Temporal stability of genetic diversity revealed by microsatellite markers in restocked populations of Caspian roach, Rutilus caspicus (Yakovlev, 1870)

Abstract Rutilus caspicus is considered one of the most important bony fish with high economic value in the Caspian Sea. Since the population size of Caspian roach has decreased during recent decades, restocking of the populations is done through releasing hatchery-produced larvae into the wild. In the present study, the genetic diversity of wild and hatchery populations of R. caspicus was investigated using ten microsatellite loci. Also, microsatellite analysis was performed to compare the population structure of Caspian roach over a time frame of about 11 years. Although the allelic and gene diversity of hatchery populations tended to be lower than those of the wild populations, no significant differences in genetic diversity parameters were observed among the wild and hatchery populations. Similar variation levels were noticed among temporal samples of the same population, suggesting temporal stability in the genetic diversity of the wild populations. In most cases, significant departure from the Hardy-Weinberg equilibrium was observed after sequential Bonferroni correction. Results from analysis showed that a captive hatchery population was the most differentiated group. Also, the UPGMA dendrogram showed that the captive population was the most distant group. The stability of genetic composition between the two periods was noticed by the low and non-significant and estimates. The results from this study are anticipated to provide important information for setting up more efficient strategies for the conservation and restocking of R. caspicus.

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Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers

Forests ◽

10.3390/f10111019 ◽

2019 ◽

Vol 10 (11) ◽

pp. 1019 ◽

Cited By ~ 1

Author(s):

Zhong ◽

Yang ◽

Li ◽

Zhang ◽

Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

South China ◽

Expressed Sequence Tag ◽

Gene Diversity ◽

Jiangxi Province ◽

Group Method ◽

Cinnamomum Camphora ◽

Wild Populations ◽

Arithmetic Means

Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei’ gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs.

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Genetic diversity in wild and hatchery populations of stinging catfish (Heteropneustes fossilis Bloch) revealed by RAPD analysis

Journal of Bio-Science ◽

10.3329/jbs.v19i0.13005 ◽

2012 ◽

Vol 19 ◽

pp. 81-87

Author(s):

Md Nazrul Islam ◽

Abhishak Basak ◽

Dr Ashrafullah ◽

Md Samsul Alam

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Gene Diversity ◽

Similarity Index ◽

Heteropneustes Fossilis ◽

Wild Populations ◽

Polymorphic Loci

Context: DNA fingerprinting using genetic markers such as Random Amplification of Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), microsatellite (Simple sequence repeat), Amplified Fragment Length Polymorphism (AFLP) etc. can be successfully used to reveal genetic variation within and among different populations. Objective: The aim of the present study was to assess genetic diversity in two wild and one hatchery populations of stinging catfish Heteropneustes fossilis by RAPD fingerprinting. Materials and Methods: A total of 90 live fish (H. fossilis), 30 from each source, were collected from a beel in Patuakhali, a beel in Jessore and Rupali Hatchery, Mymensingh. Genomic DNA was extracted from fin tissues. The concentration of DNA was estimated using a spectrophotometer. Fifteen decamer primers of random sequence from three kits (six from kit A, seven from kit B and two from kit C) (Operon technologies, Inc., Alameda, CA, USA) were screened on sub-samples of one randomly chosen H. fossilis DNA sample from the each population to test their suitability for amplifying RAPDs. The amplified products from each sample were separated by electrophoresis on 1.4% agarose gel containing ethidium bromide. The sizes of the bands were calculated using the software DNAFRAG and the sizes in base pair (bp) were used for identification of the bands (RAPD markers). The similarity index values (SI) between the RAPD fingerprint of any two individuals on the same gel were calculated from RAPD band sharing. Results: A total of 28 RAPD bands were obtained using four decamer random primers, among which 21 bands were polymorphic. The percentage of polymorphic loci, intra-population similarity indices and Nei's gene diversity values were 85.71%, 78.75 and 0.304±0.183 for Jessore population, 83.71%, 82.62 and 0.280±0.159 for Patuakhali population, 82.14%, 85.25 and 0.271±0.165 for Rupali hatchery population, respectively. The overall gene flow (Nm) among the populations was 5.755. The highest inter-similarity (Sij) was found between Patuakhali - Rupali hatchery populations. Among the three populations, the highest genetic distance (0.069) was found between Jessore and Patuakhali population. Considering polymorphic loci, intrapopulation similarity index and gene diversity the genetic variation in the Jessore population was higher than the other two populations. The genetic variation of the hatchery population was found to be lower than the two wild populations. Conclusion: The result of the present study can be used as baseline information regarding the genetic variation and population structure before undertaking any breeding programme. Study indicated that the genetic variation in the hatchery populations were slightly lower than those of the wild populations. DOI: http://dx.doi.org/10.3329/jbs.v19i0.13005 J. bio-sci. 19 81-87, 2011

