Assessment of Genetic Diversity of Some Wild Populations of Thymus Kotschyanus Usingrapd Molecular Markers

Abstract RAPD molecular markers were used to assess the genetic diversity of some population of thyme (Thymus kotschyanus) from Iran. The 17 tennucleotide primers used that produced 185 high-resolution bands, which 21 of these were monomorphic and 162 were polymorphic. An average, 10.88 bands were obtained per primer and 9.52 of these were polymorphic. POPGENE software was used to calculate Nei's genetic distance among populations and based on the cluster analysis of this matrix, a UPGMA dendrogram was drawn using the software NTSYS-pc. On the basis of dendrogram among populations of wild mountain thyme, Avan (Qazvin) and Siahkal (Gilan province) populations was the most similar between studied populations with the distance of 0.094 high disimilarity was observed between Qazvin and Mazandaran 2 populations with the distance of 0.185 within populations variation based on Shannon's information index and Nei genetic diversity index showed that Takestan (I= 0.26; H= 0.3) and Alamut (I= 0.24; H= 0.15) had a highest and lowest within populations variation compared to other populations, respectively. Average of Fst and Nm indices, which represent the amount of gene flow between populations, were recorded as 0.26 and 1.361, respectively, which reflects the high level of gene exchange between ten populations of Thymus kotschyanus.

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Genetic diversity of eight millet genera assessed by using molecular and morphological markers

Crop and Pasture Science ◽

10.1071/cp15202 ◽

2016 ◽

Vol 67 (2) ◽

pp. 181

Author(s):

Zdislava Dvořáková ◽

Petra Hlásná Čepková ◽

Iva Viehmannová ◽

Lenka Havlíčková ◽

Dagmar Janovská

Keyword(s):

Genetic Diversity ◽

Morphological Variability ◽

Aflp Markers ◽

Morphological Data ◽

Plant Materials ◽

Morphological Attributes ◽

Shannon’S Index ◽

High Level ◽

Close Relatedness ◽

Nei's Genetic Distance

In this study, the genetic diversity and relationships among eight millet genera were investigated by molecular and morphological data analyses. Sixty-nine millet accessions were analysed by using amplified fragment length polymorphism (AFLP) markers, and evaluated for morphological traits. Eight AFLP primer pairs were amplified successfully and 779 bands were scored for all accessions, with a high level of polymorphism detected. Nei’s genetic distance among all accessions varied from 0.0123 to 0.4246 and the Shannon’s index was estimated at 0.9708. The neighbour joining tree, using the unweighted neighbour-joining method and Dice’s dissimilarity coefficient, was constructed. The AFLP markers revealed the close relatedness between the Eragrostis and Panicum genera, whereas the greatest distance was found the Pennisetum and Echinochloa genera. Cluster analysis based on the AFLP profiles revealed that the majority of accessions of a given millet genus tend to group together. Clustering from morphological data allocated individuals into three main clusters with high variation. The genetic variability found between the analysed accessions was weakly negatively correlated (r = –0.074) with their morphological attributes. However, high molecular and morphological variability indicated that this collection includes rich and valuable plant materials for millet breeding.

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Genetic Diversity and Population Structure of Endangered Catfish Rita rita (Hamilton, 1822) Revealed by Heterologous DNA Microsatellite Markers

Asian Fisheries Science ◽

10.33997/j.afs.2021.34.2.007 ◽

2021 ◽

Vol 34 (2) ◽

Author(s):

MUHAMMAD FORHAD ALI ◽

◽

MD. RAFIQUL ISLAM SARDER ◽

MOHAMMAD MATIUR RAHMAN ◽

MD. FAZLUL AWAL MOLLAH ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Genetic Difference ◽

