scholarly journals Selection of ISSR Primers to Study the Genetic Diversity of Myrciaria floribunda O. Berg

2020 ◽  
pp. 23-28
Author(s):  
Luiz Sergio Costa Duarte Filho ◽  
Danielson Ramos Ribeiro ◽  
Allison Vieira da Silva
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
South America ◽  
Central America ◽  
Dna Extraction ◽  
Endemic Species ◽  
Germplasm Bank ◽  
Slow Growing ◽  
Selection Of ◽  
Issr Primers

The species Myrciaria floridunda O. Berg, popularly known as cambuí, belongs to the Myrtaceae family. Cambui is a native, non-endemic species that occur in diverse environments in Central America and South America. They are slow-growing plants with a shrub or sub-shrub habit. The fruits, the product of interest of the species, are small, spherical berries orange or red in colorturning to wine colorwhen they are ripe. The exploitation of the species is still mostly extractivist, carried out by traditional local families who, in times of fruiting of the species, leverage their income by selling fruits at fairs. The fruits can be eaten fresh, in the form of jellies, liquor or wine. To study the genetic diversity of the species using ISSR-type molecular markers, it is necessary to first isolate DNA in sufficient quality and quantity. Here, leaves for DNA extraction were collected from the active germplasm bank of the Federal University of Alagoas, Brazil. The DNA of the species was extracted using CTAB detergent methodology with modifications adapted to the species. Twelve ISSR primers were tested on DNA from two cambui genotypes. Of the twelve primers, eight were selected due to their polymorphism index above 50%, namely: UFAL-2, UFAL-3, UFAL-5, UFAL-6, UFAL-7, UFAL-8, UFAL-9 and UFAL-10.

scholarly journals AVALIAÇÃO DE DOIS MÉTODOS DE TRITURAÇÃO FOLIAR DE Acianthera ciliata (Orchidaceae) PARA EXTRAÇÃO DE DNA

Nativa ◽  
2020 ◽  
Vol 8 (1) ◽  
pp. 97
Author(s):  
Eliane Cristina Moreno de Pedri ◽  
Catiane Dos Santos Braga ◽  
Carlos Alberto Da Cunha Oliveira ◽  
Auana Vicente Tiago ◽  
Ana Aparecida Bandini Rossi
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Liquid Nitrogen ◽  
Dna Extraction ◽  
Plant Species ◽  
Genomic Dna ◽  
Extraction Buffer ◽  
Foliar Tissue ◽  
Genomic Regions ◽  
Issr Primers

O estabelecimento de protocolo de extração de DNA de espécies vegetais é uma técnica empregada para a obtenção de um DNA puro e de qualidade. Diante disso, objetivou-se neste estudo padronizar um protocolo para a extração de DNA da espécie Acianthera ciliata, visando posteriores estudos de diversidade genética. Foram testados dois métodos de trituração do tecido foliar, sendo eles: Tampão STE e nitrogênio líquido. Para cada método de trituração foram testadas duas concentrações de β-mercaptoetanol (0% e 2%). Os dois métodos utilizados, foram eficientes na extração do DNA genômico de A. ciliata. As amostras extraídas com 0% de β-mercaptoetanol, para os dois métodos, STE e nitrogênio líquido, apresentaram menor quantidade de DNA quando comparado com as amostras extraídas com 2% de β-mercaptoetanol. Os dois primers testados amplificaram regiões do genoma de A. ciliata. Para a extração de DNA de A. ciliata indica-se a utilização de CTAB 5% no tampão de extração e β-mercaptoetanol a 2%. Os iniciadores ISSR foram eficientes na amplificação e são recomendados para estudos de diversidade genética de A. ciliata.Palavras-chave: diversidade genética; CTAB; marcadores moleculares; orquídeas. EVALUATION OF TWO MACERATION METHODS IN Acianthera ciliata (Orchidaceae) LEAVES FOR DNA EXTRACTION ABSTRACT: The establishment of DNA extraction protocol for plant species is a technique employed to obtain pure and good quality DNA. In this study, we standardized a protocol for the extraction of DNA of the species Acianthera ciliata, aiming studies of genetic diversity subsequently. Two maceration methods for foliar tissue were tested, and they were STE buffer and liquid nitrogen. Two concentrations of β-mercaptoethanol (0% and 2%) were tested for each method. The two methods used were efficient for genomic DNA extraction of A. ciliata. In both methods the samples extracted using 0% of β-mercaptoethanol, they presented lesser amount of DNA than the samples extracted using 2% of β-mercaptoethanol. The two tested primers amplified genomic regions of A. ciliata. For the DNA extraction of A. ciliata, we indicated the use of CTAB 5% in the extraction buffer as well as β-mercaptoethanol to 2%. The ISSR primers were efficient in amplification and thus they are indicated for studies of genetic diversity of A. ciliata.Keywords: genetic diversity; CTAB; molecular markers; orchids.