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Evaluation of genetic diversity of Rubus hyrcanus using Inter Simple Sequence Repeat (ISSR) and morphological markers

Biologia ◽

10.1515/biolog-2015-0039 ◽

2015 ◽

Vol 70 (3) ◽

Author(s):

Ehsan Sedighi ◽

Mehdi Rahimmalek

Keyword(s):

Genetic Diversity ◽

Caspian Sea ◽

Gene Diversity ◽

Inter Simple Sequence Repeat ◽

Morphological Markers ◽

The Caspian Sea ◽

Geographical Regions ◽

North Eastern ◽

North Western ◽

Simple Sequence

AbstractRubus hyrcanus is considered as an important wild blackberry species scattered around the Caspian Sea. In this research, ISSR and morphological markers were used to assess genetic diversity in several populations of R. hyrcanus from various geographical regions of Caspian Sea in Iran. Twenty-five populations of R. hyrcanus from three regions (North- Western (NW), North- Eastern (NE) and Central (C)) and one population from R. discolor were applied in this research. Ten primers were used to amplify bands out of which 157 (77.13%) were polymorphic. Cluster and Principle coordinate analyses (PCoA) showed the higher similarity of NE and NW populations. Analysis of molecular variance (AMOVA) revealed that the differences among three collection regions only accounted for 28.09% of the total variation, whereas differences among populations within groups were 66.03%. Analyses among three regions showed that the minimum gene diversity over loci was observed in NW (0.16) and NE (0.17), while the highest one was found in C (0.238) region. Furthermore, narrow genetic base and relatively high genetic differentiation obtained for studied R. hyrcanus genotypes. The results of morphological analysis in most cases corresponded to those obtained through molecular analyses.

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Genetic Diversity Analysis, Population Structure and Gene-flow Estimates among Citrus Macroptera Mont. Collections from Garo Hills, Meghalaya using SPAR Approach

Journal of Agriculture and Horticulture Research ◽

10.33140/jahr.04.01.03 ◽

2021 ◽

Vol 4 (1) ◽

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Gene Diversity ◽

Time Frame ◽

Conservation Strategies ◽

North East India ◽

Information Index ◽

North East ◽

Garo Hills ◽

Single Primer

North East India is extremely rich in natural resources and is a biodiversity hotspot. Many plant species, including Citrus are known to have originated from this region. Citus macroptera Mont. is a wild, endangered species which have been found to exist naturally in various parts of this region, including Meghalaya. To access the genetic variability among genotypes and their phylogeny, 30 genotypes of wild C. macroptera Mont. were collected from Garo Hills of Meghalaya. Single primer based DNA markers viz. RAPD, ISSR, DAMD were utilized to ascertain genetic diversity. The percentage polymorphic bands for RAPD, ISSR, DAMD were found to be 97.71%, 94.67% and 100% respectively. ISSR showed the highest values for both RP (7.67) and MI (5.03) highlighting its efficacy in determining genetic variations. A concatenated approach, Single Primer Amplification Reaction (SPAR) was also followed to assess their genetic diversity. Dendogram generated from SPAR data showed that the South-West Garo Hills population is the most recently evolved amongst all others while West Garo Hills collections retain an ancestral position in the evolutionary time-frame. Population genetics parametres such as Gene flow (Nm) and the diversity among populations (GST) were found to be 1.9894 and 0.2009 respectively. Gene flow estimates (Nm>1) suggests appreciable gene flow in the populations. AMOVA data further supported this with high percentage of variations (92%) within populations whereas variations among populations were about 8% only. Shannon’s information index (I) values and Nei’s gene diversity (h) varied between 0.303-0.423and 0.201-0.285 respectively. The use of SPAR method yields a clear and concise picture of the underlying genetic variabilities, and a detailed and comprehensive data analysis will help conceive efficient and sustainable conservation strategies for this important plant.

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Estimating the stability of heartbeat counting in middle childhood: a twin study

10.31234/osf.io/xnqjr ◽

2019 ◽

Author(s):

Jennifer Murphy ◽

Rosa Cheesman ◽

Alice M Gregory ◽

Jennifer Lau ◽

Anke Ehlers ◽

...

