scholarly journals Genetic diversity of Pseudomonas syringae pv. syringae causing leaf blight of litchi in Bangladesh

2014 ◽  
Vol 12 (1) ◽  
pp. 150-161
Author(s):  
S Afrose ◽  
I Hossain ◽  
MD Hossain ◽  
MAH Khan
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Pseudomonas Syringae ◽  
Disease Incidence ◽  
Severe Disease ◽  
Molecular Study ◽  
Genetic Distances ◽  
Leaf Blight ◽  
Severity Of The Disease ◽  
Different Origins

Leaf blight of caused by Pseudomonas syringae pv. syringae is a severe disease of litchi saplings, which is considered as a threat for raising healthy sapling of the fruit in Bangladesh. A survey was conducted to find out incidence and severity of the disease in five regions of Bangladesh namely Rajshahi, Dinajpur, Mymensingh, Barishal and Khagrachari. The highest disease incidence was recorded in Dinajpur and Kagrachari regions and the lowest in Mymensingh region. On the other hand, the highest disease severity was found in Dinajpur and Kagrachari regions and the lowest in Mymensingh region. Another experiment was conducted to determine genetic diversity of the causal bacterium following molecular study. Twenty five diseased samples of bacterial leaf blight of litchi were collected from 25 locations in five regions and one isolate of P. syringae pv. syringae was isolated from each sample. The values of pair-wise comparisons of Nei’s (1972) genetic distance among5 different locations of P. syringae pv. syringae were computed. From the UPGMA dendrogram drawn on the basis of Nei’s (1972) genetic distances and comparatively the highest genetic distance (0.9163) was observed in Khajrachari vs Barishal, Mymensingh vs Barishal and Rajshahi vs Mymensingh but Dinajpur was close to the Barishal with the least genetic distance (0.3567). Thus, the results indicate that remarkable genetic diversity exists among the isolates of P. syringae pv. syringae from different origins Bangladesh. DOI: http://dx.doi.org/10.3329/sja.v12i1.21121 SAARC J. Agri., 12(1): 150-161 (2014)

Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

2015 ◽  
Vol 3 (1) ◽  
pp. 1-11
Author(s):  
Rezq Basheer-Salimia
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Vitis Vinifera L ◽  
Similarity Matrix ◽  
Breeding Programs ◽  
Local Varieties ◽  
Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

Detection of genetic diversity in rough fescue (Festuca campestris Rydb) populations of southern Alberta and British Columbia, Canada, using RAPD markers

2008 ◽  
Vol 88 (2) ◽  
pp. 307-312
Author(s):  
Zhao Mengli ◽  
Han Bing ◽  
Walter D Willms
Keyword(s):  
Genetic Diversity ◽  
British Columbia ◽  
Genetic Distance ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Distance ◽  
Genetic Distances ◽  
Gene Frequencies ◽  
Southern Alberta ◽  
Potential Adaptation ◽  
Rough Fescue

Mountain rough fescue (Festuca campestris Rydb.) is a tufted native grass in southern Alberta and British Columbia, Canada, and has attracted interest for use in reclamation. However, its seed is often available from only a few localized sources and may not be adapted for areas removed from the collection site. We conducted a study to determine the genetic variability among rough fescue populations to assess its potential adaptation. Thirty plants were collected from each of six populations and analyzed using Random Amplified Polymorphic DNA (RAPD). One population (Kamloops, BC) was separated by several mountain ranges from the five easterly Alberta populations.The Kamloops population was also separated from the Alberta populations by genetic distance in two clusters. Of the total genetic variation present in the data, 21% was found among populations while the remaining (79%) was found within populations. Nei’s genetic distances among populations were related to their geographical distances. Genetic differences among populations appeared to be caused primarily by differences in gene frequencies rather than rare genes. Also, genetic diversity appeared to increase from west to east suggesting that the more easterly populations had greater adaptation potential. We speculate that the more easterly populations are less likely to share genes since the prevailing winds are from the west. Germplasm from the more easterly populations may be used with suitable precautions within Alberta and possibly around Kamloops. Key words: Genetic distance, geographic distance, reclamation, potential adaptation

scholarly journals Genetic Diversity Based on ISSR Markers of Apple Genotypes in Ardahan/Turkey

2018 ◽  
Vol 10 (4) ◽  
pp. 554-558
Author(s):  
Emre SEVİNDİK ◽  
Hüseyin UYSAL ◽  
Zehra Tuğba MURATHAN
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Uv Light ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Genetic Distances ◽  
The Matrix ◽  
Commercial Kits ◽  
Issr Primers

