Genetic diversification of local onion populations under different production systems in Uruguay

2014 ◽  
Vol 13 (3) ◽  
pp. 238-246 ◽  
Author(s):  
Eliana Monteverde ◽  
Guillermo A. Galván ◽  
Pablo Speranza
Keyword(s):  
Production Systems ◽  
Genetic Material ◽  
Inter Simple Sequence Repeat ◽  
Group Method ◽  
Male Sterile ◽  
Pair Group ◽  
Cytoplasm Type ◽  
Low Degree ◽  
European Immigrants ◽  
And Cluster Analysis

In Uruguay, onion (Allium cepa L.) germplasm is mainly derived from the genetic material introduced by several waves of European immigrants and subsequently multiplied by household farmers, resulting in a wealth of locally adapted populations. This study examined the genetic diversity in a collection of 27 local onion populations and two cultivars derived from them. A total of 843 onion plants were fingerprinted, and 83 inter-simple sequence repeat polymorphic bands were generated. Analysis of molecular variance showed high diversity within the populations (66% of the total variation). Some short-day populations from different geographical origins were grouped together by the unweighted pair-group method using arithmetic averages, principal coordinate analysis and cluster analysis, while the more extensively sampled long- and intermediate-day populations showed a widespread distribution, with no significant subgrouping among them. This weakly structured gene pool is probably the consequence of seed and bulb exchange between farmers and natural inter-pollination. Nevertheless, a Bayesian analysis allowed the distinction of four genetic backgrounds of alleles in the whole collection, and populations were predominately assigned to each genetic background. In addition, mitochondrial variants determining normal (N) pollen fertility or the sterile S or T types were analysed for the same set of plants using specific primers. Most accessions showed a proportion of male-sterile individuals. Cytoplasm type T was the most represented (26 out of 29 accessions), and cytoplasm type S was found in a low proportion of individuals in seven populations. Uruguayan onion germplasm maintains a low degree of genetic differentiation despite the small cultivated area and intense seed exchange, probably due in part to different market purposes based on the growing cycle.

scholarly journals Genetic Characterization of an Endangered Chilean Endemic Species, Prosopis burkartii Muñoz, Reveals its Hybrids Parentage

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 744
Author(s):  
Roberto Contreras ◽  
Liesbeth van den Brink ◽  
Boris Burgos ◽  
Marlene González ◽  
Sandra Gacitúa
Keyword(s):  
Endemic Species ◽  
Genetic Material ◽  
Inter Simple Sequence Repeat ◽  
Group Method ◽  
Trnl Intron ◽  
Arithmetic Average ◽  
Pair Group ◽  
Upgma Cluster Analysis ◽  
Species Specific ◽  
Simple Sequence

The hybridization of Prosopis burkartii, a critically endangered endemic species, and the identification of its paternal species has not been genetically studied before. In this study we aimed to genetically confirm the origin of this species. To resolve the parental status of P. burkartii, inter-simple sequence repeat (ISSR), simple sequence repeats (SSR) and intron trnL molecular markers were used, and compared with Chilean species from the Algarobia and Strombocarpa sections. Out of seven ISSRs, a total of 70 polymorphic bands were produced in four species of the Strombocarpa section. An Multi-dimensional scaling (MDS) and Bayasian (STRUCTURE) analysis showed signs of introgression of genetic material in P. burkartii. Unweighted pair group method with arithmetic average (UPGMA) cluster analysis showed three clusters, and placed the P. burkartii cluster nested within the P. tamarugo group. Sequencing of the trnL intron showed a fragment of 535 bp and 529 bp in the species of the Algarobia and Strombocarpa sections, respectively. Using maximum parsimony (MP) and maximum likelihood (ML) trees with the trnL intron, revealed four clusters. A species-specific diagnostic method was performed, using the trnL intron Single Nucleotide Polymorphism (SNP). This method identified if individuals of P. burkartii inherited their maternal DNA from P. tamarugo or from P. strombulifera. We deduced that P. tamarugo and P. strombulifera are involved in the formation of P. burkartii.

