background of this endemic species and provide valuable insights into its environmental adaptation, allowing for further exploration of the underlying mechanisms.

scholarly journals Phenotypic Characterisation for Growth and Nut Characteristics Revealed the Extent of Genetic Diversity in Wild Macadamia Germplasm

Agriculture ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 680
Author(s):  
Thuy T. P. Mai ◽  
Craig M. Hardner ◽  
Mobashwer M. Alam ◽  
Robert J. Henry ◽  
Bruce L. Topp
Keyword(s):  
Genetic Diversity ◽  
Growth Traits ◽  
Principal Component ◽  
Conservation Strategies ◽  
Wild Germplasm ◽  
Phenotypic Characterisation ◽  
Wide Range ◽  
Genetic And Environmental Factors ◽  
Positive Correlations ◽  
Wild Accessions

Macadamia is a recently domesticated Australian native nut crop, and a large proportion of its wild germplasm is unexploited. Aiming to explore the existing diversity, 247 wild accessions from four species and inter-specific hybrids were phenotyped. A wide range of variation was found in growth and nut traits. Broad-sense heritability of traits were moderate (0.43–0.64), which suggested that both genetic and environmental factors are equally important for the variability of the traits. Correlations among the growth traits were significantly positive (0.49–0.76). There were significant positive correlations among the nut traits except for kernel recovery. The association between kernel recovery and shell thickness was highly significant and negative. Principal component analysis of the traits separated representative species groups. Accessions from Macadamia integrifolia Maiden and Betche, M. tetraphylla L.A.S. Johnson, and admixtures were clustered into one group and those of M. ternifolia F. Muell were separated into another group. In both M. integrifolia and M. tetraphylla groups, variation within site was greater than across sites, which suggested that the conservation strategies should concentrate on increased sampling within sites to capture wide genetic diversity. This study provides a background on the utilisation of wild germplasm as a genetic resource to be used in breeding programs and the direction for gene pool conservation.

scholarly journals Genetic diversity and population structure analysis of Lateolabrax maculatus from Chinese coastal waters using polymorphic microsatellite markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wei Wang ◽  
Chunyan Ma ◽  
Longling Ouyang ◽  
Wei Chen ◽  
Ming Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Principal Component ◽  
Genetic Constitution ◽  
Southern Group ◽  
Population Structure Analysis ◽  
Lateolabrax Maculatus ◽  
Geographic Populations ◽  
Geographic Separation

AbstractIn order to provide valuable guidelines for the conservation of germplasm of Lateolabrax maculatus, the genetic diversity and population structure analysis were evaluated for eight geographic populations along coastal regions of China, using 11 microsatellite DNA markers. The genetic parameters obtained showed that, eight populations can be clustered into two groups, the Northern group and the Southern group, concordant with their geographical positions. The UPGMA tree constructed according to the Nei’s genetic distance along with the structure analysis and discriminant analysis of principal component also supported this result. This might be explained by the geographic separation and the divergent environmental conditions among the populations. It's worth noting that, QD (Qingdao) population from northern area was assigned to the Southern group and showed a close genetic relationship and similar genetic constitution with the southern populations. We speculated that large scales of anthropogenic transportation of wild fries from QD populations to the southern aquaculture areas in history should be the primary cause. The populations from GY (Ganyu), RD (Rudong) and BH (Binhai) had higher genetic diversity and showed limited genetic exchange with other populations, indicating better conservation of the natural resources in these regions. All populations were indicated to have experienced bottleneck events in history.

Geographic patterns of genetic variation and population structure in Pinus aristata, Rocky Mountain bristlecone pine

2012 ◽  
Vol 42 (1) ◽  
pp. 23-37 ◽  
Author(s):  
Anna W. Schoettle ◽  
Betsy A. Goodrich ◽  
Valerie Hipkins ◽  
Christopher Richards ◽  
Julie Kray
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Bark Beetles ◽  
Climatic Factors ◽  
Rocky Mountain ◽  
Conservation Strategies ◽  
Restricted Gene Flow ◽  
Populations At Risk ◽  
Bristlecone Pine ◽  
Pinus Aristata

Pinus aristata Engelm., Rocky Mountain bristlecone pine, has a narrow core geographic and elevational distribution, occurs in disjunct populations, and is threatened by rapid climate change, white pine blister rust, and bark beetles. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Sixteen sites across four mountain ranges in the core distribution of P. aristata were sampled and genetic diversity was assessed with 21 isozyme loci. Low species and population level genetic diversity (He = 0.070 and 0.062, respectively) occurred with moderate among-population differentiation (FST = 0.131). Genetic diversity correlated with longitude, latitude, and elevation and a strong mountain island effect may contribute to substructuring and isolation. Using multiple complementary analyses, sampled trees were assigned to three genetic lineages that varied in diversity and admixture and were associated with different climatic factors. The distribution of genetic diversity and substructuring of P. aristata may be an outcome of a combination of restricted gene flow due to geographic and phenological isolation, random processes of genetic drift, life history traits, natural selection, and postglacial migrations. The combination of low genetic diversity, moderate population isolation, and a protracted regeneration dynamic puts populations at risk for extirpation by novel stresses.

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