Keyword(s):

Environmental Factors ◽

Middle Childhood ◽

Internal State ◽

Environmental Influences ◽

Temporal Stability ◽

Time Frame ◽

Genetic Influences ◽

Future Research ◽

Counting Task ◽

The Stability

There is growing interest in interoception, the perception of the body’s internal state, and its relevance for health and higher-order cognition across development. To date, most evidence linking interoception to health and cognition has used the heartbeat counting task. However, the stability of the measure across time, particularly during childhood, and the etiological factors that underlie individual differences in stability remain largely unexamined. Using data from the ECHO twin sample (N=204 twin pairs), we estimated the magnitude of genetic and environmental influences on the stability of heartbeat counting across a two-year period (8-10 years), the longest time-frame examined. We found a relatively modest correlation between heartbeat counting accuracy across time (r=.35), with accuracy on the heartbeat counting task improving with age. In our longitudinal twin analysis, we found that the heritability of heartbeat counting dropped between Time 1 and Time 2 from 30% to 6%. No new genetic influences were observed at Time 2, suggesting that genetic influences across this age-range are entirely stable. In contrast, shared environmental influences increased from 6% to 22%, with most of the influence at Time 2 due to new environmental factors. Of note, nonshared environmental factors accounted for the greatest proportion of variance at both time points, 64% and 73% respectively, and were the main contributors to temporal stability in heartbeat counting accuracy. Future research should seek to identify these non-shared environmental factors and elucidate whether this relatively modest stability reflects variability of interoception across development or unreliability of the heartbeat counting task.

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Characterization of microsatellite markers for Narcissus dubius, N. cuatrecasasii, N. assoanus and N. rupicola (Amaryllidaceae)

Plant Genetic Resources ◽

10.1017/s1479262118000412 ◽

2018 ◽

Vol 17 (03) ◽

pp. 285-288 ◽

Cited By ~ 1

Author(s):

Daniel Barranco ◽

Violeta I. Simón-Porcar ◽

Juan Arroyo

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genomic Library ◽

Gene Diversity ◽

Model System ◽

Polymorphic Loci ◽

The Stability

AbstractThe genusNarcissusL. (Amaryllidaceae) provides a model system to study the evolution and maintenance of sexual polymorphisms. In this study, we characterized microsatellite markers forN. dubius,N. cuatrecasasii,N. assoanusandN. rupicolafor studies of genetic diversity and paternity analyses to investigate the stability of stylar dimorphism. We proved 40 new primer pairs from a genomic library ofN. papyraceusand 12 microsatellite markers characterized also forN. papyraceusin a previous study (52 primer pairs overall). Twenty markers amplified, but their transferability and variability were different among species. Polymorphism was tested at least on 74 individuals and one population per species. The number of polymorphic loci per species ranged from four to eight. The number of alleles per locus ranged from two to 19 and the observed heterozygosity and gene diversity, from 0.107 to 0.729 and 0.103 to 0.894, respectively. These markers can be used for studies of genetic diversity and paternity analyses among individuals ofN. dubius,N. cuatrecasasii,N. assoanusandN. rupicolato study the stability of stylar dimorphism.

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Genetic variability in wild and hatchery populations of commercially important fish: The common carp (Cyprinus carpio)

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d190437 ◽

2018 ◽

Vol 19 (4) ◽

pp. 1468-1474

Author(s):

MARYAM AHMADI ◽

HADISEH KASHIRI ◽

ALI SHABANI ◽

ABASALI AGHAEI MOGHADAM

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Common Carp ◽

Cyprinus Carpio ◽

Caspian Sea ◽

Wild Populations ◽

The Caspian Sea ◽

Common Carp Cyprinus Carpio ◽

Carp Cyprinus Carpio ◽

The Common

Ahmadi M, Kashiri H, Shabani A, Moghadam AA. 2018. Genetic variability in wild and hatchery populations of commerciallyimportant fish: The common carp (Cyprinus carpio). Biodiversitas 19: 1468-1474. Common carp, Cyprinus carpio, is considered as oneof the most important bony fish with high economic value in the Caspian sea. Since the population size of common carp has decreasedduring recent decades, restocking of the populations is done through releasing the hatchery-produced larvae into the Caspian Sea. In thepresent study, the genetic diversity of hatchery and wild populations of C. carpio was investigated using eight microsatellite loci(MFW7, MFW9, MFW13, MFW16, MFW17, MFW20, MFW26 and MFW28). A total of 145 different alleles were observed across allloci, with some of them being unique to each population. Although the allelic and gene diversity of hatchery populations tended to belower compared to the wild populations, no significant differences (P>0.05) in genetic diversity parameters were observed among thewild and hatchery populations. In most cases, significant departure from Hardy-Weinberg equilibrium was observed, mainly because ofthe heterozygosity deficiency. Results from FST, RST and UPGMA analysis showed that the hatchery-reared population was the mostdifferentiated and distant group. The results from this study are anticipated to provide important information for setting up moreefficient strategies in conservation and restocking of C. carpio.

