ISSR Analysis of Genetic Diversity and Structure of Plum Varieties Cultivated in Southern China

Plums (Prunus spp.) are important deciduous fruit crops in the world. China is a major producer of P. salicina Lindl., but the genetic relationship of Chinese plums in key production regions remain unclear. In this study, 14 University of British Columbia (UBC) inter simple sequence repeats (ISSR) primers were used to analyze 33 plum varieties cultivated in Fujian Province to determine their genetic diversity and population structure. A total of 146 bands were generated, of which 130 were polymorphic. Mean percentage of polymorphic bands was 89.04%, Shannon’s information index value was 0.38, and the Nei’s genetic index value was 0.24. Using unrooted trees (Neighbor-Joining method), 33 varieties were classified into four groups. Split graph separated them into two major groups, each with two subgroups. The two phylogenetic trees indicate that environmental or natural selection pressure is an important factor influencing their genetic relationship. Analysis of population structure revealed that they have frequent genetic exchanges among closed subpopulations; thus, genetic variation mainly occurs within the population. Additionally, based on the phylogenetic analysis and unique morphological characteristics of fruits, we propose that the Chinese landrace Nai could contribute significantly to development of the famous variety Wickson.

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Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

Malaria Journal ◽

10.1186/s12936-021-03734-x ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Fehintola V. Ajogbasile ◽

Adeyemi T. Kayode ◽

Paul E. Oluniyi ◽

Kazeem O. Akano ◽

Jessica N. Uwanibe ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Population Structure ◽

Microsatellite Loci ◽

Control Strategies ◽

Population Diversity ◽

Parasite Population ◽

Nested Polymerase Chain Reaction ◽

Public Health Burden ◽

Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

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Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

10.21203/rs.3.rs-673512/v1 ◽

2021 ◽

Author(s):

Varun Hiremath ◽

Kanwar Pal Singh ◽

Neelu Jain ◽

Kishan Swaroop ◽

Pradeep Kumar Jain ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Structure Analysis ◽

Genetic Relationships ◽

Crop Improvement ◽

Test Analysis ◽

Average Value ◽

Population Structure Analysis ◽

Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

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How diverse can rare species be on the margins of genera distribution?

AoB Plants ◽

10.1093/aobpla/plz037 ◽

2019 ◽

Vol 11 (4) ◽

Author(s):

Alice Backes ◽

Geraldo Mäder ◽

Caroline Turchetto ◽

Ana Lúcia Segatto ◽

Jeferson N Fregonezi ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Variability ◽

Habitat Loss ◽

Evolutionary History ◽

Founder Effects ◽

Geographical Isolation ◽

Genetic Diversity And Structure ◽

Genetic Patterns

Abstract Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.

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Genetic diversity and structure of the noxious alien grass Praxelis clematidea in southern China

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2015.01.021 ◽

2015 ◽

Vol 59 ◽

pp. 183-189 ◽

Cited By ~ 5

Author(s):

Qizhi Wang ◽

Min Huang ◽

Stephen R. Downie ◽

Zhenxi Chen ◽

Yating Chen

Keyword(s):

Genetic Diversity ◽

Southern China ◽

Genetic Diversity And Structure

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GENETIC DIVERSITY OF HONEY BEE POPULATIONS IN TURKEY BASED ON MICROSATELLITE MARKERS: A COMPARISON BETWEEN MIGRATORY VERSUS STATIONARY APIARIES AND ISOLATED REGIONS VERSUS REGIONS OPEN TO MIGRATORY BEEKEEPING

10.31237/osf.io/gkusw ◽

2019 ◽

Cited By ~ 1

Author(s):

Mert Kükrer

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Honey Bee ◽

Honey Bees ◽

Phylogenetic Trees ◽

The Status ◽

Genetic Impact ◽

Geographic Populations ◽

Ecological Importance

The honey bee (Apis mellifera L.) is a globally significant species of apparent economic and ecological importance. Recent reports from Spain, Italy and Greece point to an intense admixture of honey bee populations signified by a loss of population structure. This is mostly attributed to migratory beekeeping practices and replacement of queens or colonies with commercial ones that are usually from non-native races or hybrids of different subspecies. These two practices are also heavily carried out in parts of Turkey where almost three-quarters of the 6 million colonies are transferred seasonally from one region to other.Past research using microsatellite and RAPD markers, mtDNA, allozymes and geometric morphometry revealed the presence of five different subspecies of honey bees (meda, syriaca,caucasica, anatoliaca and an ecotype from Carniolan subspecies group) inTurkey. Here, we carried out an analysis of population structure of Turkish honeybees sampled from six different regions (n = 250) during the period 2010-2012. A total of 29 microsatellite markers were used in four multiplex reactions. The results show that population structure is preserved in general although there are signs of gene flow between the clusters.Overall FST between stationary colonies was calculated as 0,067. For migratory colonies the value was 0,015 and for all the 250 samples the value was 0,047. Four different clusters corresponding to geographical distributions of four subspecies were revealed in structure analysis. The differentiation between the clusters was also apparent in PCA and FCA as well as phylogenetic trees constructed based on genetic distances.The genetic impact of migratory beekeeping was demonstrated for the first time based on a comparison of assignment probabilities of individuals from migratory and stationary colonies to their geographic populations. Another comparison between regions that are either open to migratory beekeeping or closed let us to evaluate the status of isolated regions and showed the importance of establishing such regions. The effects of queen and colony trade were revealed by the presence of introgression from the highly commercial Caucasian bees. Our findings confirm the previously observed high levels geographically structured genetic diversity in honey bees of Turkey and emphasize the need to develop policies to maintain this diversity.

