Inter-simple sequence repeat (ISSR)-based diversity assessment among faba bean genotypes

2011 ◽  
Vol 62 (9) ◽  
pp. 755 ◽  
Author(s):  
Salem S. Alghamdi ◽  
Sulieman A. Al-Faifi ◽  
Hussein M. Migdadi ◽  
Megahed H. Ammar ◽  
K. H. M. Siddique
Keyword(s):  
Faba Bean ◽  
Simple Sequence Repeat ◽  
Molecular Data ◽  
Inter Simple Sequence Repeat ◽  
Group Method ◽  
Sequence Repeat ◽  
Arithmetic Average ◽  
Pair Group ◽  
Diversity Assessment ◽  
Simple Sequence

Thirty-four faba bean (Vicia faba L.) including local and exotic materials were subjected to molecular diversity assessment using 12 inter-simple sequence repeat primers. The molecular data showed unambiguous and qualitative (present or absent) fragments that gave repeatable patterns were considered for the analysis. The 12 selected primers produced a total of 71 fragments (loci), all of which were polymorphic using the 34 collected faba genotypes. The results of clustering Nei’s genetic distance using the unweighted pair group method with arithmetic average algorithm at the 0.52 dissimilarity separated genotypes to six main clusters with many subclusters. The local genotypes were distributed to most of all clusters. Genotypes collected from Egypt and King Saud University was grouped together in two clusters, ICARDA’s genotypes in two clusters and two genotypes (H8, local determent genotype and 987–255–95 line) formed a single cluster. The high number of subclusters formed in this study indicated that there is a high genetic variability related to collection sites and it should be utilised in faba bean improvement.

scholarly journals Variation Among and Within Populations of the Parasitic Weed Orobanche crenata from Spain and Israel Revealed by Inter Simple Sequence Repeat Markers

2002 ◽  
Vol 92 (12) ◽  
pp. 1262-1266 ◽  
Author(s):  
Belén Román ◽  
Zlatko Satovic ◽  
Diego Rubiales ◽  
Ana M. Torres ◽  
José Ignacio Cubero ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Group Method ◽  
Sequence Repeat ◽  
Orobanche Crenata ◽  
Parasitic Weed ◽  
Arithmetic Average ◽  
Pair Group ◽  
Spanish Populations ◽  
Simple Sequence

The patterns of genetic variation among Orobanche crenata populations from Spain and Israel were studied using radiolabeled inter simple sequence repeat amplification products that were separated in sequencing polyacrylamide gels. The analysis of molecular variance indicated that most of the genetic diversity was attributable to differences among individuals within a population although significant divergences were found between regions. The Jaccard's similarity matrix was analyzed by unweighted pair-group method with arithmetic average and the resultant dendrogram clearly divided six populations by region, with the Spanish populations being more similar to each other than the Israeli populations. These results are consistent with the predominantly allogamous behavior of O. crenata and the extremely efficient dispersal of its seeds.

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 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

Genetic diversity of pummelo (Citrus grandis Osbeck) and its relatives based on simple sequence repeat markers

2006 ◽  
Vol 3 (2) ◽  
pp. 119-126 ◽  
Author(s):  
Liu Yong ◽  
Liu De-Chun ◽  
Wu Bo ◽  
Sun Zhong-Hai
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Similarity Coefficient ◽  
Group Method ◽  
Allelic Polymorphism ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Arithmetic Average ◽  
Pair Group ◽  
Simple Sequence

AbstractGenetic diversity in 122 accessions of pummelo (Citrus grandis Osbeck) and its related varieties was assessed using simple sequence repeat (SSR) markers. Thirty-one pairs of SSR informative primers generated a total of 335 alleles. The average number of alleles per locus was 9.85. The value of allelic polymorphism information content (PIC) ranged from 0.1939 to 0.9073, with an average of 0.7085 per primer. The 122 accessions of pummelo and its related varieties could be clustered into seven groups by the unweighted pair-group method arithmetic average (UPGMA), in which the 110 pummelo accessions could be divided into 18 subgroups at similarity coefficient of 0.712. These subgroups were mainly composed of the Shatian pummelo variety group, the Wendan variety group and many of the hybrid pummelo groups. The classification method can be used in targeting many varieties in order to widen the genetic background of pummelo.

scholarly journals Variabilidade genética entre acessos de Umbu-Cajazeira mediante análise de marcadores ISSR

2011 ◽  
Vol 33 (3) ◽  
pp. 868-876 ◽  
Author(s):  
Ivonilda Barbosa Brito Santana ◽  
Eder Jorge de Oliveira ◽  
Walter dos Santos Soares Filho ◽  
Rogério Ritzinger ◽  
Edson Perito Amorim ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Group Method ◽  
Sequence Repeat ◽  
Pair Group ◽  
Simple Sequence ◽  
Unweighted Pair Group Method

