Microsatellite analysis of genetic diversity and structure of Bruguiera gymnorrhiza and Kandelia obovate

Microsatellite loci were used for estimating genetic diversity and structure for three populations of B. gymnorrhiza and K. obovata (Rhizophoracea) in Okinawa, Japan. Thirty propagules of individual samples representing the population of both species were genotyped at five microsatellites. The level of observed heterozygosity (HO) was observed for several population, overall loci, ranged 0.422-0.800 with an average 0.627 for B. gymnorrhiza and 0.477-0.822 with an average 0.665 for K. obovata, indicating both species had relatively low genetic diversity. Both species showed low levels of allelic diversity, 3-5 and 3-5 alleles per locus, respectively. Gene diversitywas also maintained within populations (HS: 0.741 and 0.954). Additionally, an analysis of molecular variance (AMOVA) based on the immeasurable alleles model (F-statistics), for B. gymnorrhiza and K. obovata found that most of the variation resided within individuals in the total populations, i.e. 79.78 % and 69.90 % respectively, and among individuals within populations, i.e.14.30 % and 27.95 % respectively. There was little variation between populations, i.e. 5.92 % and 2.15 % for B. gymnorrhiza and K. obovata, respectively. The high-level genetic differentiation within individuals and populations both species may be due to the geographic range of the species, mating system, and environmental factors.

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Genetic comparison of Altai and Gobi argali sheep (Ovis ammon) populations using mitochondrial and microsatellite markers: Implication on conservation

Proceedings of the Mongolian Academy of Sciences ◽

10.5564/pmas.v59i3.1247 ◽

2019 ◽

pp. 54-61

Author(s):

Baatar Delgerzul ◽

Zunduibaatar Unudbayasgalan ◽

Tsenddorj Bilguun ◽

Chuluunbat Battsetseg ◽

Baranz Galbadrahk ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genetic Difference ◽

Haplotype Diversity ◽

Allelic Diversity ◽

Mitochondrial Control Region ◽

Microsatellite Analysis ◽

North West ◽

Low Genetic Diversity ◽

Subspecies Level

Argali sheep is an ungulate, which inhabits the north, west, south and central regions of Mongolia. There are two major populations (Altai and Gobi) in Mongolia, but their taxonomic classification as subspecies is often disputed among researchers. Furthermore, there is no recent study about the population genetic structure of argali sheep in Mongolia. In the present study, we have investigated genetic diversity and difference between Altai and Gobi argali populations using mitochondrial control region hyper variable segment (HVS) sequence (598bp) and 3 microsatellite markers. Mitochondrial HVS haplotype analysis showed high haplotype diversity (0.982±0.012) and low nucleotide diversity (0.02589). In microsatellite analysis, total of 9 alleles were found across all loci while mean Ho were 0.59±0.13 for Altai and 0.53±0.1 for Gobi populations, indicating low allelic diversity with moderate heterozygosity. Neighbor-joining tree separated haplotypes into two clusters, Altai and Gobi population, implying distinct genetic difference between the two subspecies. Additionally, Pairwise FST and Kimura-2 parameter showed 0.127 and 0.0413±0.0068, respectively. These genetic distance analyses hinted genetic difference between Altai and Gobi populations are in subspecies level. In summary, mitochondrial HVS and microsatellite analysis demonstrated that Altai and Gobi populations had low genetic diversity but might be genetically distinct from each other in subspecies level, suggesting conservation should be separately managed.

