Target Region Amplification Polymorphism (TRAP) for Assessing Genetic Diversity and Relationships Among Cultivated Populations of Dendrobium officinale

2020 ◽  
Vol 14 (5) ◽  
pp. 624-631
Author(s):  
Bingzhong Ding ◽  
Benhou Zhang ◽  
Chao Li ◽  
Qingyun Xue ◽  
Wei Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Dendrobium Officinale ◽  
Target Region ◽  
Target Region Amplification Polymorphism ◽  
Rare And Endangered Species ◽  
Upgma Dendrogram ◽  
Rare And Endangered ◽  
Cultivated Populations ◽  
High Level

Dendrobium officinale (Orchidacesae) is one of the rare and endangered species of herbs in China. Therefore, it will be beneficial to investigate the genetic diversity and relationships of cultivated populations of D. officinale for quality improvement. In this study, eight target region amplification polymorphism (TRAP) primer combinations were selected from fifty-four combinations, which were designed based on the related genes of the polysaccharides and alkaloids. A total of 148 fragments were scored in nine cultivated populations of D. officinale, including 130 (87.84%) polymorphic fragments. The analysis of genetic diversity revealed high level of genetic diversity in cultivated populations of D. officinale (H = 0.4125, I = 0.5985). Based on analysis of genetic structure, there was a moderate variation (Gst = 0.4706) and lower gene flow (Nm = 0.5625) among the cultivated populations due to some isolated measures, and domestication of excellent cultivars. Moreover, UPGMA dendrogram and Principal Coordinate Analysis (PCoA) indicated that nine cultivated populations were divided into four major groups. The results suggested that genetic relationships were associated with geographical germplasm sources instead of cultivation locations. Therefore, TRAP markers can be effectively employed to analyze genetic diversity and relationships among cultivated populations of D. officinale.

Genetic diversity and genetic structure of the rare and endangered species, Primula ranunculoides

2014 ◽  
Vol 21 (5) ◽  
pp. 601-609
Author(s):  
Wang Deyun ◽  
Peng Jie ◽  
Chen Yajing ◽  
Lü Guosheng ◽  
Zhang Xiaoping ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Endangered Species ◽  
Rare And Endangered Species ◽  
Rare And Endangered

Assessment of genetic variability amongst cultivated populations of Khasi mandarin (Citrus reticulata Blanco) detected by ISSR

2021 ◽  
pp. 1-11
Author(s):  
Karishma Kashyap ◽  
Rasika M. Bhagwat ◽  
Sofia Banu
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Inter Simple Sequence Repeat ◽  
Northeast India ◽  
Issr Markers ◽  
Citrus Reticulata ◽  
Brahmaputra Valley ◽  
Indian Food ◽  
Cultivated Populations ◽  
High Level

Abstract Khasi mandarin (Citrus reticulata Blanco) is a commercial mandarin variety grown in northeast India and one of the 175 Indian food items included in the global first food atlas. The cultivated plantations of Khasi mandarin grown prominently in the lower Brahmaputra valley of Assam, northeast India, have been genetically eroded. The lack in the efforts for conservation of genetic variability in this mandarin variety prompted diversity analysis of Khasi mandarin germplasm across the region. Thus, the study aimed to investigate genetic diversity and partitioning of the genetic variations within and among 92 populations of Khasi mandarin collected from 10 cultivated sites in Kamrup and Kamrup (M) districts of Assam, India, using Inter-Simple Sequence Repeat (ISSR) markers. The amplification of genomic DNA with 17 ISSR primers yielded 216 scorable DNA amplicons of which 177 (81.94%) were polymorphic. The average polymorphism information content was 0.39 per primer. The total genetic diversity (HT = 0.28 ± 0.03) was close to the diversity within the population (HS = 0.20 ± 0.01). A high mean coefficient of gene differentiation (GST = 0.29) reflected a high level of gene flow (Nm = 1.22), indicating high genetic differentiation among the populations. Analysis of Molecular Variance (AMOVA) showed 78% of intra-population differentiation, 21% among the population and 1% among the districts. The obtained results indicate the existence of a high level of genetic diversity in the cultivated Khasi mandarin populations, indicating the need for preservation of each existing population to revive the dying out orchards in northeast India.

Genetic diversity and relationships among Secale L. based on RAMP markers

2004 ◽  
Vol 1 (2) ◽  
pp. 73-78 ◽  
Author(s):  
Shang Hai-Ying ◽  
Zheng You-Liang ◽  
Wei Yu-Ming ◽  
Wu Wei ◽  
Yan Ze-Hong
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Group Method ◽  
Transitional Region ◽  
Arithmetic Average ◽  
Pair Group ◽  
Broad Leaf ◽  
Polymorphic Bands ◽  
High Level

