GENETIC VARIABILITY IN Sechium spp. (Cucurbitaceae) EVALUATED WITH AFLP MARKERS

Agrociencia ◽  
2021 ◽  
Vol 55 (7) ◽  
pp. 611-626
Author(s):  
María Isabel Iñiguez Luna ◽  
Jorge Cadena Iñiguez ◽  
Moisés Cortés Cruz† ◽  
Francisco Javier Morales Flores ◽  
Kazuo N. Watanabe ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Fragment Length Polymorphism ◽  
Distance Matrix ◽  
Fixation Index ◽  
Separate Species ◽  
Sechium Edule ◽  
Genetic Distance Matrix ◽  
Genetic Complexity ◽  
Genetic Cross ◽  
Very High

There are few studies in Mexico aimed at evaluating the genetic variability of Sechium spp. Despite certain biological variants are reported with very high potential to develop antineoplastic supplements to treat public health conditions. Using the Amplified Fragment Length Polymorphism (AFLP) technique, the genetic variability of a sample of 95 accessions of three species of Sechium (S. edule, S. chinantlense, S. compositum) was evaluated, with leaf DNA from the Banco Nacional de Germoplasma de Sechium edule en Mexico. Four combinations of AFPL were applied (EcoRI + ACC/MseI + CAC, EcoRI + ACC/MseI + CAT, EcoRI + ACC/MseI + CGC, and EcoRI + ACC/MseI + CGG). DNA samples were classified into three groups based on the flavour of the fruit (sweet, neutral, bitter). An average of 47.91% polymorphism, 0.16 heterozygosity, 32.83 number of polymorphic bands, and a zero Wright fixation index (Fst) was obtained. The evidence showed that the domesticated accessions (sweet, neutral) were separated from the bitter-taste genotypes. A monophyletic tree was generated with the genetic distance matrix and the neighbour-joining methodology. Analyses showed S. edule as the root taxon, deriving S. compositum and S. chinantlense as subgroups, and suggesting that there is not enough differentiation to treat them as separate species. The evaluated sample showed that there is no apparent reproductive barrier for genetic cross breeding. Genotypes behaved as a complex with evolutive dynamism; that genetic complexity would allow the design of new variants.

scholarly journals Molecular characterization of papaya genotypes using AFLP markers

2011 ◽  
Vol 33 (3) ◽  
pp. 849-858 ◽  
Author(s):  
Eder Jorge de Oliveira ◽  
Juliana Leles Costa ◽  
Lucas Ferraz dos Santos ◽  
Fabiana Moraes de Carvalho ◽  
Aline dos Santos Silva ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Genetic Distance ◽  
Carica Papaya ◽  
Fragment Length Polymorphism ◽  
Distance Matrix ◽  
Inbred Lines ◽  
Genetic Distance Matrix ◽  
Pair Method ◽  
Polymorphic Bands

Due to the low genetic variability reported in the commercial plantations of papaya (Carica papaya L.), the objective of this study was analyze the genetic diversity of 32 genotypes including cultivars, landraces, inbred lines, and improved germplasm using the AFLP technique (Amplified Fragment Length Polymorphism). The genetic distance matrix was obtained using the Nei and Li genetic distance and clustering was performed using the unweighted pair-method with arithmetic mean (UPGMA). Using 11 combinations of EcoRI/MseI primers, 383 polymorphic bands were obtained. On average, 34.8 polymorphic bands were obtained per primer combination. Five clusters were formed. The traditional cultivar 'Sunrise' and the inbred line CMF-L30-08 were the closest genotypes, and the improved germplasm (CMF041) and landrace (CMF233) the most distant. The main papaya cultivars commercially grown in Brazil, as well as four inbred lines and three improved germplasm, were clustered together, however, were not grouped in the same branch. The genetic distance between the Sunrise and Golden cultivars was 0.329, and even arising from mutation and selection within the Sunrise variety, the Golden stores considerable genetic variability. Additional variability was observed in the inbred lines derived from papaya breeding program at Embrapa Cassava and Fruits.

