Application of DNA fingerprinting for the classification of selected almond [Prunus dulcis (Miller) D. A. Webb] cultivars

2000 ◽  
Vol 40 (7) ◽  
pp. 995 ◽  
Author(s):  
F. M. Woolley ◽  
G. G. Collins ◽  
M. Sedgley
Keyword(s):  
Middle East ◽  
Prunus Dulcis ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Breeding Lines ◽  
Pair Group ◽  
Commercial Cultivars ◽  
Unweighted Pair Group Method ◽  
Prunus Webbii

Almond cultivars developed in Australia are thought to have descended from 2 breeding lines, 1 from hard-shelled Spanish/Jordan types, and the other from paper-shell Californian types. However, the precise derivation of many individual Australian cultivars is uncertain. Randomly amplified polymorphic DNA (RAPD) was used to estimate the genetic similarities between 50 accessions of almond cultivars derived from Australia, California, Europe and the Middle East, and individual accessions of Prunus orientalis (Miller) D. A. Webb and Prunus webbii (Spach) Vieh. Amplification products were analysed using the simple matching coefficient and the unweighted pair group method with arithmetic averages to cluster individuals into a dendrogram. Cultivars known to have originated in Europe or the Middle East clustered in a different group from those known to have originated in California confirming the 2 suspected breeding lines. The origin of some common Australian commercial cultivars was inferred by their placement on the dendrogram, and the possible parentage of some Australian selections is discussed.

scholarly journals Inter- and Intraspecific RAPD Variation in Four Ipomoea Species

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 773A-773
Author(s):  
Dapeng Zhang ◽  
Wanda W. Collins
Keyword(s):  
Genetic Similarity ◽  
Rapd Analysis ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Similarity Coefficients ◽  
Ipomoea Trifida ◽  
Pair Group ◽  
Ipomoea Triloba ◽  
Ipomoea Species ◽  
Unweighted Pair Group Method

Randomly amplified polymorphic DNA (RAPD) analysis was performed on 18 accessions belonging to four different species of the genus Ipomoea, including sweetpotato and three related species. Twenty-two out of 30 primers tested revealed polymorphisms among these four species. Eight primers were selected on the basis of the number and repeatability of polymorphism produced. With these, a total of 98 different DNA bands were obtained and 85% of them were polymorphic. Based on the presence/absence of the bands, a genetic similarity among accessions and among species was calculated. Unweighted pair-group method with arithmetical averages (UPGMA) based on the similarity coefficients clearly discriminated these four species. Ipomoea trifida and sweetpotato share more genetic similarity. Ipomoea triloba and I. leucantha fall into another cluster. This study demonstrated that RAPD techniques can be a very useful tool for genotype/accession identification and studying the genetic relationship among genotypes/accessions of sweetpotato and among species of Ipomoea.

scholarly journals Rose Germplasm Analysis with RAPD Markers

HortScience ◽  
1999 ◽  
Vol 34 (2) ◽  
pp. 341-345 ◽  
Author(s):  
C.H. Jan ◽  
D.H. Byrne ◽  
J. Manhart ◽  
H. Wilson
Keyword(s):  
Rapd Markers ◽  
Group Method ◽  
Similarity Matrix ◽  
Arithmetic Means ◽  
Pair Group ◽  
Traditional Classification ◽  
Germplasm Analysis ◽  
The Rose ◽  
Unweighted Pair Group Method

The genus Rosa consists of more than 100 species classified into four subgenera, Eurosa, Platyrhodon, Hesperhodos, and Hulthemia, and distributed widely throughout the northern hemisphere. The subgenus Eurosa includes 11 sections. The other subgenera are monotypic. One hundred and nineteen accessions and 213 markers of 36 rose species that include eight sections of the subgenus Eurosa and one species each from the subgenera Hesperhodos and Platyrhodon were used to calculate a similarity matrix, which was clustered with the unweighted pair group method using arithmetic means (UPGMA). The RAPD markers distinguished between all the rose accessions, and species grouped into their respective sections. Therefore, classification of Rosa using RAPD data generally supports traditional classification. The Asian rose sections (Laevigatae, Banksianae, Bracteatae, Pimpinellifoliae, Chinenses, and Synstylae) were consistently separated from the primarily North American sections (Cassiorhodon and Carolinae). The Cassiorhodon and Carolinae sections were grouped together with the subgenera Hesperhodos and Platyrhodon. Both subgenera separated out at the same level as sections within the subgenus Eurosa, suggesting that they are more appropriately classified as sections within the subgenus Eurosa. Sections Cassiorhodon and Carolinae overlapped, and are probably best grouped as one section as previously suggested.