AbstractGenetic diversity and relationships among 21 accessions of Secale L., including three species and 10 subspecies, were evaluated using RAMP markers. Forty-one out of 80 (50.5%) RAMP primers, which produced clear and polymorphic bands, were selected for PCR amplification of genomic DNA. A total of 446 bands were amplified from the 41 primers, and 428 of these bands (about 96%) were polymorphic. Three to 19 polymorphic bands could be amplified from each primer, with an average of 10.4 bands. The RAMP-based genetic similarity (GS) values among the 21 Secale accessions ranged from 0.266 to 0.658, with a mean of 0.449. A high level of genetic variation was found between or within the wild populations and the cultivars. Based on the GS matrix, a dendrogram was constructed using the unweighted pair group method with arithmetic average (UPGMA). All 21 accessions could be distinguished by RAMP markers. Clustering results showed that the genetic diversity of Secale based on RAMP markers was correlated with geographical distribution. Six rye cultivars, originating from Poland, Portugal, Mexico, Hungary, Armenia and Ukraine, were clustered into one group. The six countries are all located in the transitional region of broad-leaf forests between maritime and continental temperate zones, with narrow latitude span. In comparison, the other five cultivars from countries scattered over a region with large latitude span were distributed within different groups or subgroups. Genetic relationships based on RAMP markers had great deviation from the original taxonomy. Some subspecies of the same species were distributed within different groups, while some accessions of different species were closely clustered into one subgroup. These results suggest that RAMP markers could be an effective technique for detecting genetic diversity among Secale and give some useful information about its phylogenic relationships.

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 Target Region Amplification Polymorphism (TRAP) as a Tool for Detecting Genetic Variation in the Genus Pelargonium

HortScience ◽  
2007 ◽  
Vol 42 (5) ◽  
pp. 1118-1123 ◽  
Author(s):  
Rose Palumbo ◽  
Wai-Foong Hong ◽  
Guo-Liang Wang ◽  
Jinguo Hu ◽  
Richard Craig ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ornamental Plant ◽  
The Other ◽  
Sequence Information ◽  
Extraction Techniques ◽  
Large Collection ◽  
Target Region ◽  
Breeding Lines ◽  
Target Region Amplification Polymorphism

Pelargonium was a priority genera collected by the Ornamental Plant Germplasm Center (OPGC) until a recent reorganization. To preserve genetic diversity for future breeders, OPGC collects heirloom cultivars, breeding lines, and wild species. The current Pelargonium collection at OPGC consists primarily of cultivars originating from P. ×hortorum and P. ×domesticum. Target region amplification polymorphism (TRAP) has the advantage of producing a large number of markers through use of sequence information that is already available. Our first goal was to determine the feasibility of TRAP for the analysis of this large collection, so that in the future the most diverse genotypes may be retained. To achieve this goal, we first modified existing DNA extraction techniques to account for the high levels of phenolic compounds present in some Pelargonium species by combining several washes to remove the phenolics with the addition of high levels of antiphenolic compounds. Second, we evaluated the TRAP procedure using the DNA isolated from 46 accessions. For 44 accessions, one or two primer combinations generated enough fragments to discriminate each of the accessions, and similar clades were produced by cluster analysis of the polymorphic fragments amplified by different primer combinations. All the scorable fragments were polymorphic, for one primer combination there were 148 markers from one image and the other produced 160 markers on two images. These results demonstrate that TRAP is an effective method for molecular characterization of ornamental collections.

Genetic Diversity in the Endangered Phebalium daviesii (Rutaceae) Compared to That in Two Widespread Congeners

1995 ◽  
Vol 43 (2) ◽  
pp. 181 ◽  
Author(s):  
AJJ Lynch ◽  
RE Vaillancourt
Keyword(s):  
Genetic Diversity ◽  
Population Bottleneck ◽  
Allozyme Data ◽  
Enzyme Systems ◽  
Total Genetic Diversity ◽  
Rare And Endangered ◽  
Ecological Habitat ◽  
Hardy Weinberg Equilibrium ◽  
High Level ◽  
Adult Plants

Genetic diversity in the rare and endangered Phebalium daviesii was compared to that in P. squamulosum subsp. squamulosum and P. glandulosum subsp. glandulosum using allozyme analysis. Phebalium daviesii was once presumed extinct, but 43 adult plants have so far been rediscovered. Phebalium squamulosum subsp. squamulosum and P. glandulosum subsp. glandulosum are widespread in the south-eastern part of the Australian mainland. Morphologically, these two taxa are the closest relatives of P. daviesii and share a similarity with P. daviesii in their ecological habitat. The level of genetic diversity and deviations from Hardy-Weinberg equiibrium were investigated using allozyme data with 18 enzyme systems. Nei's total genetic diversity, the proportion of polymorphic loci and the average number of alleles per locus were all slightly lower in P. daviesii than in P. squamulosum subsp. squamulosum and P. glandulosum subsp. glandulosum. Deviations from expected Hardy-Weinberg equilibrium were present in all three taxa and were more frequent in P. glandulosum subsp. glandulosum. This suggests that inbreeding may be occurring in all three Phebalium taxa and that P. daviesii does not suffer from increased inbreeding due to rarity. Phebalium daviesii has a high level of genetic diversity (Ht = 0.30) for such a rare species and should be able to recover from its population bottleneck with appropriate management.