Within the present study, it was conducted a genetic diversity analysis using ISSR markers for some apple genotypes grown in Ardahan region, Turkey. Total genomic DNA (gDNA) isolation from apple leaves was performed using commercial kits. Five ISSR primers were used to determine the genetic diversity among the genotypes studied. Polymerase Chain Reaction (PCR) was performed with all gDNA samples to produce bands to score. PCR products were run in agarose gel and visualized under UV light. Bands on the gels were scored as “1”, while no bands at the corresponding positions were scored as “0”, to generate the matrix file. Five ISSR primers produced a total of 35 bands, and 20 of them were polymorphic. The polymorphic bands rated approximately 57%. Phylogenetic relationships and genetic distances between the genotypes were calculated by using the PAUP [Phylogenetic Analysis Using Parsimony (and Other Methods)] program.  According to the PAUP data, the closest genetic distance was 0.03704 between ‘Kaburga’ and ‘Japon Apple’ genotypes, while the furthest genetic distance was 0.48148 between ‘Karanfil Apple’ and ‘Sisli Uruset’. The phylogenetic analysis obtained using UPGMA algorithm produced a phylogenetic tree with two clades. The results suggest that ISSR markers are useful tools for determining genetic relationships among apple genotypes.

scholarly journals Assessing Taro (Colocasia esculenta (L.) Schott) Leaf Blight Incidence, Severity, and Farmers’ Knowledge of the Disease in Fako Division of Cameroon

2020 ◽  
pp. 17-29
Author(s):  
Mandah Cicelia Takor ◽  
Ekwa Yawa Monono ◽  
Ojong Agbor Ntane ◽  
Jemimah Evenye Ngale ◽  
Lum A. Fontem
Keyword(s):  
Disease Severity ◽  
Disease Incidence ◽  
Management Strategies ◽  
Leaf Blight ◽  
Cultural Methods ◽  
Randomized Design ◽  
High Prevalence ◽  
Severity Of The Disease ◽  
Blight Disease ◽  
Taro Leaf Blight

Taro leaf blight (TLB), a major disease of taro plant caused by Phytophthora colocasiae, a pseudo-fungus, that occurs in many taro producing areas, especially in the South West of Cameroon. A Survey was conducted to assess farmers’ knowledge, as well as to determine the incidence and the severity of the disease in taro fields. Structured questionnaires were administered in selected locations (Bokova, Ekona, Muea, Mile 16, Mutengene, and Likomba) of taro production. Two farms were selected with two quadrats of 64 m2 each were carved to assess disease incidence and severity on taro. The number of plants infected with taro leaf blight were counted and the area of the affected leaves measured was used to evaluate the disease incidence and disease severity. Data collected were subjected to ANOVA for complete randomized design and the means were compared using Tukey test at 0.05 probability levels. The results revealed that most of the farmers could identify the disease while practicing cultural methods in controlling the disease. The results also revealed significant differences (p = 0.001) in disease incidence and disease severity in all the localities, with Mile 16 showing the highest percentage mean of 96.53% and 85.59%, respectively. The severity scored showed high infection range of 3 – 3.95 in all locations except in Likomba (2.60).  It could be concluded from the results that there were high prevalence of taro leaf blight disease in Fako Division. Good management strategies are therefore required to control Taro leaf blight and improve taro production in the area.

scholarly journals Genetic diversity and species identity of the critically endangered Rote Island snake-necked turtle, Chelodina mccordi Rhodin, 1994

2021 ◽  
Vol 948 (1) ◽  
pp. 012001
Author(s):  
N A Devi ◽  
R Eprilurahman ◽  
D S Yudha ◽  
S Raharjo ◽  
M As-Singkily ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Dna Sequences ◽  
Captive Breeding ◽  
Haplotype Diversity ◽  
Genetic Distances ◽  
Ex Situ ◽  
Species Identity ◽  
Natural Habitats ◽  
Diversity Assessment

Abstract The endemic Chelodina mccordi is considered extinct in the wild; however, ex-situ populations are thriving and sampled for our genetic diversity assessment. We used three sequences resulting from blood and tissue samples of five individual turtles amplified for 650-bp cytochrome oxidase I (COI) fragment of the mitochondrial DNA. We analysed a total of 30 barcoding DNA sequences for phylogenetic relationships and genetic distances among Chelodina spp. Nucleotide diversity of eight C. mccordi samples is 0.007 ± 0.001 with a haplotype diversity of 0.893 ± 0.086. All these samples form a monophyletic clade that is sister to a clade of Australian and New Guinean long-necked turtles. Genetic distances calculated using Kimura 2-paramater model among C. mccordi sequences range between 0.2% and 1.5%, while a few others are without distance. The shortest genetic distance is between individuals from Rote Island, whereas the longest distance was found between individuals, each of which was derived from parental stocks originating in Rote and Timor islands. A genetic distance of 1.1% - 1.5% is likely to denote distinction at subspecies level. Results of this study could help in reintroducing captive individuals into their natural habitats. Thus, captive breeding programme of this species may help its conservation.