scholarly journals Analysis of Genetic Variability Amongst Polyploid Genotypes of Pteris vittata L. From Various Geographic Locales of India

2021 ◽  
Vol 9 ◽  
Author(s):  
Jyoti Mathur ◽  
P. B. Khare ◽  
Apurva Panwar ◽  
S. A. Ranade
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Genomic Structure ◽  
Inter Simple Sequence Repeat ◽  
Pteris Vittata ◽  
Group Method ◽  
Bootstrap Analysis ◽  
Pair Group ◽  
Fern Species ◽  
Outgroup Taxon ◽  
Effective Multiplex Ratio

Pteris vittata L. is very common and a widely distributed species belongs to the family Pteridaceae. Various cytotypes from diploid to octaploid is available in this fern species. The present work has been carried out for genetic diversity in this fern both within and between the cytotypes. The molecular analysis at inter- as well as intra-species has been carried out with 57 accessions of P. vittata as well as of other species of Pteris with Microsorium punctatum considered as an out group taxon. For the present study 48 P. vittata (36 tetraploid and 12 pentaploid) and five of other species (four P. cretica, one P. pellucida, one P. tremula, one P. quadriaurita, and two P. ensiformis) accessions were used. The UPGMA (unweighted pair group method with arithmetic mean) dendrograms were generated for each method separately, as well as for all methods cumulatively, after a 1000 replicate bootstrap analysis. In order to determine the utility of each of the method, a comparative statistical assessment was done and marker index (MI), expected average heterozygosity, fraction of polymorphic loci and effective multiplex ratio (EMR) were calculated in case of each of the methods used in the present study. At the level of individual methods highest MI was obtained for directed amplification of minisatellites DNA (DAMD) method. Our findings of the present study concluded that out of the three methods Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat (ISSR), and Directed Amplification of Minisatellite DNA (DAMD), DAMD was the best in term of polymorphism and heterozygosity as scores exhibited highest MI. The different accessions of P. vittata collected from different phytogeographical regions falls into six groups. Out of six clusters, one cluster is of pentaploid cytotype, four clusters are of tetraploid cytotype and one for outgroup taxon (M. punctatum). The result thus showed that within tetraploid, heterozygosity with variable genomic structure exists.

Inter Simple Sequence Repeat (ISSR) markers to assess genetic diversity and relatedness within strawberry genotypes

2008 ◽  
Vol 88 (2) ◽  
pp. 313-322 ◽  
Author(s):  
S. C. Debnath ◽  
S. Khanizadeh ◽  
A. R. Jamieson ◽  
C. Kempler
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Breeding Lines ◽  
Pair Group ◽  
Simple Sequence

The goal of this study was to determine the level of genetic diversity and relatedness among 16 strawberry (Fragaria H ananassa Duch.) cultivars and 11 breeding lines developed in Canada, using Inter Simple Sequence Repeat (ISSR) markers. Seventeen primers generated 225 polymorphic ISSR-PCR bands. Cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) revealed a substantial degree of genetic similarity among the genotypes ranging from 63 to 77% that were in agreement with the principal coordinate (PCO) analysis. Geographical distribution for the place of breeding program explained only 1.4% of total variation as revealed by analysis of molecular variance (AMOVA). The ISSR markers detected a sufficient degree of polymorphism to differentiate among strawberry genotypes, making this technology valuable for cultivar identification and for the more efficient choice of parents in current strawberry breeding programs. Key words: Fragaria × ananassa, DNA fingerprinting, multivariate analysis, breeding, genetic similarity

Genetic diversity of male sterile and low fertility germplasm of Citrus revealed using SSR markers

2007 ◽  
Vol 4 (2) ◽  
pp. 99-104 ◽  
Author(s):  
Cao Qing-Qin ◽  
Meng Hai-Jun ◽  
Wen Xiao-Peng ◽  
Yi Hua-Lin ◽  
Deng Xiu-Xin
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Low Fertility ◽  
Group Method ◽  
Male Sterile ◽  
Pair Group ◽  
Male Sterile Cytoplasm ◽  
Group 3 ◽  
Group 2 ◽  
Method Analysis