scholarly journals A geometrical framework for f –statistics

2020 ◽  
Author(s):  
Gonzalo Oteo–García ◽  
José–Angel Oteo
Keyword(s):  
Numerical Simulation ◽  
Phylogenetic Tree ◽  
Distance Matrix ◽  
Fixation Index ◽  
Population Admixture ◽  
Admixture Proportion ◽  
Genetic Distance Matrix ◽  
Detailed Derivation ◽  
Coalescence Times ◽  
F Statistics

AbstractA detailed derivation of the f–statistics formalism is made from a geometrical framework. It is shown that the f–statistics appear when a genetic distance matrix is constrained to describe a four population phylogenetic tree. The choice of genetic metric is crucial and plays an outstanding role as regards the tree–like–ness criterion. The case of lack of treeness is interpreted in the formalism as presence of population admixture. In this respect, four formulas are given to estimate the admixture proportions. One of them is the so–called f4–ratio estimate and we show that a second one is related to a known result developed in terms of the fixation index FST. An illustrative numerical simulation of admixture proportion estimates is included. Relationships of the formalism with coalescence times and pairwise sequence differences are also provided.

scholarly journals Molecular characterization of elephantgrass accessions through RAPD markers

2005 ◽  
Vol 29 (3) ◽  
pp. 568-574 ◽  
Author(s):  
Leônidas Paixão Passos ◽  
Marco Antonio Machado ◽  
Maria Coletta Vidigal ◽  
Ana Lúcia Campos
Keyword(s):  
Genetic Variability ◽  
Genetic Distance ◽  
Binary Data ◽  
Rapd Markers ◽  
Dna Amplification ◽  
Distance Matrix ◽  
Genetic Distances ◽  
Average Genetic Distance ◽  
Genetic Distance Matrix

Elephantgrass pastures are limited by yield variations and reductions in forage quality and availability, thus making the search for genotypes with reduced seasonality a major concern. In order to verify the extent of genetic variability among contrasting cultivars, ten elephantgrass accessions were analyzed through DNA amplification by RAPD technique. A total of 160 DNA bands were generated with the use of 44 random primers and 23% of these bands were monomorphic for all accessions. Gel-obtained binary data (1 for presence and 0 for absence) were used for generating a genetic distance matrix, which was utilized in a UPGMA grouping analysis. Elephantgrass cultivars Cameroon and Vruckwona were the accessions mostly divergent from the others, with an average genetic distance of 0.34. The accessions with the lowest average genetic distances from the others were Pioneiro and CNPGL 27-5, both with a distance of 0.25. Overall, genetic distances ranged from 0.06 to 0.43, indicating little genetic variability for the set of accessions, despite the contrasting morphology of the studied genotypes.

scholarly journals Differentiation and genetic structure of Sclerophoma pythiophila (Corda) v. hoehn. strains associated with various damage and disease symptoms on Pinus sylvestris L.

2012 ◽  
Vol 62 (1) ◽  
pp. 57-65 ◽  
Author(s):  
Wojciech Kraj ◽  
Tadeusz Kowalski ◽  
Marcin Zarek
Keyword(s):  
Genetic Variability ◽  
Pinus Sylvestris ◽  
Genetic Similarity ◽  
Distance Matrix ◽  
Mean Value ◽  
Shoot Tips ◽  
Disease Symptoms ◽  
Genetic Distance Matrix ◽  
Dead Shoot ◽  
High Level