scholarly journals Genetic diversity of different breeds of Kazakh sheep using microsatellite analysis

2019 ◽  
Vol 62 (1) ◽  
pp. 305-312
Author(s):  
Kairat Dossybayev ◽  
Zarina Orazymbetova ◽  
Aizhan Mussayeva ◽  
Naruya Saitou ◽  
Rakhymbek Zhapbasov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Microsatellite Loci ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Sheep Breed ◽  
Expected Heterozygosity ◽  
The Mean ◽  
High Level ◽  
Short Tandem

Abstract. A total of 75 individuals from five sheep populations in Kazakhstan were investigated based on 12 STR (short tandem repeat, also known as microsatellite) markers in order to study their genetic structure and phylogenetic relationship based on genetic distances. These sheep had a high level of genetic diversity. In total, 163 alleles were found in all the populations using 12 microsatellite loci. The mean number of alleles, effective number of alleles, and polymorphism information content (PIC) values per loci were 13.4, 5.9, and 0.78, respectively. Comparing the allelic diversity between the populations, the highest genetic diversity was observed in the Edilbay-1 sheep breed (8.333±0.644), and the lowest parameter was for Kazakh Arkhar-Merino (7.083±0.633). In all populations, there is a deficiency of heterozygosity. The largest genetic diversity was found in loci INRA023 and CSRD247 with 16 alleles, and the smallest polymorphism was noted for the locus D5S2 with 8 alleles. The level of observed heterozygosity was in the range 0.678±0.051 for Kazakh Arkhar-Merino and 0.767±0.047 for Kazakh fat-tailed coarse wool. The expected heterozygosity level range was from 0.702±0.033 for Kazakh Arkhar-Merino to 0.777±0.023 for Edilbay-1. When 12 microsatellite loci are compared, the OarFCB20 locus showed the highest level of genetic variability. Excess of heterozygosity was observed at three loci; MAF065, McM042, and OarFCB20. The highest genetic distance was observed between Kazakh Arkhar-Merino and Edilbay-1, whereas the genetic distance between Edilbay-1 and Edilbay-2 is the smallest using Nei's standard genetic distance. The Edilbay-1 sheep breed possesses the largest genetic diversity among these five populations.

Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

2015 ◽  
Vol 3 (1) ◽  
pp. 1-11
Author(s):  
Rezq Basheer-Salimia
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Vitis Vinifera L ◽  
Similarity Matrix ◽  
Breeding Programs ◽  
Local Varieties ◽  
Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

Genetic variation in 26 populations of Racospermaauriculiforme and Racospermamangium using allozymes

1994 ◽  
Vol 24 (6) ◽  
pp. 1123-1132 ◽  
Author(s):  
P.D. Khasa ◽  
W.M. Cheliak ◽  
J. Bousquet
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Unknown Origin ◽  
Population Level ◽  
Genetic Distances ◽  
Starch Gel Electrophoresis ◽  
Introduced Populations ◽  
Linear Relationships ◽  
Starch Gel ◽  
The Mean

Racospermaauriculiforme (Cunn. ex Benth.) Pedley and Racospermamangium (Willd.) Pedley are two fast-growing multipurpose leguminous species that have great potential for reforestation in the subhumid and humid tropics. The level and distribution of genetic variability were evaluated among and within 13 populations of each species at 18 loci encoding 10 enzymes, using starch gel electrophoresis. At the population level, the mean number of alleles per locus, the mean percentage of polymorphic loci, and mean expected heterozygosity were, respectively, 1.9, 52.1%, and 0.122 for R. auriculiforme, and 1.5, 24.3%, and 0.064 for R. mangium. Therefore, R. mangium appeared genetically depauperate compared with R. auriculiforme. The proportion of the total genetic diversity that resided among populations in R. auriculiforme (18%) was twice that in R. mangium (9%). No linear relationships were detected between genetic and geographic distances among populations. Cluster analysis of Nei's genetic distances and discriminant analysis did not show any significant geographic pattern of population differentiation for R. mangium. These same analyses revealed two distinct clusters of populations for R. auriculiforme, one in Queensland, Australia, and Papua New Guinea, and the other in the Northern Territory of Australia and Indonesia. For both taxa, seed of unknown origin of some introduced populations in Zaire and Congo could be identified. The genetic distance between the two species (D = 0.097) was, as expected, much larger than the average intraspecific genetic distance derived from comparisons of conspecific populations (D = 0.034 for R. auriculiforme and D = 0.007 for R. mangium). However, the amplitude of the interspecific genetic distance calculated is representative of divergence levels usually observed among subspecific taxa. Based on this, and the lower levels of genetic diversity found in R. mangium, it is suggested that R. mangium derived recently from R. auriculiforme.

