scholarly journals Genetic Diversity Of Plukenetia Volubilis L. Assessed By ISSR Markers

2015 ◽  
Vol 46 (4) ◽  
pp. 145-153 ◽  
Author(s):  
M. Ocelák ◽  
P. Hlásná Čepková ◽  
I. Viehmannová ◽  
Z. Dvořáková ◽  
D.C. Huansi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Diversity Indices ◽  
Issr Markers ◽  
Information Index ◽  
Geographical Distances ◽  
Plukenetia Volubilis ◽  
Polymorphic Bands

Abstract The diversity and genetic relationships in 173 sacha inchi samples were analyzed using ISSR markers. Thirty ISSR primers were used, only 8 showed variability in tested samples. ISSR fragments ranged from 200 to 2500 bp. The mean number of bands per primer was 12 and the average number of polymorphic bands per primer was 11. The lowest percentages of polymorphic bands (27%), gene diversity (0.103), and Shannon’s information index (0.15) were exhibited by the Santa Lucia population, which was also geographically most distant. This fact may be attributed to a very small size of this group. In contrast, the Dos de Mayo population exhibited the highest percentage of polymorphic bands (78%), and the Santa Cruz population the highest Nei’s gene diversity index (0.238) and Shannon’s information index (0.357). The obtained level of genetic variability was 36% among tested populations and 64% within populations. Although the diversity indices were low, a cluster analysis revealed 8 clusters containing mainly samples belonging to individual populations. Principal coordinate analysis clearly distinguished Chumbaquihui, Pucallpa, Dos de Mayo, and Aguas de Oro populations, the others were intermixed. The obtained results indicated the level of genetic diversity present in this location of Peru, although it is influenced by anthropological aspects and independent on the geographical distances.

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

Biologia ◽  
2013 ◽  
Vol 68 (4) ◽  
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).

Inter-Simple Sequence Repeat (ISSR) Markers Revealed Genetic Diversity and Population Structure Among 9 Wild Species of Clematis L.

2021 ◽  
Vol 15 (5) ◽  
pp. 580-588
Author(s):  
Yonghui Li ◽  
Shipeng Li ◽  
Jingjing Li ◽  
Xiangli Yu ◽  
Fawei Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Diversity Index ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Mantel Test ◽  
Information Index ◽  
Ctab Method ◽  
Different Populations

To analyze the genetic diversity of 9 species of Clematis from 31 different populations, we extracted DNA by the improved CTAB method, used ISSR-PCR for amplification, and then selected 9 primers with clear amplified bands from amongst 220 primers. A total of 127 clear bands were amplified, of which 126 were polymorphic bands, yielding a ratio of 99.2%. The polymorphism information index (PIC) of the primers ranged from 0.9326 to 0.9649. The Nei’s genetic diversity index (H) was 0.2750, the total gene diversity (Ht) was 0.2845, and the genetic differentiation coefficient (Gst) was 0.6696, indicating high genetic differentiation among populations of Clematis. After cluster analysis, the 31 Clematis populations were divided into 3 categories. Principal coordination analysis (PCoA) of 9 Clematis species then showed that the genetic relationship between samples of the same Clematis germplasms was closer than that of samples from the same region. The mantel test revealed a significant positive correlation between genetic distance and geographical distance among the populations. The population clustering results are broadly consistent with the clustering graphs of UPGMA and PCoA. We can conclude the polymorphism of the 9 primers is good, and that the genetic diversity of 31 Clematis populations is rich. Individual Clematis germplasms are closely related and will gather together preferentially.

ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

2021 ◽  
Author(s):  
Lalit Arya ◽  
Ramya Kossery Narayanan ◽  
Anjali Kak ◽  
Chitra Devi Pandey ◽  
Manjusha Verma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Morinda Citrifolia ◽  
Species Differentiation ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

scholarly journals Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

2015 ◽  
Vol 71 (1) ◽  
pp. 81-95 ◽  
Author(s):  
Hoda Moradkhani ◽  
Ali Ashraf Mehrabi ◽  
Alireza Etminan ◽  
Alireza Pour-Aboughadareh
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Issr Marker ◽  
D Genome ◽  
Ploidy Levels ◽  
Marker Data ◽  
Geographical Regions ◽  
High Level

AbstractThe aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions ofAegilopsandTriticumspecies with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA) revealed that 81% (ISSR) and 84% (SSR) of variability was partitioned among individuals within populations. Comparing the genetic diversity ofAegilopsandTriticumaccessions, based on genetic parameters, shows that genetic variation ofAe. crassaandAe. tauschiispecies are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA) for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA), also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

scholarly journals Genetic Differentiation of Jack Pine (Pinus banksiana) and Red Pine (P. resinosa) Populations From Metal Contaminated Areas in Northern Ontario (Canada) Using ISSR Markers

2008 ◽  
Vol 57 (1-6) ◽  
pp. 333-340 ◽  
Author(s):  
M. Ranger ◽  
K. K. Nkongolo ◽  
P. Michael ◽  
P. Beckett
Keyword(s):  
Genetic Diversity ◽  
Pinus Banksiana ◽  
Metal Accumulation ◽  
Gene Diversity ◽  
Jack Pine ◽  
Issr Markers ◽  
Red Pine ◽  
Northern Ontario ◽  
Polymorphic Loci ◽  
Information Index

Abstract Metal accumulation in soil and plant tissues has caused severe ecological damage in forest ecosystems in the Sudbury region. The main objective of the present study was to determine the levels of genetic diversity in jack and red pine populations growing in metal contaminated and uncontaminated areas. Newly introduced populations were compared to 40 to 60 old populations. For jack pine, the percentage of polymorphic loci (P %) ranged from 14.6% to 45.8% with a mean of 31.6%. Nei’s gene diversity (h) varied from 0.046 to 0.169 with an average of 0.100, and Shannon’s index (I) ranged from 0.070 to 0.250 with an average of 0.153. The level of genetic variation was much lower in the red pine populations. For this species, the level of polymorphic loci varied from 4.55% to 27.27%. The mean for Nei’s gene diversity and Shannon’s information index, were 0.034 and 0.053, respectively. The highest genetic diversity values were observed in new plantations being developed by the Sudbury reforestation program. Overall, the genetic distance among the Pinus banksiana populations revealed that all the populations analyzed were genetically close to each other. There was no association between metal accumulation and genetic diversity for both species.

Genetic structure and proposed conservation strategy for natural populations of Calycanthus chinensis Cheng et S.Y. Chang (Calycanthaceae)

2008 ◽  
Vol 88 (1) ◽  
pp. 179-186 ◽  
Author(s):  
Chu-Chuan Fan ◽  
Nicola Pecchioni ◽  
Long-Qing Chen
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Population Level ◽  
Conservation Strategy ◽  
Information Index

Calycanthus chinensis Cheng et S.Y. Chang, a tertiary relic species in China, is a shade-loving and deciduous bush withan elegant shape and beautiful flower of high ornamental value. It was widely planted in gardens and miniature scapes in China.The objective of this study was to characterize the genetic variation and structure in the three extant populations of the species, in order to provide useful information for a future conservation strategy. Twenty-two of 120 RAPD primers were selected and a total of 257 stable and clear DNA fragments were scored. Calycanthus chinensis showed a lower level of genetic diversity. At the population level, the percentage of polymorphic loci, Nei's gene diversity and Shannon’s information index were 40.9%, 0.1641 and 0.2386, respectively; while at the species level, the corresponding values were 59.1%, 0.2097 and 0.3123, respectively. The estimates of genetic differentiation based on Shannon’s information index (0.2360), Nei’s gene diversity (0.2175) and AMOVA (24.94%) were very similar, and significantly higher than the average genetic differentiation reported in outcrossed spermatophyte. So it suggested high genetic differentiation emerged among populations of C. chinensis. Genetic relationships among populations were assessed by Nei’s standard genetic distance, which suggested that the Tiantai population was genetically distinct from the other two populations. Moreover, the genetic distance was significantly correlated with geographical distance among populations (r = 0.997, t > t0.05). The gene flow (Nm) was 0.8994, indicating that gene exchange among populations was restricted. A conservation strategy was proposed based on the low gene flow and habitat deterioration, which are contributing to the endangered status of this species. Key words: Genetic diversity, endangered plant, population genetics, RAPD

scholarly journals Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
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.