scholarly journals Characterization of genetic diversity of cactus species (Opuntia spp.) in Morocco by morphological traits and molecular markers

2017 ◽  
Vol 5 (2) ◽  
pp. 149-159 ◽  
Author(s):  
Y. El Kharrassi ◽  
M.A. Mazri ◽  
M.H. Sedra ◽  
A. Mabrouk ◽  
B . Nasser ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Morphological Traits ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Group Method ◽  
Rapd Primer ◽  
Opuntia Spp ◽  
Issr Primers

The genetic diversity within and among 124 accessions of Opuntia spp. collected from different regions of Morocco was assessed using morphological descriptors and molecular markers. Based on 10 morphological traits, the accessions were separated into 3 main clusters; each cluster was containing accessions from different regions and species. Polymerase chain reaction (PCR) was then performed on 22 accessions from different regions and species, with 10 inter-simple sequence repeat (ISSR) primers and one random amplified polymorphic DNA (RAPD) primer. ISSR primers produced 66 bands overall, 64 (96.9 %) of which were polymorphic while 6 bands were generated by the RAPD marker, all polymorphic. The polymorphic information content (PIC) values ranged from 0.62 to 0.97, with an average of 0.82. The dendrogram of genetic differences generated using the unweighted pair-group method using arithmetic averages (UPGMA) method showed 7 different clusters at a similarity of 0.76, which was confirmed by the principal component analysis (PCA). The main conclusion of our work is the high genetic similarity between Opuntia ficus indica and Opuntia megacantha species in Morocco. Our results will be useful for plant breeding and genetic resource conservation programs.

scholarly journals Increase of the genetic diversity of the germplasm bank of Cactus pear using RAPD molecular markers

Phyton ◽  
2012 ◽  
Vol 81 (1) ◽  
pp. 143-148
Author(s):  
Escalante-Gonz醠ez JG ◽  
EA Garc韆-Zambrano ◽  
A Guti閞rez-Diez ◽  
RE V醶quez-Alvarado ◽  
JA Torres-Castillo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Germplasm Bank ◽  
Cactus Pear

scholarly journals Comparison among Methods and Statistical Software Packages to Analyze Germplasm Genetic Diversity by Means of Codominant Markers

J ◽  
2018 ◽  
Vol 1 (1) ◽  
pp. 197-215 ◽  
Author(s):  
Mario Pagnotta
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Open Access ◽  
Basic Principles ◽  
Statistical Software ◽  
Germplasm Collections ◽  
Software Packages ◽  
Dominant Markers ◽  
Selection Of

Co-dominant markers’ data are often analysed as if they were dominant markers, an over-simplification that may be misleading. Addressing this, the present paper aims to provide a practical guide to the analysis of co-dominant data and selection of suitable software. An overview is provided of the computational methods and basic principles necessary for statistical analyses of co-dominant molecular markers to determine genetic diversity and molecular characterization of germplasm collections. The Hardy–Weinberg principle is at the base of statistical methods to determine genetic distance, genetic diversity, and its distribution among and within populations. Six statistical software packages named GenAlEx, GDA, Power Marker, Cervus, Arlequin, and Structure are compared and contrasted. The different software packages were selected based on: (i) The ability to analyze co-dominant data, (ii) open access software, (iii) ease of downloading, and (iv) ease of running using a Microsoft Window interface. The software packages are compared analyzing the same dataset. Differences among parameters are discussed together with the comments on some of the software outputs.