scholarly journals Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary

2021 ◽  
Vol 186 (2) ◽  
pp. 237-244
Author(s):  
M. Domán ◽  
L. Makrai ◽  
Gy. Lengyel ◽  
R. Kovács ◽  
L. Majoros ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Molecular Diversity ◽  
Genetic Relatedness ◽  
Group Method ◽  
Pair Group ◽  
Degree Of Separation ◽  
Avian Origin ◽  
Species Specific ◽  
Sequence Types ◽  
Unweighted Pair Group Method

AbstractThe molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The remaining isolates were clustered into Clade 7 (5 isolates; 20.8%), Clade 10 (4 isolates; 16.6%), Clade 8 (2 isolates; 8.3%), Clade 4 (1 isolate; 4.2%) and Clade 16 (1 isolate; 4.2%). Unweighted pair group method with arithmetic averages (UPGMA) and eBURST analyses showed that the genetic construction of avian origin C. albicans population is fairly diverse. Although species-specific lineages were not found, some degree of separation in the evolution of bird and human strains could be observed.

scholarly journals Padrões de infestação de comunidades de plantas daninhas no agroecossistema de cana-crua

2008 ◽  
Vol 26 (3) ◽  
pp. 549-557 ◽  
Author(s):  
M.A. Kuva ◽  
A.S. Ferraudo ◽  
R.A. Pitelli ◽  
P.L.C.A. Alves ◽  
T.P. Salgado
Keyword(s):  
Group Method ◽  
Pair Group ◽  
Unweighted Pair Group Method

Objetivou-se neste trabalho a obtenção de padrões de infestação de plantas daninhas na cultura de cana-de-açúcar com histórico de colheita mecanizada sem queima prévia da palha. Foram realizadas amostragens em 28 talhões na região de Ribeirão Preto, SP; em cada talhão foram demarcadas unidades de avaliação e coleta, na proporção de duas por hectare, que consistiram de áreas (quatro linhas de 4 metros de comprimento) mantidas sem controle de plantas daninhas e onde foram realizadas as amostragens de plantas emergidas. As amostragens foram realizadas aos 120 dias após o corte, com quadrados vazados (0,5 x 0,5 m) lançados aleatoriamente duas vezes em cada uma das unidades de avaliação e coleta. Com os dados obtidos, calculou-se a importância relativa e o índice de agregação das espécies ou grupo de espécies. Esses índices foram usados no processamento da análise de agrupamento hierárquica, utilizando como medida de semelhança a distância euclidiana e como estratégia de agrupamento o método UPGMA (Unweighted Pair-Group Method using arithmetic Averages). Foi possível distinguir quatro grupos em função da importância relativa e cinco grupos de talhões em função do índice de agregação; dentro de alguns grupos houve formação de subgrupos.

scholarly journals Caracterização Biométrica dos Caprinos da República de Cabo Verde

2019 ◽  
Vol 68 (263) ◽  
pp. 384-394
Author(s):  
L.C. Pires ◽  
T.M. Machado ◽  
J. de D. Fonseca ◽  
J.F. Fonseca ◽  
E. Pile ◽  
...  
Keyword(s):  
Arithmetic Mean ◽  
Group Method ◽  
Cabo Verde ◽  
Pair Group ◽  
Unweighted Pair Group Method

Objetivou-se discernir populações caprinas de cinco ilhas da República de Cabo Verde (n=533) por meio de dados biométricos e análises estatísticas. Foram avaliadas 16 características de fêmeas adultas, através da estatística descritiva simples, análise de variância, teste de multicolinearidade, distância generalizada de Mahalanobis (D²) e algoritmo UPGMA (Unweighted Pair Group Method Arithmetic Mean). Após o teste de multicolinearidade foi identificada e descartada a variável profundidade torácica. As D² foram calculadas com base nas 15 medidas biométricas. O maior valor da D² foi entre as populações das ilhas do Fogo e São Nicolau (22,73), e a menor D² foi entre Santo Antão e São Vicente (3,71). O dendrograma a partir de 15 variáveis em cinco populações colocou as cabras da ilha de Fogo em ramo a parte das demais. Agruparam-se num ramo as cabras das ilhas de Santo Antão e São Vicente. Este resultado está de acordo com a distância geográfica entre as ilhas de Cabo Verde e o histórico recente de intercâmbio de animais entre elas.