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Structure and genetic diversity of Theobroma speciosum (Malvaceae) and implications for Brazilian Amazon conservation

Rodriguésia ◽

10.1590/2175-7860202172023 ◽

2021 ◽

Vol 72 ◽

Author(s):

Juliana de Freitas Encinas Dardengo ◽

Ana Aparecida Bandini Rossi ◽

Luiz Orlando de Oliveira ◽

Guilherme Ferreira Pena ◽

Luiz Henrique Rivas ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Molecular Genetic ◽

Economic Value ◽

Natural Populations ◽

Brazilian Amazon ◽

Fixation Index ◽

Breeding Programs ◽

Expected Heterozygosity ◽

Refuge Area

Abstract The genetic diversity of Theobroma speciosum is important because its use in breeding programs, once the species is closely related to species of great economic value such as Theobroma cacao (cocoa) and Theobroma grandiflorum (cupuaçu). Thus, the objective of this work is to characterize the intra and interpopulational genetic diversity of Theobroma speciosum in natural populations in the Brazilian Amazon. Ninety individuals of T. speciosum from four populations localized in different states of legal Amazon were selected and genotyped. The data were obtained by fluorescence microsatellite analysis and the number of alleles, number of private alleles, fixation index, observed and expected heterozygosity were analyzed. Bayesian analysis, AMOVA and PCOa were used to reveal the molecular genetic structure of the populations, using the programs Structure and GenAIEx 6.5, respectively. All populations studied present great levels of gene diversity, although, there was a greater similarity among the AUR, API and MAC populations, while RBC population presented higher heterozygosity and less inbreeding than the others, becoming a possible refuge area in the Amazon, and the most important population for T. speciosum conservation.

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Development of CAPS Markers for Evaluation of Genetic Diversity and Population Structure in the Germplasm of Button Mushroom (Agaricus bisporus)

Journal of Fungi ◽

10.3390/jof7050375 ◽

2021 ◽

Vol 7 (5) ◽

pp. 375

Author(s):

Hyejin An ◽

Hwa-Yong Lee ◽

Donghwan Shim ◽

Seong Ho Choi ◽

Hyunwoo Cho ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Agaricus Bisporus ◽

Gene Diversity ◽

Economic Value ◽

Button Mushroom ◽

Major Allele Frequency ◽

Cultivated Mushroom ◽

New Varieties ◽

Caps Markers

Agaricus bisporus is a globally cultivated mushroom with high economic value. Despite its widespread cultivation, commercial button mushroom strains have little genetic diversity and discrimination of strains for identification and breeding purposes is challenging. Molecular markers suitable for diversity analyses of germplasms with similar genotypes and discrimination between accessions are needed to support the development of new varieties. To develop cleaved amplified polymorphic sequences (CAPs) markers, single nucleotide polymorphism (SNP) mining was performed based on the A. bisporus genome and resequencing data. A total of 70 sets of CAPs markers were developed and applied to 41 A. bisporus accessions for diversity, multivariate, and population structure analyses. Of the 70 SNPs, 62.85% (44/70) were transitions (G/A or C/T) and 37.15% (26/70) were transversions (A/C, A/T, C/G, or G/T). The number of alleles per locus was 1 or 2 (average = 1.9), and expected heterozygosity and gene diversity were 0.0–0.499 (mean = 0.265) and 0.0–0.9367 (mean = 0.3599), respectively. Multivariate and cluster analyses of accessions produced similar groups, with F-statistic values of 0.134 and 0.153 for distance-based and model-based groups, respectively. A minimum set of 10 markers optimized for accession identification were selected based on high index of genetic diversity (GD, range 0.299–0.499) and major allele frequency (MAF, range 0.524–0.817). The CAPS markers can be used to evaluate genetic diversity and population structure and will facilitate the management of emerging genetic resources.

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Implications of Person Fluctuation for the Stability and Validity of Test Scores

Methodology ◽

10.1027/1614-2241.2.4.142 ◽

2006 ◽

Vol 2 (4) ◽

pp. 142-148 ◽

Cited By ~ 1

Author(s):

Pere J. Ferrando

Keyword(s):

Item Response ◽

Test Scores ◽

Temporal Stability ◽

Person Fit ◽

Item Parameters ◽

Individual Trait ◽

The Stability ◽

The Individual ◽

Different Levels ◽

Fluctuation Model

In the IRT person-fluctuation model, the individual trait levels fluctuate within a single test administration whereas the items have fixed locations. This article studies the relations between the person and item parameters of this model and two central properties of item and test scores: temporal stability and external validity. For temporal stability, formulas are derived for predicting and interpreting item response changes in a test-retest situation on the basis of the individual fluctuations. As for validity, formulas are derived for obtaining disattenuated estimates and for predicting changes in validity in groups with different levels of fluctuation. These latter formulas are related to previous research in the person-fit domain. The results obtained and the relations discussed are illustrated with an empirical example.

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