A umbu-cajazeira (Spondias sp.) é uma frutífera nativa do Semiárido brasileiro, ainda em fase de domesticação, cujos frutos apresentam excelentes perspectivas de aproveitamento comercial. O objetivo deste trabalho foi caracterizar a variabilidade genética entre acessos de umbu-cajazeira pertencentes ao Banco Ativo de Germoplasma de Fruteiras Tropicais da Embrapa Mandioca e Fruticultura, por meio de marcadores moleculares ISSR (Inter Simple Sequence Repeat). Foram analisados 17 acessos de umbu-cajazeira, com 25 marcadores ISSR, os quais produziram um total de 249 bandas, sendo 201 bandas polimórficas e 48 monomórficas. As dissimilaridades genéticas entre os acessos variaram de 0,247 a 0,665, com base no coeficiente de Jaccard. O método UPGMA (Unweighted Pair-Group Method Average) agrupou os acessos em cinco grupos, sendo que 'Preciosa' e 'Suprema' foram os acessos mais similares. A maior dissimilaridade foi observada entre os acessos 'Esperança' e 'Pomar'. O alto grau de polimorfismo encontrado demonstrou a eficiência dos marcadores ISSR, indicando que estes podem ser utilizados com sucesso na caracterização molecular de germoplasma e em futuros trabalhos de melhoramento genético dessa frutífera. Existe considerável variabilidade genética entre os acessos de umbu-cajazeira presentes no BAG Fruteiras Tropicais, que pode ser explorada para a conservação e o melhoramento da espécie.

scholarly journals Genetic diversity and distance of Iranian goat breeds (Markhoz, Mahabadi and Lori) compared to the Beetal breed using inter-simple sequence repeat (ISSR) markers

2016 ◽  
Vol 59 (4) ◽  
pp. 477-483 ◽  
Author(s):  
Leila Simaei-Soltani ◽  
Alireza Abdolmohammadi ◽  
Alireza Zebarjadi ◽  
Saheb Foroutanifar
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Genetic Diversity And Structure ◽  
Simple Sequence

Abstract. The aim of this study was to investigate the genetic diversity and structure in three Iranian native goat breeds (Markhoz, Mahabadi and Lori) and the Beetal imported breed using inter-simple sequence repeat (ISSR) markers and also to investigate ISSR markers' potential in order to genetically separate single (S) and twin-birth (T) subpopulations. Blood samples were collected from 210 animals for this purpose. In total, 16 primers were used, and finally 5 primers were selected based on the number of clear bands and the level of polymorphisms. The result of this study showed that 76 of 86 observed fragments were polymorphic. Genetic diversity for each breed ranged from 0.23 in the Beetal breed to 0.26 in the Markhoz breed; this represents a relatively similar genetic diversity in these breeds. An unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on the Nei's standard genetic distance between the breeds studied showed that three Iranian goat breeds (Mahabadi, Lori and Markhoz) were clustered closer together, while the Beetal breed formed a separate cluster. In the constructed dendrogram of the subpopulations, the S and T subpopulations of each breed were clustered together. The constructed dendrogram of the Beetal breed and the S and T subpopulations of all breeds studied showed a separate cluster for the Beetal breed as an imported breed and another cluster for the S and T subpopulations as Iranian native breeds. The current study showed that the ISSR markers studied had no potential to genetically separate S and T subpopulations. On the other hand, these ISSR markers can be used for the clustering of distinct populations.

Inter simple sequence repeat (ISSR) to assess genetic diversity within a collection of wild lingonberry (Vaccinium vitis-idaea L.) clones

2007 ◽  
Vol 87 (2) ◽  
pp. 337-344 ◽  
Author(s):  
Samir C. Debnath
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Germplasm Management ◽  
Sequence Repeat ◽  
Pair Group ◽  
Canadian Provinces ◽  
Simple Sequence

Forty-three wild lingonberry [Vaccinium vitis-idaea ssp. minus (Lodd) Hult.] clones collected from four Canadian provinces were assessed for genetic variability by using inter simple sequence repeat (ISSR). Fifteen primers generated 356 polymorphic ISSR-PCR bands. A substantial degree of genetic diversity was found am ong the wild collections. Cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) separated the wild clones into four main clusters, and identified the two remaining clones as outliers. Furthermore, within four clusters, the genotypes tended to form sub-clusters that were in agreement with the principal coordinate (PCO) analysis. Geographical distribution explained 10% of total variation as revealed by analysis of molecular variance (AMOVA). The ISSR markers detected a sufficient degree of polymorphism to differentiate among lingonberry clones, making this technology valuable for germplasm management and the more efficient choice of parents in current lingonberry breeding programs. Key words: Vaccinium vitis-idaea, DNA fingerprinting, molecular marker

scholarly journals Genetic diversity and interspecific relationships of some Allium species using inter simple sequence repeat markers