scholarly journals Efficiency of different PCR-based marker systems for assessment of Iris pumila genetic diversity

Biologia ◽  
2013 ◽  
Vol 68 (4) ◽  
Author(s):  
Olena Bublyk ◽  
Igor Andreev ◽  
Ruslan Kalendar ◽  
Kateryna Spiridonova ◽  
Viktor Kunakh
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Issr Markers ◽  
Genetic Distances ◽  
Resolving Power ◽  
Abiotic Stress Response ◽  
Genetic Population ◽  
Iris Pumila ◽  
Polymorphic Bands

AbstractWe investigated informativeness and effectiveness of different marker types (ISSR, IRAP, REMAP, RGAP and LP-PCR that employ primers based on the conservative sequences of abiotic stress response genes) to study genetic diversity of Iris pumila L. By the number of amplicons per primer, number of polymorphic amplicons per primer and resolving power index (Rp), ISSR-markers were the most efficient followed by LP-PCR-markers. In order of decreasing value of indicators of genetic diversity “the percentage of polymorphic bands”, and “the average Jaccardś genetic distance between plants”, marker systems may be arranged as follows: ISSR > RAPD > LP-PC > RGAP ≈ IRAP. For ISSR-markers, the percentage of polymorphic bands was 1.3–1.7 times higher than for the others, and the average genetic distance was 1.2–1.3 times higher. Different marker systems were ranked by the value of Neiś gene diversity and the Shannonś index as follows: ISSR > RAPD ≈ LP-PCR > RGAP ≈ IRAP, with the highest and the lowest values differing 1.4 times. Genetic population structure was investigated with program Structure 2.3. The data of all marker systems suggest that all genomes under study belonged to one population. The PCoA and cluster analyses based on genetic distances showed distinctions in clustering generated from different markers data and summarized data, as well as the lack of strong clusters. Mantel test revealed significant positive correlation between the matrices of genetic distances generated by the data of almost all marker systems. The strongest correlation was found between RGAP- and IRAP-markers (r = 0.452, p = 0.01) and between RGAP and ISSR (r = 0.430, p = 0.01). ISSR, RAPD and LP-PCR proved to be more effective for the study of I. pumila genetic diversity, nevertheless, joint use of different marker systems will provide a more comprehensive assessment of variation in different genomic regions.

scholarly journals Genetic diversity analysis of thirteen mungbean (Vigna radiata (L.) Wilczek) cultivars using RAPD markers

2013 ◽  
Vol 41 (2) ◽  
pp. 169-175 ◽  
Author(s):  
Sonia Khan Sony ◽  
Md Ahashan Habib ◽  
Mohammad Nurul Islam
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Distances ◽  
Polymorphic Band ◽  
Group Method ◽  
Diversity Analysis ◽  
Arithmetic Means ◽  
Genetic Diversity Analysis ◽  
Pair Group ◽  
Band Size

Genetic diversity analysis among 13 mungbean cultivars from Bangladesh was performed through polymerase chain reaction (PCR) based random amplification of polymorphic DNA (RAPD). Out of 20 arbitrary decamer oligonucleotide primers used, 10 produced a total of 379 different bands with an average of 37.9 bands per primer. Based on the observed banding pattern all the primers were found to be 100% polymorphic. Band size of the amplicons ranged from 250 - 5000 bp. A total of 10 unique DNA fragments was amplified from the 13 mungbean cultivars genome. The values of pair-wise genetic distances ranged from 0.0700 - 1.0852, indicating the presence of wide genetic diversity. The highest genetic distance (1.0852) was found between cultivar BARI Mung-2 and 6 while the lowest (0.0700) between cultivar BINA Mung-2 and 7. Dendogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Means (UPGMA) has segregated the 13 mungbean cultivars into two major clusters. BARI Mung-1, 2, 3, 4 and 5 formed cluster 1 and BARI Mung-6, BINA Mung-1, 2, 7, 6, 4, 5 and 8 have made cluster 2. DOI: http://dx.doi.org/10.3329/bjb.v41i2.13444 Bangladesh J. Bot. 41(2): 169-175, 2012 (December)

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