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Genetic variation in lowland and mountain populations of Tofieldia calyculata and their ability to survive within low levels of genetic diversity

10.21203/rs.3.rs-341613/v1 ◽

2021 ◽

Author(s):

Tomáš Vlasta ◽

Zuzana Műnzbergová

Keyword(s):

Genetic Diversity ◽

Suitable Habitat ◽

Herbarium Specimens ◽

The Past ◽

Low Genetic Diversity ◽

Genetic Diversity And Structure ◽

Population Sizes ◽

Range Periphery ◽

Low Levels ◽

European Mountains

Abstract Loss of genetic diversity is expected to be a common reason for decline of populations of many rare species. To what extent this is true for populations at the range periphery remains to be explored. Alpine species with peripheral lowland populations are ideal but poorly known model system to address this issue. We investigated genetic diversity and structure of populations of Tofieldia calyculata, species common in central European mountains but highly endangered in lowlands using 17 microsatellite loci. We showed that lowland populations have lower genetic diversity than mountain populations and they are not clearly differentiated from mountain populations. Species probably survived the last glaciation in refugia in margins of Alps and western Carpathians. Some lowland populations are probably relict as well and contain unique genetic information. Their low genetic diversity is likely the result the of reduction of population sizes, gene flow during the Holocene and selfing. However postglacial colonization is also a case of some lowland populations. Based on data from herbarium specimens from extinct lowland populations, we demonstrated that lowland populations had low genetic diversity also in the past and main part of the genetic diversity was lost due to extinction of whole populations. Within population genetic diversity has not changed since the last century suggesting that these populations are able to survive with low levels of genetic diversity under suitable habitat conditions. This idea is also supported by finding of large viable recent populations with very low genetic diversity. We conclude that lowland populations are unique and deserve adequate conservation.

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Genetic diversity of rice stem borer (Chilo suppressalis Walker) from Northern Iran and comparison with other countries

Journal of Entomological and Acarological Research ◽

10.4081/jear.2016.5507 ◽

2016 ◽

Vol 48 (3) ◽

pp. 360 ◽

Cited By ~ 2

Author(s):

M. Shayanmehr ◽

E. Yoosefi-Lafooraki

Keyword(s):

Genetic Diversity ◽

Stem Borer ◽

Chilo Suppressalis ◽

Mazandaran Province ◽

Northern Iran ◽

Low Genetic Diversity ◽

High Gene ◽

Major Pest ◽

Different Populations ◽

Low Levels

Rice striped stem borer, Chilo suppressalis Walker (Lepidoptera: Crambidae) is considered the major pest of rice in Iran. Because of the serious damage on rice in Northern Iran, the present study was conducted to investigate genetic diversity within populations of C. suppressalis, from Mazandaran using a template of cytochrome oxidase I gene, 750 bps, (COI). Later the haplotypes from Iran were compared with those found in other countries. According to the results of this study, there is very low genetic diversity (two haplotypes) among different populations of this pest in populations of Northern Iran. The genetic similarity and low levels of genetic diversity of these populations suggest that the pest colonization occurred relatively recently and there is high gene flow between these populations of the province. In addition, haplotypes of Mazandaran province are different with those found in other countries. The similarity of Iranian population (Simorgh) with one population from China indicated that China might be the origin of C. suppresalis.

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Unusually Low Levels of Genetic Variation among Giardia lamblia Isolates

Eukaryotic Cell ◽

10.1128/ec.00138-07 ◽

2007 ◽

Vol 6 (8) ◽

pp. 1421-1430 ◽

Cited By ~ 52

Author(s):

Smilja Teodorovic ◽

John M. Braverman ◽

Heidi G. Elmendorf

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Giardia Lamblia ◽

Diarrheal Disease ◽

Regulation Of Gene Expression ◽

Genetic Exchange ◽

Disease Etiology ◽

Noncoding Regions ◽

Low Genetic Diversity ◽

Low Levels

ABSTRACT Giardia lamblia, an intestinal pathogen of mammals, including humans, is a significant cause of diarrheal disease around the world. Additionally, the parasite is found on a lineage which separated early from the main branch in eukaryotic evolution. The extent of genetic diversity among G. lamblia isolates is insufficiently understood, but this knowledge is a prerequisite to better understand the role of parasite variation in disease etiology and to examine the evolution of mechanisms of genetic exchange among eukaryotes. Intraisolate genetic variation in G. lamblia has never been estimated, and previous studies on interisolate genetic variation have included a limited sample of loci. Here we report a population genetics study of intra- and interisolate genetic diversity based on six coding and four noncoding regions from nine G. lamblia isolates. Our results indicate exceedingly low levels of genetic variation in two out of three G. lamblia groups that infect humans; this variation is sufficient to allow identification of isolate-specific markers. Low genetic diversity at both coding and noncoding regions, with an overall bias towards synonymous substitutions, was discovered. Surprisingly, we found a dichotomous haplotype structure in the third, more variable G. lamblia group, represented by a haplotype shared with one of the homogenous groups and an additional group-specific haplotype. We propose that the distinct patterns of genetic-variation distribution among lineages are a consequence of the presence of genetic exchange. More broadly, our findings have implications for the regulation of gene expression, as well as the mode of reproduction in the parasite.