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

scholarly journals 523 PB 489 INCORPORATION OF USEFUL TRAITS FROM NATIVE ALMOND SPECIES INTO CULTIVATED ALMOND VARIETIES. II. GENE INTROGRESSION

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 506d-506
Author(s):  
Thomas M. Gradziel ◽  
Dale E. Kester
Keyword(s):  
Gene Pool ◽  
Prunus Dulcis ◽  
Tree Size ◽  
Gene Introgression ◽  
Breeding Lines ◽  
Commercial Use ◽  
Selected Traits ◽  
Prunus Webbii

Breeding lines have been developed incorporating introgressed genes from three native almond species Prunus fenzliana, Prunus webbii and Prunus argentea. Selected traits include self-fertility and autogamy, late bloom, smaller tree size, early nut maturity, improved cropping potential, and a well-sealed shell (endocarp) with high kernel/shell crack-out percentages. Fertility barriers, while present were easily overcome though linkage to introgressed genes with undesirable phenotypes remains an important obstacle to commercial use. Current breeding results, however, support a general conclusion that the wide diversity present within the range of species related to the cultivated almond (Prunus dulcis) provides an valuable gene pool for variety improvement.

scholarly journals Identificação de parentais e híbridos entre Vitis vinifera e Vitis rotundifolia utilizando polimorfismo enzimático e marcador RAPD

Bragantia ◽  
1996 ◽  
Vol 55 (2) ◽  
pp. 221-230 ◽  
Author(s):  
Haiko Enok Sawazaki ◽  
Celso Valdevino Pommer ◽  
Ilene Ribeiro Da Silva Passos ◽  
Maurilo Monteiro Terra ◽  
Erasmo José Paioli Pires
Keyword(s):  
Vitis Vinifera ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Vitis Rotundifolia ◽  
Pair Group ◽  
Unweighted Pair Group Method

Identificaram-se parentais e híbridos entre Vitis vinifera (videiras comuns) e V. rotundifolia (muscadínias), utilizando-se o polimorfismo enzimático e marcador RAPD (Random Amplified Polymorphic DNA). Os sistemas GOT (glutamato-oxalo-acetato-transaminase), IDH (isocitrato desidrogenase) e PGI (fosfoglucose isomerase) diferenciaram a muscadínia, sendo observadas cinco aloenzimas para o GOT, duas para o LAP (leucina aminopeptidase) e quatro para o EST (esterase). Os sistemas PGI e IDH apresentaram-se como diméricos com o fenótipo de quatro aloenzimas em duas regiões e três em uma região respectivamente. O marcador RAPD apresentou polimorfismo que permitiu a diferenciação entre todos os cultivares. Os dendrogramas UPGMA (unweighted pair-group method with aritmetic mean) obtidos pelas isoenzimas e pelo marcador RAPD foram semelhantes, sendo a aproximação mais forte entre 'Itália' e 'Rubi' que se ligaram aos cultivares Patrícia e A Dona. Os cultivares Piratininga e Eugênio, também bastante próximos, foram os seguintes a se ligarem às demais viníferas. Pelo polimorfismo enzimático e marcador RAPD, a muscadínia ficou bastante isolada dos outros grupos. Pelo método RAPD, aplicado às muscadínias, ao híbrido da Carolina do Norte NC66 C203-9, a um possível híbrido e seu parental feminino, observou-se o seguinte: os híbridos foram intermediários às muscadínias e viníferas, porém o possível híbrido se assemelhou ao parental feminino, enquanto o NC66203-9 apresentou bandas provenientes das muscadínias e viníferas, comprovando sua origem híbrida.

scholarly journals Discrimination among Cultivars of Cabbage Using Randomly Amplified Polymorphic DNA Markers

HortScience ◽  
2000 ◽  
Vol 35 (6) ◽  
pp. 1155-1158 ◽  
Author(s):  
Rogério L. Cansian ◽  
Sergio Echeverrigaray
Keyword(s):  
Rapd Markers ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Base Pairs ◽  
Arithmetic Average ◽  
Pair Group ◽  
Similarity Indices ◽  
Upgma Cluster Analysis ◽  
Group A

Randomly amplified polymorphic DNA (RAPD) markers were used to discriminate among 16 commercial cultivars of cabbage (Brassica oleracea L. Capitata Group). A set of 18 decamer primers was selected from 100 random sequences and used to characterize cultivars and to evaluate distances. The selected primers produced 105 (54%) polymorphic bands ranging in size from 100 and 2500 base pairs, out of a total of 195 bands, which allowed for discrimination of all cultivars. Similarity indices between cultivars were computed from RAPD data, and ranged from 0.72 to 0.87 with an average of 0.82. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis revealed two groups, one formed by two cultivars recommended for summer cropping, and the other by 14 cultivars. This large group was additionally divided into two subgroups. RAPD analysis provides a quick and reliable alternative for the identification of cabbage cultivars and for determination of the relationships among them.