scholarly journals Characterization of the nearly extinct ‘Albilla’ cultivar from Galicia and its relationships with other Spanish ‘Albillos’

OENO One ◽  
2013 ◽  
Vol 47 (4) ◽  
pp. 261
Author(s):  
Emilia Díaz-Losada ◽  
Sandra Cortés-Diéguez ◽  
Inmaculada Rodríguez-Torres ◽  
José Manuel Mirás-Avalos ◽  
Ignacio Orriols-Fernández ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Vitis Vinifera ◽  
Canary Islands ◽  
Germplasm Collection ◽  
Morphological Descriptors ◽  
Germplasm Bank ◽  
The Future

<p style="text-align: justify;"><strong>Aims</strong>: This work contributes to the knowledge of the genetic diversity of <em>Vitis vinifera</em> L. with the characterization of the non-referenced cultivar ‘Albilla’ by ampelographic description and molecular markers. This will be useful for the preservation, identification and propagation of this cultivar in the future.</p><p style="text-align: justify;"><strong>Methods and results</strong>: Six microsatellites (SSRs), 55 OIV (International Organisation of Vine and Wine) morphological descriptors and 45 phylometric traits were evaluated in two accessions of ‘Albilla’ preserved in the Germplasm Bank of EVEGA (Estación de Viticultura e Enoloxía de Galicia), Xunta de Galicia. Additionally, we set out to determine whether this cultivar was distinct from the yet uncharacterized ‘Albillo’ cultivars found in the Canary Islands. These methods allowed us to describe the cultivar known as ‘Albilla’ and to compare it with other homonym cultivars.</p><p style="text-align: justify;"><strong>Conclusions</strong>: The ‘Albilla’ cultivar is different from other genotypes denominated ‘Albillo’ and any other genotype described until now. This may indicate that it could be an autochthonous cultivar from Galicia.</p><p style="text-align: justify;"><strong>Significance and impact of the study</strong>: The characterization of cultivars is still necessary in order to identify any homonyms or synonyms, develop measures for their conservation (germplasm collection) and evaluate their potential for producing quality wines.</p>

scholarly journals Genetic diversity assessment of ancient mulberry (Morus spp.) in Lebanon using morphological, chemical and molecular markers (SSR and ISSR)

2021 ◽  
Vol 35 (3) ◽  
pp. 243-253
Author(s):  
Aline Kadri ◽  
Shoaib Saleh ◽  
Ahmad Elbitar ◽  
Ali Chehade
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Crop Improvement ◽  
Germplasm Management ◽  
Diversity Assessment ◽  
Geographical Regions ◽  
Relative Separation ◽  
Morus Spp ◽  
High Level ◽  
Issr Primers

Lebanon has ancient mulberry trees which are the remnants of the abundant orchards that dominated its lands during the nineteenth century. Lebanese mulberry germplasm has not been assessed yet. This study aims to collect local old rainfed mulberry accessions from different geographical regions and assess their diversity by using morphological and molecular markers (SSR and ISSR). Genetic diversity of 70 accessions of mulberry were evaluated by using 27 morphological traits. The dendrogram based on the morphological attributes showed a relative separation of the different accessions based on fruits color and taste. Molecular analysis was performed for the accessions by using selected SSR and ISSR primers. The primers marked a high discriminating power (0.7 to 0.89). The dendrogram constructed on the base of UPGMA method showed 13 different groups. The clustering patterns indicated no location nor local name specificity among mulberry accessions. The combination of SSR and ISSR primers was informative for estimating the extent of mulberry genetic diversity. It can be concluded that there is a high level of genetic diversity within mulberry trees in Lebanon. These results will be useful for mulberry germplasm management in terms of biodiversity protection and as a valuable source of gene pool for crop improvement.