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Analysis of genetic diversity of Ficus carica L. (Moraceae) collection using simple sequence repeat (SSR) markers

Acta Scientiarum Polonorum Hortorum Cultus ◽

10.24326/asphc.2019.4.9 ◽

2019 ◽

Vol 18 (4) ◽

pp. 93-109

Author(s):

Ilaria Marcotuli ◽

Andrea Mazzeo ◽

Domenica Nigro ◽

Stefania Lucia Giove ◽

Angelica Giancaspro ◽

...

Keyword(s):

Genetic Diversity ◽

Ficus Carica ◽

Accurate Information ◽

Main Crop ◽

Polymorphic Pattern ◽

Genetic Diversity And Structure ◽

The Mean ◽

High Level ◽

Simple Sequence ◽

Modern Technologies

Modern technologies and accurate information on genetic diversity and structure are contributing to improve the plant breeding, in particular for all the minor species with a lack of data. Genetic diversity of 139 different Ficus carica L. genotypes collected from Italy and Croatia, and divided into two subgroups: uniferous (only main crop) and biferous (breba and main crop), was investigated using 49 microsatellite markers. A total of 70 alleles were generated, of which 64 (91.4%) showed a polymorphic pattern indicating high level of genetic diversity within the studied collection. The mean heterozygosity over the 64 single locus microsatellites was 0.33 and the expected and observed averaged variance were 16.50 and 184.08, respectively. The 139 fig genotypes formed two clusters in the PCoA analysis, suggesting a division between Italian and Croatian genotypes. Moreover, the fig accessions could be divided into two main clusters based on the STRUCTURE analysis according to the biological type, uniferous or biferous, with partly overlapping varieties. In conclusion, our results demonstrated that molecular markers were able to discriminate among genotypes and useful for the authentication of fig tree varieties (homonymies and synonymies).

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De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

10.21203/rs.2.18797/v4 ◽

2020 ◽

Author(s):

Duy Dinh Vu ◽

Syed Noor Muhammad Shah ◽

Mai Phuong Pham ◽

Van Thang Bui ◽

Minh Tam Nguyen ◽

...

Keyword(s):

Genetic Diversity ◽

Endangered Species ◽

De Novo ◽

Average Length ◽

Species Conservation ◽

Illumina Hiseq ◽

Bottleneck Analysis ◽

Genetic Diversity And Structure ◽

Geographical Distances ◽

High Level

Abstract Background: Understanding the genetic diversity in endangered species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeqTM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

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Genetic diversity and structure in Leishmania infantum populations from southeastern Europe revealed by microsatellite analysis

Parasites & Vectors ◽

10.1186/1756-3305-6-342 ◽

2013 ◽

Vol 6 (1) ◽

pp. 342 ◽

Cited By ~ 24

Author(s):

Evi Gouzelou ◽

Christos Haralambous ◽

Maria Antoniou ◽

Vasiliki Christodoulou ◽

Franjo Martinković ◽

...