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Genetic diversity and population structure of Rhipicephalus sanguineus sensu lato across different regions of Colombia

Parasites & Vectors ◽

10.1186/s13071-021-04898-w ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Luisa Páez-Triana ◽

Marina Muñoz ◽

Giovanny Herrera ◽

Darwin A. Moreno-Pérez ◽

Gabriel A. Tafur-Gómez ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Dna Sequences ◽

Phylogenetic Trees ◽

Statistical Tests ◽

Population Expansion ◽

Rhipicephalus Sanguineus ◽

Tick Population ◽

12S Rdna ◽

Haplotype Networks

Abstract Background There has been a long-standing debate over the taxonomic status of Rhipicephalus sanguineus sensu lato. Different studies worldwide have reported the occurrence of different well-defined lineages, in addition to Rhipicephalus sanguineus sensu stricto. To date, there are very few studies examining the diverse aspects of this tick in Colombia. We assessed the population structure and genetic diversity of R. sanguineus s.l. in eight departmental regions across Colombia. Methods A total of 170 ticks were collected from dogs in different departments of Colombia. All specimens were morphologically compatible with R. sanguineus s.l. and subjected to genetic analysis. DNA sequences were obtained for the 12S rDNA, cytochrome oxidase I (COI) and internal transcribed spacer 2 (ITS2) markers. A concatenated set of all mitochondrial markers was also constructed. Next, maximum likelihood phylogenetic trees were constructed using the sequences generated herein and sequences available in GenBank. Finally, we assessed different summary statistics and analysed population structure and divergence with Fst and Dxy and demographic changes with Tajima's D and Fu and Li’s statistical tests. Results Analysis of the 12S rDNA and COI revealed that all R. sanguineus s.l. specimens collected across different regions of Colombia clustered within the tropical lineage. Micro-geographical analyses showed that the tick population from Amazonas formed a distinct cluster separated from the other sequences, with moderate Fst and Dxy values. However, no signs of a robust population structure were found within the country. The results of Fu’s FS tests, together with the haplotype networks and diversity values, signal a possible population expansion of this tick species in Colombia. Conclusions Evidence provided herein supports the tropical lineage as the main circulating lineage in Colombia, exhibiting a general lack of genetic structure except for the Amazonas region. Graphical Abstract

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Genetic Diversity and Population Structure of Races of Fusarium oxysporum Causing Cotton Wilt

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401187 ◽

2020 ◽

Vol 10 (9) ◽

pp. 3261-3269

Author(s):

Hannah C Halpern ◽

Peng Qi ◽

Robert C Kemerait ◽

Marin T Brewer

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Fusarium Oxysporum ◽

Principal Components ◽

Phylogenetic Trees ◽

Elongation Factor ◽

Intergenic Spacer ◽

Pathogenic Fungi ◽

The United States ◽

Intergenic Spacer Region

Abstract To better understand the evolution of virulence we are interested in identifying the genetic basis of this trait in pathogenic fungi and in developing tools for the rapid characterization of variation in virulence among populations associated with epidemics. Fusarium oxysporum f. sp. vasinfectum (FOV) is a haploid fungus that causes devastating outbreaks of Fusarium wilt of cotton wherever it is grown. In the United States, six nominal races and eleven genotypes of FOV have been characterized based on the translation elongation factor (EF-1α) gene and intergenic spacer region (IGS), but it is unclear how race or genotype based on these regions relates to population structure or virulence. We used genotyping-by-sequencing to identify SNPs and determine genetic diversity and population structure among 86 diverse FOV isolates. Six individuals of Fusarium oxysporum closely related to FOV were genotyped and included in some analyses. Between 193 and 354 SNPs were identified and included in the analyses depending on the pipeline and filtering criteria used. Phylogenetic trees, minimum spanning networks (MSNs), principal components analysis (PCA), and discriminant analysis of principal components (DAPC) demonstrated that races and genotypes of FOV are generally not structured by EF-1α genotype, nor are they monophyletic groups with the exception of race 4 isolates, which are distinct. Furthermore, DAPC identified between 11 and 14 genetically distinct clusters of FOV, whereas only eight EF-1α genotypes were represented among isolates; suggesting that FOV, especially isolates within the widely distributed and common race 1 genotype, is more genetically diverse than currently recognized.