Information Index ◽

Hardy Weinberg Equilibrium ◽

High Gene ◽

High Level ◽

Dna Microsatellite

Genetic information is essential for conservation and future aquaculture development of the endangered catfish Rita rita (Hamilton, 1822). Two hundred catfish, R. rita, 50 from four rivers, the Old Brahmaputra, Jamuna, Meghna and Kangsa were collected and analysed to evaluate the genetic diversity and population structure using five microsatellite primers (Cba06-KUL, Cba08-KUL, Cba09-KUL, Phy03-KUL and Phy07-KUL). Four of the five amplified loci were found polymorphic (P95) in all the populations and 46 alleles were recorded with 9 to 14 alleles per locus. Differences were observed in the total number of alleles ranging from 41 to 44, effective number of alleles from 29.96 to 37.46, observed heterozygosity from 0.57 to 0.76, Shannon’s information index from 2.09 to 2.30 and polymorphic information content from 0.84 to 0.88 among the four populations. Results exposed the highest levels of genetic diversity in the Meghna population while the lowest in the Kangsa population of R. rita. All the populations were significantly deviated (P < 0.001) from the Hardy-Weinberg equilibrium for all the loci. Nei’s genetic distance between populations ranged 0.007 to 0.017 with low overall genetic difference FST = 0.011 and high gene flow Nm = 24.333, indicating that R. rita populations were not subdivided. This study revealed a high level of gene diversity with deficiency in genetic heterogeneity in all the populations of R. rita, emphasising natural management, conservation and rehabilitation measures of this species.

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Genetic diversity in maize dent landraces assessed by morphological and molecular markers

Genetika ◽

10.2298/gensr1303811r ◽

2013 ◽

Vol 45 (3) ◽

pp. 811-824 ◽

Cited By ~ 4

Author(s):

Danijela Ristic ◽

Vojka Babic ◽

Violeta Andjelkovic ◽

Jelena Vancetovic ◽

Snezana Mladenovic-Drinic ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Molecular Markers ◽

Genetic Distance ◽

Morphological Traits ◽

Mean Value ◽

Ecological Data ◽

Phenotypic Analysis ◽

High Level ◽

Maize Research Institute

Maize Research Institute ?Zemun Polje? genebank maintains a collection of landraces grouped into 18 agro-ecological collected from ex-Yugoslavia territories. The application and comparison of different marker systems are important for the characterization and use of maize landraces in breeding program, as potential sources of desirable traits. In this study, 15 morphological traits, 7 RAPD primers and 10 SSR primer pairs were applied to i) to determine genetic distance between 21 maize dent landraces and ii) compare results obtained on morphological and molecular markers. Phenotypic analysis showed high level of heterogeneity between landraces. Higher level of genetic diversity was obtained with SSR than with RAPD. Genetic distance mean value for RAPD data was 0.35 i.e. for SSR 0.48. Based on the morphological traits and molecular markers, unweighted pairgroup method (UPGMA) analysis was applied for cluster analysis, using statistical NTSYSpc program package. Cluster analysis of morphological and molecular markers distances did not show the same population grouping. Better agreement with agro-ecological data was obtained with RAPD markers. Correlations between dissimilarity matrices for different types of markers were low. Data obtained in this work could be useful for further study of a larger number of landraces, and conservation of genetic resources and their genetic diversity.

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Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

BioMed Research International ◽

10.1155/2018/7658032 ◽

2018 ◽

Vol 2018 ◽

pp. 1-11 ◽

Cited By ~ 20

Author(s):

Saba Jasim Aljumaili ◽

M. Y. Rafii ◽

M. A. Latif ◽

Siti Zaharah Sakimin ◽

Ibrahim Wasiu Arolu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Diversity Index ◽

Gene Diversity ◽

Allelic Diversity ◽

Peninsular Malaysia ◽

Breeding Program ◽

Aromatic Rice ◽

Information Index ◽

Rice Germplasm

Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon’s information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He) of 0.60 and mean Nei’s gene diversity index of 0.36. The dendrogram based on UPGMA and Nei’s genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

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Breeding potential and genetic diversity of "Híbrido do Timor" coffee evaluated by molecular markers

Cropp Breeding and Applied Biotechnology ◽

10.1590/s1984-70332010000400003 ◽

2010 ◽

Vol 10 (4) ◽

pp. 298-304 ◽

Cited By ~ 12

Author(s):

Tesfahun Alemu Setotaw ◽

Eveline Teixeira Caixeta ◽

Guilherme Ferreira Pena ◽

Eunize Maciel Zambolim ◽

Antonio Alves Pereira ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Molecular Markers ◽

Genetic Structure ◽

Gene Diversity ◽

High Genetic Diversity ◽

Breeding Programs ◽

Information Index ◽

Upgma Cluster Analysis ◽

Potential Use

AFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon's information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breeding programs are discussed.