Keyword(s):

Genetic Diversity ◽

Leishmania Infantum ◽

Microsatellite Analysis ◽

Southeastern Europe ◽

Genetic Diversity And Structure

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Genetic variation within and among populations of Camelliajaponica (Theaceae) in Korea

Canadian Journal of Forest Research ◽

10.1139/x26-061 ◽

1996 ◽

Vol 26 (4) ◽

pp. 537-542 ◽

Cited By ~ 18

Author(s):

Myong Gi Chung ◽

Soon Suk Kang

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Pollen Dispersal ◽

Island Populations ◽

Generation Times ◽

Genetic Diversity And Structure ◽

Stump Sprouting ◽

Ability To Regenerate ◽

The Mean ◽

High Level

The genetic diversity and structure of 17 Korean populations of Camelliajaponica L., a broad-leaved evergreen tree, was examined. Although most populations are restricted to several islands near the southern and southwestern coast of the Korean Peninsula, they maintain higher levels of genetic variation within populations than do long-lived, woody angiosperms. For example, 13 of 16 loci examined were polymorphic in at least one population, the mean number of alleles per locus was 2.63, and mean expected heterozygosity was 0.265. These values were comparable with those for continuously distributed, mainland populations of C. japonica in Japan. However, a considerably high level of heterozygote deficiency was observed in Korean populations of C. japonica (mean FIS = 0.202). About 13% of the total genetic variation was found among populations (GST = 0.129). Indirect estimates of the number of migrants per generation (1.69, calculated from FST; 2.14, calculated from the mean frequency of eight private alleles) indicate that gene flow among island populations is moderate. Factors contributing to the high levels of genetic diversity found in the entire species of C. japonica include long generation times, ability to regenerate by stump sprouting, predominant outcrossing induced by animal vectors, and occasional pollen dispersal by birds.

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A Major Disjunction in Genetic Diversity Over the Geographic Range of Acacia melanoxylon R.Br

Australian Journal of Botany ◽

10.1071/bt9930355 ◽

1993 ◽

Vol 41 (3) ◽

pp. 355 ◽

Cited By ~ 23

Author(s):

J Playford ◽

JC Bell ◽

GF Moran

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Genetic Distance ◽

Allozyme Variation ◽

Geographic Range ◽

Considerable Time ◽

High Genetic Diversity ◽

Acacia Melanoxylon ◽

River Region ◽

High Level

A study of allozyme variation in Acacia melanoxylon R. Br. in 27 populations from across the geographic range of the species indicated high genetic diversity compared to other Australian trees and plants generally. Clines of increasing genetic variability with increasing latitude were found for four measures of genetic diversity. Most of the genetic diversity is found within populations but there was an unusually high level of the variation between populations (37.7%). A distinct genetic separation between the northern and southern populations was located approximately at the Hunter River region, where there is also a disjunction in the distribution of the species. The Nei (1978) genetic distance between these populations within this species is larger than observed between some plant species. Clearly the species has evolved separately in the two regions for a considerable time.

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Genetic Diversity and Structure of Common Carp (Cyprinus carpio L.) in the Centre of Carpathian Basin: Implications for Conservation

Genes ◽

10.3390/genes11111268 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1268

Author(s):

Bianka Tóth ◽

Rasoul Khosravi ◽

Mohammad Reza Ashrafzadeh ◽

Zoltán Bagi ◽

Milán Fehér ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Common Carp ◽

Assignment Test ◽

Original Strain ◽

Genetic Purity ◽

Animal Genetic Resources ◽

Genetic Diversity And Structure ◽

Low Levels ◽

Few Data

Hungary is one of the largest common carp-production countries in Europe and now, there is a large number of local breeds and strains in the country. For proper maintenance of the animal genetic resources, information on their genetic diversity and structure is essential. At present, few data are available on the genetic purity and variability of the Hungarian common carp. In this study, we genetically analyzed 13 strains in Hungary and, in addition, the Amur wild carp, using 12 microsatellite markers. A total of 117 unique alleles were detected in 630 individuals. Low levels of genetic differentiation (Fst and Cavalli–Sforza and Edwards distance) were estimated among strains. The AMOVA showed the low but significant level of genetic differentiation among strains (3.79%). Bayesian clustering analysis using STRUCTURE classified the strains into 14 different clusters. The assignment test showed that 93.64% of the individuals could be assigned correctly into their original strain. Overall, our findings can be contributed to complementing scientific knowledge for conservation and management of threatened strains of common carp.

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