Eighty-three strains of <i>Sclerophoma pythiophila</i> were isolated in the period between 1996 and 2006 from needles and shoots of <i>Pinus sylvestris</i> displaying various types of disease symptoms or damages caused by <i>Contarinia baeri</i> or <i>Thecodiplosis brachyntera</i>. On the basis of fifty-six RAMS markers, very high genetic variability of examined strains was ascertained (mean value of Jaccard's coefficient 0.58). The highest genetic similarity was shown by strains related with needles damaged by <i>Contarinia baeri</i> (0.65), whereas the lowest by those derived from dead shoot tips (0.53). No monomorphic markers were found for individual groups of strains, yet on the basis of Nei's genetic distance matrix, it was possible to determine a group of closely related fungus populations which was connected with the damaging of the needles by <i>C. baeri</i> or <i>T. brachyntera</i> (Nei's coefficient ranging from 0.035 to 0.059) and populations related with the occurrence of necrosis on shoots or decay of their tips (Nei's coefficient - 0.066). The PCA confirmed genetic similarity of strains related with damaging of the needles by insects and strains isolated from local necroses on shoots and withered shoot tips. A high level of genetic variability between populations was shown by AMOVA analysis. A high level (14.9%) and statistically significant (P=0.001) share of between-population genetic variability were ascertained.

scholarly journals Disentangling Species Delineation and Guiding Conservation of Endangered Magnolias in Veracruz, Mexico

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 673
Author(s):  
Fabián Augusto Aldaba Aldaba Núñez ◽  
Emily Veltjen ◽  
Esteban Manuel Martínez Martínez Salas ◽  
Marie-Stéphanie Samain
Keyword(s):  
Conservation Status ◽  
Full Range ◽  
Genetic Evidence ◽  
Primary Forest ◽  
Volcanic Area ◽  
Conservation Units ◽  
Separate Species ◽  
Representative Sampling ◽  
Conservation Projects ◽  
Very High

The Mexican state of Veracruz has suffered very high deforestation rates in the last few decades, and despite the establishment of protected areas and conservation projects, primary forest is now mainly persisting in mostly small, scattered, fragmented remnants. New species of Magnolia section Talauma in this state have been described with little to no reference to the already existing ones, potentially resulting in over-splitting, obscuring their taxonomic delineation and conservation status, and consequently conservation programs. To study the conservation units and their genetic diversity, we here employ 15 microsatellite markers on a highly representative sampling of 254 individuals of what are presumed to be five Magnolia species. The results support at least three species and maximum five main conservation units. We propose downgrading the latter to four, given morphological, ecological, demographical, and geographical considerations. Two out of the three sympatrically occurring species in the rainforest in the Los Tuxtlas volcanic area have weak genetic evidence to be considered separate species. Similarly, the individuals in the Sierra de Zongolica in central Veracruz, who bear a very high morphological and genetic similarity to Magnolia mexicana, have weak genetic evidence to be recognised as a separate species. Nonetheless, the individuals could be identified as Magnolia decastroi based on morphology, and further research including the full range of this species is recommended.

scholarly journals Genetic variation among South Brazilian accessions of Lippia alba Mill. (Verbenaceae) detected by ISSR and RAPD markers

2009 ◽  
Vol 69 (2) ◽  
pp. 375-380 ◽  
Author(s):  
MF. Manica-Cattani ◽  
J. Zacaria ◽  
G. Pauletti ◽  
L. Atti-Serafini ◽  
S. Echeverrigaray
Keyword(s):  
Genetic Variability ◽  
Rapd Markers ◽  
Molecular Data ◽  
Chemical Characteristics ◽  
Hierarchical Analysis ◽  
Rio Grande Do Sul ◽  
Medicinal Species ◽  
Lippia Alba ◽  
Very High ◽  
Issr Primers

Twenty-seven accessions of Lippia alba Mill. collected in Rio Grande do Sul state, Brazil, were analysed by ISSR and RAPD markers to evaluate their genetic variability and relationships. Six ISSR primers and four RAPD primers generated 120 amplified fragments, most of which were polymorphics. The overall genetic variability among accessions was very high when compared with other plant species. The hierarchical analysis of molecular data (UPGMA) showed low relationship between accessions, and no grouping between accessions of the same chemotype. Canonical functions allowed identifying some variables related with the chemical characteristics of the essential oils. Both ISSR and RAPD markers were efficient to address the genetic diversity of L. alba, and may contribute to the conservation and breeding of this increasingly important aromatic and medicinal species.