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Genetic Diversity of Tef [Eragrostis tef (Zucc.)Trotter] as Revealed by Microsatellite Markers

International Journal of Genomics ◽

10.1155/2021/6672397 ◽

2021 ◽

Vol 2021 ◽

pp. 1-9

Author(s):

Mahilet Tadesse ◽

Mulugeta Kebede ◽

Dejene Girma

Keyword(s):

Genetic Diversity ◽

Polymorphic Information Content ◽

Mean Value ◽

Eragrostis Tef ◽

Human Consumption ◽

Gene Pools ◽

Information Index ◽

Geographical Regions ◽

The Mean ◽

High Level

Genetic variability is the fundamental prerequisite of any crop-breeding program to develop superior cultivars. There are about 350 Eragrostis1 species, of which, tef is the only species cultivated for human consumption. Currently, the Ethiopian Biodiversity Institute (EBI) collected over five thousand tef accessions from different geographical regions, diverse in terms of climate and elevation, which are uncharacterized yet. The objective of this study was to evaluate the genetic diversity among 64 tef accessions using 10 selected polymorphic simple sequence repeats (SSRs) markers. A total of 314 alleles were detected with an average of 14.5 alleles per locus and amplicon size ranged from 90 bp–320 bp. The mean value of polymorphic information content (PIC) was 0.87, appearing polymorphic for all loci. The lowest Fst value (0.05) was recorded among the studied tef populations. The mean value of major allele frequency and the number of effective alleles were 0.33 and 3.32, respectively. The mean value of gene flow (Nm) and Shannon’s information index (I) was 4.74 and 1.65, respectively. The observed (Ho) and expected (He) heterozygosities varied from 0.34 to 0.56 and from 0.58 to 0.76, respectively. The cluster analysis has grouped the 64 tef accessions into three distinct clusters based on their similarity. The PCoA analysis showed that clustering is basing on the geographical origin of accessions. Analysis of molecular variance revealed 56%, 39% and 5% of the total variation due to variation within populations, among individuals and among populations, respectively. Structure bar-plot also inferred three gene pools, but with high level of admixtures. Thus, the present study shows that the identified tef accessions could be of great interest for the initiation of a planned breeding and conservation programs.

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Genetic diversity and SSR markers development of ancient Camellia sinensis in Sandu County of Guizhou Province

10.21203/rs.3.rs-208220/v1 ◽

2021 ◽

Author(s):

Yichen Zhao ◽

Runying Wang ◽

Qing Liu ◽

Xuan Dong ◽

De-Gang Zhao

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Diversity Index ◽

Molecular Genetic ◽

Diversity Indices ◽

Guizhou Province ◽

Information Index ◽

Molecular Genetic Diversity ◽

Qualitative Characters ◽

Breed Selection

Abstract Background: The genetic abundance of ancient tea germplasm has been preserved in the long evolution process, which provides valuable resources for the protection and breed selection of ancient tea germplasm. However, the limited studies related to the genetic diversity of ancient tea germplasm restrict protection and breed selection. Therefore, the genetic diversity of ancient tea germplasm in Sandu county of Guizhou Province was explored in this study. II.Methods and Results: The genetic diversity was analyzed using phenotypes and SSR markers. The ranges for the variation coefficients of the six quantitative and seven qualitative characters were 17.76%-60.37% and 18.58%-50.64%, respectively. The ranges of diversity indices of the six quantitative and seven qualitative characters were 1.72-2.74 and 0.55-0.84, respectively. Ninety-six bands were amplified using 15 pairs of SSR primers from the 145 samples, and the average polymorphism information index was 0.66. The analysis revealed that the average values of Nei’s genetic diversity index (H) and the Shannon information index (I) are 0.26 and 0.41, respectively. Further, a genetic similarity coefficient of 0.734 shown by UPGMA dendrogram classified the 145 samples decreased into four groups. III.Conclusions: This study revealed the rich phenotypic variation and high molecular genetic diversity and the genetic diversity of the arbor is higher than that of the shrub of the ancient tea germplasm in Sandu of Guizhou province. Thus, this study not only provides a theoretical basis for the protection and breed selection but also promotes further research of ancient tea germplasm.

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Habitat-related specifity of iPBS fingerprint in European populations of Hedera helix L.

Folia Oecologica ◽

10.2478/foecol-2019-0005 ◽

2019 ◽

Vol 46 (1) ◽

pp. 30-36

Author(s):

Jana Žiarovská ◽

Katarína Ražná ◽

Eloy C. Fernandéz ◽

Danka Bošeľová ◽

Matúš Kyseľ

Keyword(s):

