Genetic selection of Calophyllum brasiliense for seed orchards

Calophyllum brasiliense populations are under severe depletion and criteria to improve production and quality of propagative material are therefore necessary. Genetic measures have the potential to reduce consanguinity and maximize allelic representation within target populations. Here, we explored genetic values for this species in a small relic of natural forest in Rio de Janeiro State (Brazil). The objective was to evaluate the potential of some genetic measures for seed orchard establishment. As genomic information of native trees is still scarce, we opted to use a dominant marker: RAPD. DNA from 17 phenotypically superior trees was obtained through the CTAB method and submitted for amplification by PCR. Electrophoresis and electronic documentation was then conducted. We calculated the percentage of polymorphic bands (PPB), gene diversity (Ht), Shannon’s information index (i), genetic distance (UPGMA) and parsimony analysis. Six primers were evaluated generating 34 loci. We found high genetic diversity PPB=70.6% with Ht=0.28 and i=0.41. Genetic relationships were reported in dendrograms (maximum parsimony and distance). Simulated sampling within and among clusters suggests that inter cluster sampling is more effective to capture the genetic diversity.

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Genetic Divergence among Populations of Invasive Alien Species Lantana camara L. from Selected Areas of Bangladesh

Plants and Ecosystem ◽

10.54479/pae.v1i01.6664 ◽

2021 ◽

Vol 1 (01) ◽

pp. 9-14

Author(s):

SAILA KABIR ◽

MD ABUL KASHEM ◽

MOHAMMAD ZABED HOSSAIN

Keyword(s):

Genetic Diversity ◽

Alien Species ◽

Invasive Alien Species ◽

Gene Diversity ◽

Lantana Camara ◽

Native Plant ◽

High Genetic Diversity ◽

Native Plant Species ◽

Information Index ◽

Genetic Clustering

Lantana camara L., a well-known invasive alien species causing invasion and posing threat to native plant species community in different regions of Bangladesh. The present study aimed to investigate the genetic diversity of L. camara populations in different regions of Bangladesh. Eight RAPD markers were used in order to probe into its genetic variability. Total number of bands (202), polymorphic loci (104), per-centage of polymorphism (97.20%), average Shanon’s information index (0.3051±0.115), Nei’s gene diversity (0.4733±0.144) was found and in different populations and multiple divergent genetic clustering along with presence of unique alleles (4) for RAPD revealed high genetic diversity among the populations of L. camara in different regions of Bangladesh.

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Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of EndangeredPolyporus umbellatus

BioMed Research International ◽

10.1155/2015/941357 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 2

Author(s):

Yuejin Zhang ◽

Yuanyuan Chen ◽

Ruihong Wang ◽

Ailin Zeng ◽

Michael K. Deyholos ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tags ◽

Large Scale ◽

Gene Diversity ◽

High Genetic Diversity ◽

Information Index ◽

Polyporus Umbellatus ◽

Ssr Primers ◽

Expressed Sequence

A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences inGanoderma lucidumobtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 naturalPolyporus umbellatusaccessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13P.umbellatusaccessions showed relatively high genetic diversity. The expected heterozygosity, Nei’s gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups.

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

Canadian Journal of Plant Science ◽

10.4141/cjps07015 ◽

2008 ◽

Vol 88 (1) ◽

pp. 179-186 ◽

Cited By ~ 2

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

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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 Stephanie kwangsiensis H. S. Lo and Salvia prionitis Hance after Transplanted and Micropropagated

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.518-523.5460 ◽

2012 ◽

Vol 518-523 ◽

pp. 5460-5467

Author(s):

Chuan Ming Fu ◽

Yan Qin ◽

Feng Luan Tang ◽

Yun Ping Shi ◽

Zhi Guo Zhao ◽

...

Keyword(s):

Genetic Diversity ◽

Tissue Culture ◽

Gene Diversity ◽

Random Amplified Polymorphic Dna ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Chinese Herbs ◽

High Genetic Diversity ◽

Information Index ◽

Rapd Pcr

Stephanie Kwangsiensis H. S. Lo and Salvia prionitis Hance were two rare and valuable Chinese herbs. Genetic diversity of the two plants were studied by using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers after they were transplantation and tissue culture. Results indicated that Nei’s gene diversity (H), Shannon’s information index (I), the percentage of polymorphic loci (PPL) of source / transplantation / tissue culture materials of S. Kwangsiensis H. S. Lo were H=0.282 / 0.195/ 0.056, I=0.415 / 0.290 / 0.087, PPL=75.6% / 56.1% /19.5% based on RAPDs and H=0.295 / 0.292 / 0.111, I=0.445 / 0.435 / 0.166, PPL=85.3% / 85.3% / 32.8% based ISSRs. And the same parameters of source / transplantation / tissue culture materials of S. prionitis Hance were H=0.193 / 0.192 / 0.231, I=0.291 / 0.289 /0.347, PPL=57.8% / 57.2% / 68.6% based on RAPDs and H=0.217 / 0.217 / 0.155, I=0.327 / 0.326 /0.235, and PPL=64.2% / 64.2% / 49.1% based on ISSRs instead. For the transplanted materials, genetic diversity was slightly declining with the disappearance of adversity. And for the tissue culture materials, more genets sampled for tissue culture, less reduction of genetic diversity; and fewer genets sampled, more reduction of genetic diversity. In addition, high genetic diversity appearing in tissue culture materials of S. prionitis Hance partially generate from somatic mutations. And these mutations maybe related to RAPD-PCR regions and just had been checked out by RAPDs.

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

Journal of Biobased Materials and Bioenergy ◽

10.1166/jbmb.2021.2099 ◽

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.