AbstractThe genetic diversity of 43 male sterile and low fertility Citrus accessions, as well as 13 fertile ones, were assessed using simple sequence repeat markers (SSRs). Thirty-five polymorphic alleles were generated from eight primers (on average 4.4 alleles per primer). Cluster analysis was performed via unweighted pair group method analysis (UPGMA) using the NTSYS-pc version 2.10. The results showed that the accessions could be classified into three groups: cultivars of mandarin were classified into group 1; those of sweet orange, grapefruit, ponkan or tangor into group 2; and Microcitrus with male sterile cytoplasm into group 3. Cluster analysis also revealed that Satsuma mandarin was more closely related to Bendiguangju mandarin than to Zaoju, Mankieh or Huangyan Bendizao tangerine. The present study on genetic diversity of male sterile and low fertility Citrus will provide useful information for further collection, preservation and utilization of this plant.

Morphometric analysis in different geographical populations of Varroa destructor (Acari: Varroidae) associated with Apis mellifera colonies in Iran

2018 ◽  
Vol 23 (10) ◽  
pp. 1915
Author(s):  
Mahsa Farjamfar ◽  
Alireza Saboori ◽  
Jamasb Nozari ◽  
Vahid Hosseininaveh
Keyword(s):  
Apis Mellifera ◽  
Morphometric Analysis ◽  
Varroa Destructor ◽  
Principal Component ◽  
Group Method ◽  
Dorsal Shield ◽  
Pair Group ◽  
Geographical Regions ◽  
Geographical Populations ◽  
And Cluster Analysis

Varroa destructor is a major ectoparasitic mite which feeds on the western honey bee, Apis mellifera hemolymph. Morphometric analysis of V. destructor in Iran was performed in order to detect differences within some populations of the species. Totally, 145 female mites were collected from A. mellifera colonies in different geographical regions in Iran and Europe (Spain and France). Eight morphological variables were measured: 1) length of dorsal shield (LDS), 2) width of dorsal shield (WDS), 3) length of genital shield (LGS), 4) width of genital shield (WGS), 5) length of metapodal shield (LMS), 6) width of metapodal shield (WMS), 7) length of anal shield (LAS) and 8) width of the anal shield (WAS). The ratios of LDS/WDS, WDS/LDS, LGS/WGS and LAS/WAS were also calculated. Multivariate analyses demonstrated significant differences in means of body length (LDS) and body width (WDS) between populations. Using principal component analysis (PCA) and cluster analysis with pair group method, five morphological groups were established. PCA analyses were also shown one morphotype, A3, between samples. Collectively, our findings suggest a wide phenotypic plasticity within the populations of Varroa mite in Iran.

scholarly journals Characterization of Fusarium Spp. Inciting Vascular Wilt of Tomato and Its Management by a Chaetomium-Based Biocontrol Consortium

2021 ◽  
Vol 12 ◽  
Author(s):  
Govindan Pothiraj ◽  
Zakir Hussain ◽  
Awani Kumar Singh ◽  
Amolkumar U. Solanke ◽  
Rashmi Aggarwal ◽  
...  
Keyword(s):  
Complex Disease ◽  
Field Experiments ◽  
Geographic Origin ◽  
Inter Simple Sequence Repeat ◽  
Control Treatment ◽  
Group Method ◽  
Vascular Wilt ◽  
Indian States ◽  
Pair Group ◽  
Wilt Incidence