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Genetic Diversity and Population Structure of Kerala Rice Landraces Using Genotyping-By-Sequencing

10.21203/rs.3.rs-516783/v1 ◽

2021 ◽

Author(s):

Maya Peringottillam ◽

Smitha Kunhiraman Vasumathy ◽

Hari Krishna Kumar ◽

Manickavelu Alagu

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Genetic Purity ◽

Next Generation Sequencing Technology ◽

Distance Analysis ◽

Rice Landraces ◽

Genetic Diversity And Structure ◽

Rice Landrace

Abstract Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for creating opportunities to guide more realistic and applicable strategies for the sustainable management of genetically diverse rice resources. This study is a pioneering effort where GBS-SNP markers were employed to assess the tremendous genetic diversity and structure of rice landrace collections from northern Kerala. Kerala holds an immense diversity of rice landraces that encountered selection pressures of environmental heterogeneity, biotic and abiotic stresses, however competent rather provide good yields, whereby drawing the attention of the rice breeding sector. The population structure and diversity analyses separated the accessions into three distinct subpopulations with a huge amount of genetic variation within subpopulations. Nei’s genetic distance analysis confirmed the existence of strong genetic differentiation among rice landrace populations. The values of FST and Nm established the farmers’ effort to preserve the genetic purity of rice landraces despite the extensive seed exchange programs across the states of India. Moreover, this low level of gene flow among subpopulations could provide the opportunity for well-adapted combinations of genes to be established by natural selection. The clustering pattern based on SNP markers furnished sufficient knowledge in identifying rice genotypes that eliminates the likelihood of duplication among indigenous cultivars. Similar clustering patterns of genotypes revealed shared genetic characters among them. Collectively these analyses can be used to completely understand the population of rice landraces in Kerala while contributing insights toward the evolution and selective pressures underlying these unique landraces.

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Evaluation of the population structure and genetic diversity of Plasmodium falciparum in southern China

Malaria Journal ◽

10.1186/s12936-015-0786-0 ◽

2015 ◽

Vol 14 (1) ◽

Cited By ~ 12

Author(s):

Guiying Wei ◽

Lili Zhang ◽

He Yan ◽

Yuemeng Zhao ◽

Jingying Hu ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Population Structure ◽

Southern China

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Genetic diversity and population structure of disjunct Newfoundland and central Ontario populations of eastern white pine (Pinus strobus)

Canadian Journal of Botany ◽

10.1139/b98-021 ◽

1998 ◽

Vol 76 (3) ◽

pp. 500-508 ◽

Cited By ~ 15

Author(s):

Om P Rajora ◽

Linda DeVerno ◽

Alex Mosseler ◽

David J Innes

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Pinus Strobus ◽

Population Bottleneck ◽

Genetic Distances ◽

Population Variation ◽

White Pine ◽

Eastern White Pine ◽

Genetic Diversity And Structure ◽

Allozyme Loci

The dramatic decline of eastern white pine (Pinus strobus L.) populations in Newfoundland over the past 100 years presents an opportunity to determine and monitor population bottleneck effects on genetic diversity in trees. To provide benchmarks and indicators for monitoring genetic changes due to recent and future bottleneck events and to assist development of conservation strategies, we assessed genetic diversity and structure of six small, isolated white pine populations from two regions at the limits of its geographical range in Newfoundland for comparison with three populations from its central range in Ontario for 20 allozyme loci coding for 12 enzymes. On average, 47.8% of the loci were polymorphic, the number of alleles per locus was 1.75, and the observed and expected heterozygosities were 0.215 and 0.195, respectively. Although most of the alleles were widespread, unique alleles were found in three of the nine populations examined. The Newfoundland populations were as genetically variable as those from Ontario. Generally, all populations exhibited slight excess of heterozygotes at most loci. Only 6.1% of the detected genetic variation was among populations, and the remainder among individuals within populations. The genetic distances among the populations within a province or region were as great as those among populations between the provinces or regions. Canonical discriminant functions and cluster analysis from genetic distances separated nine populations into the same four groups. Neither provincial nor regional or geographic gradient-related patterns of population variation and differentiation were apparent. It appears that 8000 years of postglacial geographic isolation and recent population decline have had little or no detectable effect on genetic diversity or differentiation of disjunct Newfoundland white pine populations from their ancestral mainland populations. Assuming their adaptability, the Ontario seed sources may be acceptable for white pine restoration in Newfoundland.Key words : Pinus strobus, allozymes, gene conservation, genetic diversity and population structure, genetic drift, population bottleneck.

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