Agromorphological and molecular analysis discloses wide genetic variability in sunflower breeding lines from USDA, USA

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
K. T. Ramya ◽  
A. Vishnuvardhan Reddy ◽  
M. Sujatha
Keyword(s):  
Genetic Distance ◽  
Polymorphic Information Content ◽  
Distance Matrix ◽  
Coefficient Matrix ◽  
Male Sterile ◽  
Breeding Lines ◽  
Genetic Distance Matrix ◽  
Ssr Primers ◽  
Fertility Restorers ◽  
Simple Sequence

The present study investigates genetic divergence among 84 fertility restorers and 32 cytoplasmic male sterile (CMS) lines of sunflower augmented from USDA, USA along with the popular Indian parental lines using simple sequence repeats (SSR). Thirty-nine polymorphic SSR primers produced 139 alleles with an average of 3.56 alleles per locus. The polymorphic information content ranged from 0.23 to 0.69 with an average of 0.45. The average genetic distance was 0.45 and 0.42 for the R and CMS lines, respectively. Dendrogram based on the dissimilarity coefficient matrix grouped the CMS and R lines into separate clusters except for Cluster A which consisted of all CMS lines along with five R lines. Genetic distance matrix estimated from three sets of mitochondrial primers (BOX, ERIC and REP) grouped the 32 CMS lines into eight clusters. The results suggest the existence of considerable genetic diversity among the restorer and CMS lines of sunflower obtained from USDA, USA.

scholarly journals Analysis of Genetic Diversity in three Kazakh Sheep using 12 Microsatellites

2018 ◽  
Vol 7 (4.38) ◽  
pp. 122
Author(s):  
Kairat Dossybayev ◽  
Aizhan Mussayeva ◽  
Bakytzhan Bekmanov ◽  
Beibit Kulataev
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Mean Value ◽  
Fixation Index ◽  
Merino Sheep ◽  
Str Markers ◽  
Sheep Breeds ◽  
Str Loci ◽  
High Level ◽  
Two Populations

The genetic structure of three Kazakh sheep breeds was examined by using 12 microsatellite loci. A total of 144 alleles were detected from the 12 STR loci, with a mean value of 12.0. The highest allele diversity was found at the locus CSRD247 (16 alleles). PIC value showed that all studied STR markers are more informative and appropriate for genetic analysis of three Kazakh sheep populations. Beside of INRA006, all markers had high level of genetic variability. As Fixation index shows, the excess of the heterozygosity was observed only in loci MAF065. Obtained number of private alleles in Edilbai, Kazakh Arkhar Merino and Kazakh Fine-wool sheep were 25, 17 and 15 respectively. Genetic diversity was higher in Edilbai population than in other two populations. The genetic variability was lower in Kazakh Arkhar Merino sheep than in the Edilbai and Kazakh Fine-wool sheep breeds. The genetic distance was the largest between Edilbai and Kazakh Arkhar Merinos. Also, the moderate differentiation was observed between Edilbai and Kazakh Arkhar Merinos.   

scholarly journals Fluorescent Amplified Fragment Length Polymorphism and Repetitive Extragenic Palindrome-PCR Fingerprinting Reveal Host-Specific Genetic Diversity of Vibrio halioticoli-Like Strains Isolated from the Gut of Japanese Abalone

2002 ◽  
Vol 68 (8) ◽  
pp. 4140-4144 ◽  
Author(s):  
Tomoo Sawabe ◽  
Fabiano L. Thompson ◽  
Jeroen Heyrman ◽  
Margo Cnockaert ◽  
Karin Hayashi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Dna Hybridization ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Separate Species ◽  
Pcr Fingerprinting ◽  
Abalone Species ◽  
Repetitive Extragenic Palindrome

ABSTRACT When analyzed by fluorescent amplified fragment length polymorphism and repetitive extragenic palindrome-PCR fingerprinting, a total of 47 Vibrio halioticoli strains isolated from four Japanese abalone species and one turban shell species formed three clusters that roughly reflect the different species of host abalone from which they were isolated. The V. halioticoli isolates from turban shells were distributed evenly among the clusters. Representative isolates from two clusters were deemed separate species or subspecies by DNA-DNA hybridization.

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