Though the vascular wilt of tomato caused by the species of Fusarium is globally reported to be a complex disease in certain countries, for example, India, our studies indicated that the disease is caused by either Fusarium oxysporum f. spp. lycopersici (Fol) or Fusarium solani (FS) with the Fol being widely prevalent. In assessing the genetic diversity of 14 Fol strains representing the four Indian states by the unweighted pair group method with arithmetic averaging using Inter Simple Sequence Repeat (ISSR) amplicons, the strains distinguished themselves into two major clusters showing no correlation with their geographic origin. In pot experiments under polyhouse conditions, the seed dressing and soil application of a talc-based formulation of a biocontrol treatment, TEPF-Sungal-1 (Pseudomonas putida) + S17TH (Trichoderma harzianum) + CG-A (Chaetomium globosum), which inhibited Fol, was equally effective like the cell suspensions and was even better than the fungicidal mixture (copper oxychloride-0.25% + carbendazim-0.1%) in promoting the crop growth (52.3%) and reducing vascular wilt incidence (75%) over the control treatment, despite the challenge of inoculation with a highly pathogenic TOFU-IHBT strain. This was associated with significant expressions of the defense genes, indicating the induction of host resistance by a biocontrol consortium. In field experiments on two locations, the bioconsortium was highly effective in recording maximum mean fruit yields (54.5 and 60%) and a minimum mean vascular wilt incidence (37.5%) in comparison to the untreated control. Thus, Chaetomium-based bioconsortium demonstrated consistency in its performance across the two experiments in 2 years under the two field conditions.

Genetic relatedness among cultivated and wild mulberry (Moraceae: Morus) as revealed by inter-simple sequence repeat analysis in China

2006 ◽  
Vol 86 (1) ◽  
pp. 251-257 ◽  
Author(s):  
Zhao Weiguo ◽  
Zhou Zhihua ◽  
Miao Xuexia ◽  
Wang Sibao ◽  
Zhang Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Pair Group ◽  
Simple Sequence

The genetic diversity of 27 mulberry (Morus spp.) genotypes mainly from China was investigated using inter-simple sequence repeat (ISSR) markers to assist in addressing breeding objectives and conserving existing genetic resources. Of the 22 primers screened, 15 produced highly reproducible ISSR bands. Using these 15 primers, 138 discernible DNA fragments were generated with 126 (91.3%) being polymorphic, indicating considerable genetic variation among the mulberry genotypes studied. Genetic similarity ranged from 0.6014 between Yu 2 and Yu 711 to 0.9493 between Cuizhisang and Dejiang 10. The phenetic dendrogram based on ISSR data generated by the unweighed pair group method with arithmetical averages (UPGMA) method grouped the 27 accessions into two major clusters: cluster I, cultivated mulberry species (M. multicaulis Perr., M. alba Linn., M. atropurpurea oxb., M. bombycis Kiodz., M. australis Poir., M. rotundiloba Kiodz., M. alba var. pendula Dipp., M. alba var. macrophylla Loud., and M. alba var. venose Delile.); and cluster II, wild mulberry species (M. cathayana Hemsl., M. laevigata Wall., M. wittiorum Hand-Mazz., M. nigra Linn., and M. mongolica Schneid.). Our molecular analyses agree with the existing morphological classification of Morus and clarify the genetic relationships among mulberry species. Key words: Morus L., genetic diversity, inter-simple sequence repeat, relatedness

scholarly journals Genetic Variability of 21 Tea Genotypes [Camellia sinensis (L.) O. Kuntze] Based on RAPD Markers

2018 ◽  
Vol 5 (2) ◽  
pp. 77
Author(s):  
Budi Martono ◽  
Syafaruddin Syafaruddin
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Similarity ◽  
Binary Data ◽  
Rapd Markers ◽  
Group Method ◽  
Breeding Programs ◽  
Pair Group ◽  
Monomorphic Band ◽  
And Cluster Analysis