scholarly journals Genetic diversity and population structure of endangered rosewood from the Peruvian Amazon using ISSR markers

2020 ◽  
Vol 50 (3) ◽  
pp. 204-212
Author(s):  
Stalin Juan Vasquez GUIZADO ◽  
Muhammad Azhar NADEEM ◽  
Fawad ALI ◽  
Muzaffer BARUT ◽  
Ephrem HABYARIMANA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Population Level ◽  
Diversity Indices ◽  
Issr Markers ◽  
Neighbor Joining ◽  
Peruvian Amazon ◽  
Over Exploitation ◽  
Issr Primers

ABSTRACT Rosewood, Aniba rosaeodora is an endangered species in Amazon forests and its natural stands have been heavily depleted due to over-exploitation for the cosmetic industry. This study aimed to investigate the genetic diversity and population structure of 90 rosewood accessions from eight localities in the Peruvian Amazon through 11 Inter Simple Sequence Repeats (ISSR) primers. The ISSR primers produced a sum of 378 bands, of which 375 (99.2%) were polymorphic, with an average polymorphism information content (PIC) value of 0.774. The mean effective number of alleles (Ne), Shannon informative index (I), gene diversity (He) and total gene diversity (Ht) were 1.485, 0.294, 0.453 and 0.252, respectively. Analysis of molecular variance (AMOVA) showed the presence of maximum variability within populations (88%). The Structure algorithm, neighbor joining and principal coordinate analysis (PCoA) grouped the 90 rosewood accessions into three main populations (A, B and C). Diversity indices at the inter-population level revealed a greater genetic diversity in population A, due to higher gene flow. The neighbor-joining analysis grouped populations A and B, while population C was found to be divergent at the inter population level. We concluded that population A reflects higher genetic diversity and should be prioritized for future management and conservation plans.

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

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.

scholarly journals Analysis of genetic diversity among different tomato genotypes using ISSR DNA marker

Genetika ◽  
2017 ◽  
Vol 49 (1) ◽  
pp. 31-42
Author(s):  
Saida Sharifova ◽  
Sabina Mehdiyeva ◽  
Mehraj Abbasov
Keyword(s):  
Genetic Diversity ◽  
Dna Marker ◽  
Diversity Index ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Similarity Coefficient ◽  
Variation Analysis ◽  
A Value ◽  
Polymorphic Bands ◽  
Simple Sequence

Inter simple sequence repeat (ISSR) markers were used for variation analysis among 41 tomato accessions. A total of 50 scorable bands were obtained, where 32 were polymorphic, representing 63.3% of all the amplified loci. Polymorphism percentage ranged from 50 to 90% and an average number of polymorphic bands of 4.0 were observed. An average genetic diversity index was 0.61. Primer UBC860 and UBC825 generated the greatest diversity index with a value of 0.89 and 0.85 respectively. The smallest diversity identified by primer UBC808, with an index of 0.34. The genetic similarity among studied genotypes ranged from 0.52 to 0.98. The cluster analysis based on Jaccard?s similarity coefficient divided genotypes into 6 distinct clusters on a value of 0.74. The lowest genetic distance was found between ?Gronastiy? and ?AG1224? (0.52), ?Orange? and ?AG1224? (0.54), and ?Evgeniya? and ?AG1224? (0.55) accessions. The highest similarity of 0.98 was determined between ?Zafar? and ?Azerbaijan-94?, ?Khachmaz-1? and ?Azerbaijan-94?, ?Khachmaz-1? and ?Severyanka?, and ?Shakar? and ?Absheron-1? accessions.

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