scholarly journals Filogenetik Human papillomavirus (HPV) tipe 6 dan tipe 11 pada penderita recurrent respiratory papillomatosis

2014 ◽  
Vol 44 (1) ◽  
pp. 52
Author(s):  
Lenny Buana Wuriningtyas ◽  
Dwi Reno Pawarti ◽  
Achmad Chusnu Romdhoni
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Arithmetic Mean ◽  
Recurrent Respiratory Papillomatosis ◽  
Open Reading Frame ◽  
Group Method ◽  
Cross Sectional ◽  
Reading Frame ◽  
Pair Group ◽  
Unweighted Pair Group Method

Latar belakang: Papiloma saluran pernapasan berulang (recurrent respiratory papillomatosis/RRP) merupakan neoplasma jinak laring terbanyak akibat infeksi HPV tipe 6 dan tipe 11. RRP merupakan masalah terkait agresivitas dan terapi. Analisis genetik digunakan untuk membedakan varian HPV tipe 6 dan tipe 11. Filogenetik mengevaluasi evolusi sequen DNA virus. Tujuan: Penelitian bertujuan mengidentifikasi sequen DNA dan menganalisis pohon filogenetik HPV tipe 6 dan tipe 11 pada papiloma saluran pernapasan berulang. Metode: Penelitian merupakan observasional deskriptif cross sectional. Analisis menggunakan data pembanding dari GenBank. Filogenetik disusun menggunakan metodeUPGMA (Unweighted Pair Group Method with Arithmetic Mean). Didapatkan 15 sampel jaringan papiloma. Dilakukan pemeriksaan PCR dan analisis sequen DNA. Hasil: Dari 15 sampel penelitian (12 laki-laki, 3 perempuan) didapatkan 9 isolat HPV tipe 6 (8 varian dan 1 subtipe) dan 4 isolat HPV tipe 11 (3 varian dan 1 subtipe). Terdapat mutasi titik yang mengakibatkan munculnya varian dan subtipe HPV tipe 6 maupun tipe 11. Kesimpulan: sequen DNA sampel berasal dari L1 ORF (Late 1 Open Reading Frame) yang merupakan kapsid mayor virus. Proses mutasi level gen berupa substitusi, insersi, dan delesi.Subtipe HPV tipe 6 dan tipe 11 yang ditemukan diperkirakan sebagai subtipe baru dan belum pernah dilaporkan sebelumnya. Lima varian HPV tipe 6 membentuk satu cabang tersendiri pada nomenklatur filogenetik yang sudah ada sehingga diajukan sebagai sublineage baru (sublineage C). Seluruh isolat HPV tipe 11 membentuk cabang pohon tersendiri dan diajukan sebagai sublineage baru (sublineage B).Kata kunci: HPV tipe 6 dan 11, variasi sequen DNA, pohon filogenetik HPV tipe 6 and 11. ABSTRACTBackground: Recurrent respiratory papillomatosis (RRP) is the most common laryngeal benign neoplasm caused by infection of HPV type 6 and 11. RRP is still a serious problem related to agresivity and therapy. Genetic analysis used to determine the variant of HPV type 6 or 11. Phylogenetic tree used to evaluate the evolution of viral DNA squence. Purpose: This study aimed to identify DNA squences and analyse the phylogenetic tree of HPV type 6 and 11 in RRP. Methods: this was a descriptive observational cross sectional study. Data analysis used GenBank database and phylogenetic tree was constructed usedUPGMA (Unweighted Pair Group Method with Arithmetic Mean). 15 papillomas biopsies from RRP patients subjected HPV typing using PCR dan DNA sequensing analysis. Result: From 15 patients with RRP (12 male, 3 female), there were 9 isolates HPV type 6 (8 variants, 1 subtype) and 4 isolates HPV type 11 (3 variants, 1 subtype). There was a point mutation in HPV type 6 and 11. Conclusion: L1 ORF (Late 1 Open Reading Frame) sequensials DNA samples was virus major capsid. There were mutational process at gene level (substitution, insertion, deletion). Subtype of HPV-6 and 11, might be new ones, and had not been reported yet. Five variants of HPV type 6 constructed a different lineage in phylogenetic and it is proposed to be C sublineage. All samples HPV type 11 proposed as B sublineage. Keywords: HPV type 6 and 11, DNA sequences variations, phylogenetic trees HPV type 6 and 11.

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