<em>Knowing the genetic diversity in the tea germplasms collection is one of important conditions for assembling new superior varieties. Information of genetic diversity can be obtained through analysis using RAPD molecular markers. The study aimed to determine the genetic diversity of 21 tea genotypes based on RAPD markers. The research was conducted in Integrated Laboratory, Seameo Biotrop, Bogor, from July to September 2013. Genomic DNA was isolated from 21 tea genotypes leaf samples, then amplified with primer OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08. Electrophoresis result was converted into binary data. The genetic similarity and cluster analysis calculation was done using NTSYS-pc version 2.10. In this research, 50 polymorphic bands (94,34%) and 3 monomorphic band (5,66%) were obtained. Cluster analysis based on Nei's genetic distance using the unweighted pair-group method with arithmatic (UPGMA) divided 21 tea genotypes into two groups at a genetic similarity value of 0,48. Group 1 consisted of 20 tea genotypes, while the second group comprised only a one genotype (Sin 27). The range of genetic similarity matrix was between 28%–92%, the lowest genetic similarity (28%) was found between GMB 4 and Sin 27 genotypes, while the highest (92%) was found between AS 2 and AS 1 genotypes. The information obtained can be utilized in breeding programs with the support of agronomic characters as well as in the conservation of tea germplasm.</em>

scholarly journals Study of relationships among twelve Phyllanthus species with the use of molecular markers

2010 ◽  
Vol 46 (No. 3) ◽  
pp. 135-141 ◽  
Author(s):  
G.R. Rout ◽  
S.K. Senapati ◽  
S. Aparajita
Keyword(s):  
Molecular Markers ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Index ◽  
Inter Simple Sequence Repeat ◽  
Morphological Characterization ◽  
Group Method ◽  
Pair Group ◽  
Group I ◽  
Marker Loci ◽  
Rapd And Issr

The present investigation was undertaken to describe the relationships among twelve species of Phyllanthus collected in India by help of molecular markers. In total, 259 marker loci were assessed, out of which 249 were polymorphic revealing 96.13% polymorphism. Nei's similarity index varied from 0.35 to 0.76 for RAPD (Random Amplified Polymorphic DNA) and from 0.31 to 0.76 for ISSR marker systems. Cluster analysis by the unweighted pair group method (UPGMA) of Dice coefficient of similarity generated dendrogram with more or less similar topology for both the analyses that offered a better explanation for diversity and affinities between the species. The phylogenetic tree obtained from both RAPD and ISSR (Inter Simple Sequence Repeat) markers has divided the 12 species into two groups: group I consisting of only one species Phyllanthus angustifolius (Sw.) Sw and group II with the rest of 11 species. Basically, these results were in compliance with notable morphological characterization. The present study revealed high variation among the species of Phyllanthus and will help to identify different Phyllanthus species.

scholarly journals Distinguishing grapefruit and pummelo accessions using ISSR markers

2010 ◽  
Vol 46 (No. 4) ◽  
pp. 170-177 ◽  
Author(s):  
A. Uzun ◽  
O. Gulsen ◽  
T. Yesiloglu ◽  
Y. Aka-Kacar ◽  
O. Tuzcu
Keyword(s):  
Citrus Fruit ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Citrus Paradisi ◽  
Arithmetic Average ◽  
Pair Group ◽  
Citrus Maxima ◽  
Group B ◽  
Citrus Hassaku

Grapefruit is the fourth economically most important citrus fruit in the world. In this research Inter-Simple Sequence Repeat (ISSR) markers were used to distinguish twenty-nine grapefruit (Citrus paradisi Macf.), five pummelo (Citrus maxima (Burm.) Merr.) and one Citrus hassaku Hort. Ex Tanaka accessions. Twelve ISSR primers produced a total of 100 fragments and 62 of them were polymorphic. The number of average polymorphic fragments per primer was 5.2. The mean polymorphism information content (PIC) was 0.37. The unweighted pair group method arithmetic average (UPGMA) analysis demonstrated that the accessions had a similarity range from 0.79 to 1.00. The accessions were separated into two main clusters; group A with five pummelos and group B with grapefruits. In the pummelo cluster, all pummelos were distinguished whereas in the grapefruit cluster some accessions were not clearly separated. There was a low level of variation in the grapefruits due to their mutation origin.

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