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Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR and SCoT Markers

10.21203/rs.3.rs-406235/v1 ◽

2021 ◽

Author(s):

Abdurrahim YILMAZ ◽

Vahdettin Ciftci

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Genetic Relationships ◽

Genetic Distances ◽

Laurus Nobilis ◽

Information Index ◽

Geographical Regions ◽

Polymorphism Rate ◽

Amova Analysis ◽

Breeding Techniques

Abstract Laurel (Laurus nobilis L.) has been used in the Mediterranean basin since ancient ages. Nowadays, Turkey, Mexico, Portugal, Italy, Spain, France, Algeria, and Morocco use aromatic leaves for commercial purposes, and Turkey is the largest exporter in the world. In this study, molecular characterization and genetic relationships of 94 Turkish laurel genotypes were determined by ISSR and SCoT markers. The experiment was conducted with 16 ISSR and 10 SCoT markers. While 348 of 373 bands were polymorphic with a 94.04% polymorphism rate, Nei's genetic distances ranged between 0.17 and 0.70 with 0.39 mean in ISSR. In SCoT, 175 of 227 bands were polymorphic with 76.07% polymorphism rate, and Nei's distances varied between 0.12 and 0.51. Sufficient genetic diversity determined with diversity parameters consisting the average Shannon's information index (ISSR:0.46, SCoT:0.35), the overall gene diversity (ISSR:0.19, SCoT:0.18), and the effective number of alleles (ISSR:1.52, SCoT:1.38). AMOVA (Analysis of molecular variance) revealed most of the variation was within genotypes (%96). Neighbor-joining algorithms, principal coordinate analysis (PCoA), and model-based structure resulted in harmony and clustered according to the geographical regions and provinces they collected. Genotypes were divided into two groups in ISSR and SCoT with UPGMA clustering resulting in a similar polymorphism distribution. The correlation coefficient (r) determined by marker systems' Nei's genetic distance matrices was 0.88. The results of the study put forward resources for advanced breeding techniques, and contribute to the preservation of genetic diversity, and management of genetic resources for the breeders.

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Genetic Diversity Of Plukenetia Volubilis L. Assessed By ISSR Markers

Scientia Agriculturae Bohemica ◽

10.1515/sab-2015-0029 ◽

2015 ◽

Vol 46 (4) ◽

pp. 145-153 ◽

Cited By ~ 3

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.

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Genetic Diversity of Wild Oat (Avena fatua)Populations from China and the United States

Weed Science ◽

10.1614/ws-06-108.1 ◽

2007 ◽

Vol 55 (2) ◽

pp. 95-101 ◽

Cited By ~ 21

Author(s):

Runzhi Li ◽

Shiwen Wang ◽

Liusheng Duan ◽

Zhaohu Li ◽

Michael J. Christoffers ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Gene Diversity ◽

Genetic Relationships ◽

The United States ◽

Mantel Test ◽

Wild Oat ◽

Chinese Populations ◽

Nei's Distance ◽

The Impact

Weed genetic diversity is important for understanding the ability of weeds to adapt to different environments and the impact of herbicide selection on weed populations. Genetic diversity within and among six wild oat populations in China varying in herbicide selection pressure and one population in North Dakota were surveyed using 64 polymorphic alleles resulting from 25 microsatellite loci. Mean Nei's gene diversity (h) for six wild oat populations from China was between 0.17 and 0.21, and total diversity (HT) was 0.23. A greater proportion of this diversity, however, was within (Hs= 0.19) rather than among (Gst= 0.15) populations. For the wild oat population from the United States,h= 0.24 andHT= 0.24 were comparable to the values for the six populations from China. Cluster analysis divided the seven populations into two groups, where one group was the United States population and the other group included the six Chinese populations. The genetic relationships among six populations from China were weakly correlated with their geographic distribution (r= 0.22) using the Mantel test. Minimal difference in gene diversity and small genetic distance (Nei's distance 0.07 or less) among six populations from China are consistent with wide dispersal of wild oat in the 1980s. Our results indicate that the wild oat populations in China are genetically diverse at a level similar to North America, and the genetic diversity of wild oat in the broad spatial scale is not substantially changed by environment, agronomic practices, or herbicide usage.

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Genetic Diversity among Calamus brandisii Becc. (Arecaceae) Populations in Kerala Part of Western Ghats

Indian Journal of Forestry ◽

10.54207/bsmps1000-2021-xm8ipx ◽

2021 ◽

Vol 43 (1) ◽

pp. 38-42

Author(s):

Kavungal Priya ◽

◽

Indira . ◽

Vadakkethil Balakrishnan Sreekumar ◽

Renuka . ◽

...

Keyword(s):

Genetic Diversity ◽

Western Ghats ◽

Rapd Markers ◽

Gene Diversity ◽

Issr Markers ◽

High Genetic Diversity ◽

Western Ghats Of India ◽

The Mean ◽

Two Parameters ◽

Two Populations

Calamus brandisii Becc. is one of the endemic slender rattans found in the Western Ghats of India. The genetic diversity of two main populations available in Kerala was investigated using 20 RAPD and 9 ISSR markers. Two parameters viz., gene diversity and genetic diversity within and among populations were analyzed. ISSR analysis showed quite high genetic diversity in Pandimotta compared to Bonacaud population whereas in RAPD markers both these populations were moderately diverse. The percentage of total genetic differentiation (Gst) among two populations is relatively higher than the mean Gst value indicating high genetic diversity within the populations. The genetic distance between these two populations was 0.1739 with ISSR markers and 0.1971 with RAPD markers. Because of its high genetic diversity, Pandimotta population can be treated as an important population of gene diversity with potentially useful genes. This may be included in the high priority reservoir for genetic conservation also.

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