scholarly journals Genetic Diversity Analysis ofHypsizygus marmoreuswith Target Region Amplification Polymorphism

2014 ◽  
Vol 2014 ◽  
pp. 1-7
Author(s):  
Chengshu Qiu ◽  
Wenjuan Yan ◽  
Wangqiu Deng ◽  
Bin Song ◽  
Taihui Li
Keyword(s):  
Genetic Diversity ◽  
Genomic Dna ◽  
Edible Mushroom ◽  
Diversity Analysis ◽  
Target Region ◽  
Hypsizygus Marmoreus ◽  
Genetic Diversity Analysis ◽  
Target Region Amplification Polymorphism ◽  
Medium Level ◽  
The Common

Hypsizygus marmoreusis an industrialized edible mushroom. In the present paper, the genetic diversity among 20 strains collected from different places of China was evaluated by target region amplification polymorphism (TRAP) analysis; the common fragment of TRAPs was sequenced and analyzed. Six fixed primers were designed based on the analysis ofH. marmoreussequences from GenBank database. The genomic DNA extracted fromH. marmoreuswas amplified with 28 TRAP primer combinations, which generated 287 bands. The average of amplified bands per primer was 10.27 (mean polymorphism is 69.73%). The polymorphism information content (PIC) value for TRAPs ranged from 0.32 to 0.50 (mean PIC value per TRAP primer combination is 0.48), which indicated a medium level of polymorphism among the strains. A total of 36 sequences were obtained from TRAP amplification. Half of these sequences could encode the known or unknown proteins. According to the phylogenetic analysis based on TRAP result, the 20 strains ofH. marmoreuswere classified into two main groups.

Mixed Mating in Banksia brownii Baxter ex R. Br. (Proteaceae)

1994 ◽  
Vol 42 (1) ◽  
pp. 103 ◽  
Author(s):  
JF Sampson ◽  
BG Collins ◽  
DJ Coates
Keyword(s):  
Endangered Species ◽  
Minimum Variance ◽  
Outcrossing Rate ◽  
Mixed Mating ◽  
System Parameters ◽  
Rare And Endangered Species ◽  
Large Populations ◽  
Rare And Endangered ◽  
High Level ◽  
Two Populations

Mating system parameters of the rare and endangered species Banksia brownii were estimated for two populations using both the mixed mating and effective selfing models. Estimates of outcrossing rate were similar in both populations for both models (mixed mating t Pop. 1=0.68, Pop. 2=0.75; effective selfing t Pop. 1=0.65, Pop. 2=0.73) and were among the lowest reported for undisturbed Banksia populations. Banksia brownii is killed by fire and the high level of selfing found may be associated with this trait. Multilocus and minimum variance mean i estimates were similar and the covariance of selfing with gene fixation (D) was not significantly different from zero indicating that populations were not structured and that most of the inbreeding was the result of self-fertilisation. The absence of structure was attributed to gene dispersal through pollen disperse by birds, and selection against inbred seed. It is suggested that several entire, large populations of this species together with habitat sufficient to support pollinators be reserved to conserve this species.

Genetic Relationships between Tropical Sprangletop (Leptochloa virgata) Populations from Mexico: Understanding Glyphosate Resistance Spread

Weed Science ◽  
2016 ◽  
Vol 64 (4) ◽  
pp. 579-587 ◽  
Author(s):  
Ricardo Alcántara-de la Cruz ◽  
Yolanda Romano ◽  
María Dolores Osuna-Ruíz ◽  
José Alfredo Domínguez-Valenzuela ◽  
Julio Menéndez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Shikimic Acid ◽  
Genetic Relationships ◽  
Glyphosate Resistance ◽  
Long Distance ◽  
Whole Plant ◽  
Total Genetic Diversity ◽  
Susceptible Populations ◽  
High Level

The susceptibility to glyphosate and genetic diversity based on intersimple sequence repeat markers were characterized for 17 tropical sprangletop populations collected from two separate regions mainly in Persian lime groves in Veracruz, Mexico. The whole-plant dose response together with shikimic acid assays indicated different levels of glyphosate resistance in those populations. Genetic diversity values (h) estimated using POPGENE ranged from 0.119 to 0.198 and 0.117 to 0.214 within susceptible and resistant populations, respectively. The average genetic diversity (HS) within the susceptible populations was 0.157, and the total genetic diversity (HT) was 0.218. TheHSof the resistant populations was 0.144, and theHTwas 0.186. The analysis of molecular variance based on the response to glyphosate indicated that most of the genetic variation was found within groups of susceptible and resistant populations (90% of the genetic variation), whereas 10% or less was among groups. The high level of genetic diversity between glyphosate-resistant tropical sprangletop populations from distant and adjacent locations is likely due to both short- and long-distance seed dispersal and independent evolutionary events in tropical sprangletop populations among Persian lime groves in Veracruz.

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