Genetic Diversity ◽

Dna Markers ◽

Diversity Index ◽

Primer Binding Site ◽

Limited Information ◽

Hedera Helix ◽

Information Index ◽

Factors Influencing ◽

The Individual ◽

European Populations

AbstractInter primer binding site (iPBS) polymorphism was investigated for common ivy (Hedera helix, L.) to obtain the knowledge on genetic diversity in this species. Actually, a very limited information exists about application of DNA markers in Hedera helix. Natural and planted European populations of ivy were analysed using an iPBS marker 5′ACCTGGCGTGCCA3′ with a total number of 238 fragments generated. Of these, 86% were polymorphic. There were determined certain attributes of this marker such as the diversity index (DI) and polymorphism information content (PIC). The value of the diversity index was 0.79 and the polymorphic information index was 0.78. The proportion of polymorphisms of the individual amplified loci ranged from 0.32% to 6.98%. Cluster analysis was performed to determine the relationships among the European ivy populations where the distribution in the dendrogram under the habitat specifity was found for the used iPBS marker. We concluded that iPBS was very efficient in analysing the genetic diversity in Hedera helix, L. and that this marker can serve as a suitable tool to find genomically specific fingerprints relevant to the factors influencing the distribution of genetic variation.

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Genetic diversity of wild and cultured swamp eel (Monopterus albus) populations from central China revealed by ISSR markers

Biologia ◽

10.2478/s11756-013-0203-5 ◽

2013 ◽

Vol 68 (4) ◽

Cited By ~ 6

Author(s):

Wei Li ◽

Wen-Xiu Sun ◽

Jun Fan ◽

Chao-Chao Zhang

Keyword(s):

Genetic Diversity ◽

Diversity Index ◽

Gene Diversity ◽

Issr Markers ◽

Central China ◽

Commercial Fish ◽

Monopterus Albus ◽

Information Index ◽

Asian Swamp Eel ◽

Swamp Eel

AbstractAsian swamp eel is a highly commercial fish, primarily for China and other Asian countries. The aim of this paper is to evaluate the genetic diversity of wild and cultured samples of Asian swamp eel Monopterus albus using ISSR markers. A total of 129 individuals belonging to three wild samples, Xiantao (XT), Huanggang (HG), Xinyang (XY) and three cultured samples, Wuhan (WH), Jingzhou (JZ) and Nanjing (NJ) were randomly selected for genetic analysis. Twelve ISSR primers were used for screening the six populations and 110 loci were obtained. The polymorphic loci were estimated to be 54%, 56.3%, 58.2%, 60.6%, 69.5% and 71% in NJ,WH, JZ, XT, HG and XY samples, respectively. Average heterozygosity value varied from 0.1956 to 0.2449. The three wild samples showed higher genetic diversity than the cultured samples (P < 0.05), including polymorphic bands (PPB), observed number of alleles per locus (to), effective number of alleles per locus (Ne), Nei’s gene diversity index (H) and Shannon’s information index (I).

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Genetic diversity and structure among natural populations of Mytilaria laosensis (Hamamelidaceae) revealed by microsatellite markers

Silvae Genetica ◽

10.2478/sg-2018-0013 ◽

2018 ◽

Vol 67 (1) ◽

pp. 93-98 ◽

Cited By ~ 1

Author(s):

Niu Yu ◽

Jie Yuan ◽

Guangtian Yin ◽

Jinchang Yang ◽

Rongsheng Li ◽

...

Keyword(s):

Genetic Diversity ◽

Geographic Distance ◽

Natural Populations ◽

Magnetic Bead ◽

Mantel Test ◽

High Genetic Diversity ◽

Information Index ◽

Genetic Diversity And Structure ◽

High Level ◽

Mytilaria Laosensis

Abstract Mytilaria laosensis is a fast-growing tropical broadleaf tree that is extensively used for wood production and has significant ecological benefits. To investigate the genetic diversity and population structure of M. laosensis, eight major natural populations in China were analyzed by using simple sequence repeat (SSR) markers. A total of 88 microsatellite-containing fragments were obtained by the method of magnetic bead enrichment, among which 26 pairs of SSR primers were screened out and used to generate a total of 190 alleles among 152 individuals. The average of observed number of alleles, Shannon’s information index and polymorphism information content per locus were 18.3, 1.1577 and 0.7759, respectively, implying a high level of genetic diversity in M. laosensis populations. The variation within populations accounted for 81.74 % of total variation based on analysis of molecular variance. Cluster analysis divided the eight populations into four groups, among which five populations from the southern parts of Guangxi province were classified as one major group. Mantel test showed that there was highly significant correlation between Euclidean genetic distance and geographic distance, suggesting that geographic isolation contribute to the high genetic diversity of M. laosensis. Together, these could provide support for the feasibility of exploration and utilization of M. laosensis in subtropical areas of East Asia including Jiangxi, Hunan and Fujian province of China.

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