scholarly journals Diversity and genetic relatedness among genotypes of Vitis spp. using microsatellite molecular markers

2013 ◽  
Vol 35 (3) ◽  
pp. 799-808 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Cosme Damião Cruz ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Markers ◽  
Microsatellite Markers ◽  
Information Content ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Germplasm Bank ◽  
Expected Heterozygosity ◽  
Vitis Spp

The purpose of this research was to study the genetic diversity and genetic relatedness of 60 genotypes of grapevines derived from the Germplasm Bank of Embrapa Semiárido, Juazeiro, BA, Brazil. Seven previously characterized microsatellite markers were used: VVS2, VVMD5, VVMD7, VVMD27, VVMD3, ssrVrZAG79 and ssrVrZAG62. The expected heterozygosity (He) and polymorphic information content (PIC) were calculated, and the cluster analysis were processed to generate a dendrogram using the algorithm UPGMA. The He ranged from 81.8% to 88.1%, with a mean of 84.8%. The loci VrZAG79 and VVMD7 were the most informative, with a PIC of 87 and 86%, respectively, while VrZAG62 was the least informative, with a PIC value of 80%. Cluster analysis by UPGMA method allowed separation of the genotypes according to their genealogy and identification of possible parentage for the cultivars 'Dominga', 'Isaura', 'CG 26916', 'CG28467' and 'Roni Redi'.

scholarly journals Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers

2012 ◽  
Vol 47 (8) ◽  
pp. 1095-1102 ◽  
Author(s):  
Víctor Pecina‑Quintero ◽  
José Luis Anaya‑López ◽  
Alfredo Zamarripa‑Colmenero ◽  
Noe Montes‑García ◽  
Carlos Nuñez‑Colín ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Ssr Markers ◽  
Sweet Sorghum ◽  
Genetic Relationships ◽  
Biofuel Production ◽  
Germplasm Bank ◽  
New Varieties ◽  
Sorghum Genotypes ◽  
Sorghum Germplasm

The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor) germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers revealed robust amplification profiles and were able to differentiate the 41 genotypes of sweet sorghum evaluated. Analysis of the frequency and distribution of polymorphic fragments allowed for the detection of unique (AFLP) and rare (SSR) alleles in several genotypes (RBSS‑8, RBSS‑9, RBSS‑25, RBSS‑32, and RBSS‑37), indicating that these markers may be associated with a feature that has not yet been determined or may be useful for the identification of these genotypes. The genetic relationships indicated the presence of at least two types of sweet sorghum: a group of modern genotypes used for sugar and biofuel production, and another group consisting of historic and modern genotypes used for the production of syrups. Sweet sorghum genotypes may be used to develop new varieties with higher sugar and juice contents.

Ditaxis (Euphorbiaceae) from the Brazilian Caatinga, including a new species

Phytotaxa ◽  
2020 ◽  
Vol 455 (2) ◽  
pp. 152-160
Author(s):  
JOSIMAR KÜLKAMP ◽  
JOÃO R. V. IGANCI ◽  
INÊS CORDEIRO ◽  
JOSÉ FERNANDO A. BAUMGRATZ
Keyword(s):  
New Species ◽  
South America ◽  
Central America ◽  
Tropical Forests ◽  
Endemic Species ◽  
Habitat Distribution ◽  
Seasonally Dry ◽  
Seasonally Dry Tropical Forests ◽  
Dry Tropical Forests ◽  
A New Species

Ditaxis is a Neotropical genus with approximately 50 species, most of them in seasonally dry tropical forests of Brazil, Central America and the Antilles. The Brazilian Caatinga, the largest area of SDTF in South America, harbors three endemic species of Ditaxis, including the new Ditaxis grazielae, hereby described and illustrated. The new species is known from a few localities in the state of Bahia. We provide an identification key for the species occurring in the Caatinga, as well as comments on habitat, distribution and phenology. We also present amended descriptions and typifications for Ditaxis desertorum and D. malpighiacea, and propose D. gardneri as synonym of D. desertorum.

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