2015 ◽  
Vol 22 (2) ◽  
pp. 67-75 ◽  
Author(s):  
Leila Samiei ◽  
Mahnaz Kiani ◽  
Homa Zarghami ◽  
Farshid Memariani ◽  
Mohammad Reza Joharchi
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Allium Species ◽  
Interspecific Relationships ◽  
Simple Sequence

In this study genetic diversity and interspecific relationships of 11 Allium L. species from Khorassan province of Iran including 32 accessions were investigated by inter simple sequence repeat (ISSR) markers. Nine ISSR primers produced a total of 80 polymorphic markers and revealed high polymorphism among the studied species. The average gene diversity, effective number of alleles and Shannon’s information index were 0.2, 1.28 and 0.3, respectively. Allium kuhsorkhense exhibited the greatest level of variation (He: 0.18), whereas A. stipitatum demonstrated the lowest level of variability (He: 0.05). UPGMA (Unweighted Pair Group Method with Arithmetic mean) analysis showed that Allium accessions have a similarity range of 0.60 to 0.95. Allium scapriscapum composed the most distant group in the dendrogram. The clustered groups of Allium species clearly reflect the recent taxonomic concept of the genus at the subgenus and section levels. The present study showed that the ISSR technique is an effective molecular approach for analyzing genetic diversity and relationship in Allium species.Bangladesh J. Plant Taxon. 22(2): 67-75, 2015 (December)

scholarly journals Genetic variability analysis of faba bean accessions using Inter-simple sequence repeat (ISSR) markers

2015 ◽  
Vol 75 (1) ◽  
pp. 122-130 ◽  
Author(s):  
María E Salazar-Laureles ◽  
Delfina de J. Pérez-López ◽  
Andrés González-Huerta ◽  
Luis M Vázquez-García ◽  
Ernestina Valadez-Moctezuma
Keyword(s):  
Genetic Variability ◽  
Faba Bean ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Variability Analysis ◽  
Simple Sequence

scholarly journals Genetic Diversity and Phylogenetic Relationships among Plum Germplasm Resources in China Assessed with Inter-simple Sequence Repeat Markers

2007 ◽  
Vol 132 (5) ◽  
pp. 619-628 ◽  
Author(s):  
Weisheng Liu ◽  
Dongcheng Liu ◽  
Aimin Zhang ◽  
Chenjing Feng ◽  
Jianmin Yang ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Diploid Species ◽  
Inter Simple Sequence Repeat ◽  
Wild Plants ◽  
Group Method ◽  
Jaccard Coefficient ◽  
Sequence Repeat ◽  
Group Iii ◽  
Group I ◽  
Simple Sequence

Inter-simple sequence repeat (ISSR) markers were used to evaluate genetic similarity and interrelationship among 104 plum (Prunus L. spp.) and related accessions from the Chinese National Germplasm Repository for Plums and Apricots and the Tianshan Germplasm Repository for Wild Fruit Resources, including six plum species (Prunus salicina Lindl., Prunus simonii Carr., Prunus ussuriensis Kov. et Kost., Prunus domestica L., Prunus cerasifera Ehrh., and Prunus spinosa L.), two related species [apricot (Prunus armeniaca L.) and nanking cherry (Prunus tomentosa Thunb.)], eight putative hybrids between plum and apricot (plumcot), and six accessions of wild European plum (P. domestica). Out of the 42 ISSR primers, 12 were selected, which generated 103 markers in total, 99 of which were polymorphic. Possible accession-specific ISSR bands or patterns were also found. Some possible synonyms or homonyms were clarified or discussed, and closely related accessions such as bud mutants were discriminated. Based on the unweighted pair group method with arithmetic mean (UPGMA) analysis and principal coordinate analysis (PCoA) using the Jaccard coefficient, two different dendrograms were constructed—one including accessions grouped by species and one with all 104 accessions—and a two-dimensional plot was obtained. Three groups were formed in both dendrograms and PCoA plot: Group I including apricot (‘Yinxiangbai’) and plumcot types; Group II containing Asia-originated diploid species [e.g., P. cerasifera, P. ussuriensis, P. tomentosa, and Chinese plum-types (i.e., P. salicina and its hybrids)]; and Group III involving European-origin polyploid species (e.g., P. spinosa and P. domestica) and recently found wild European plum accessions in China. The dendrogram with accessions grouped by species implied that 1) plumcot types had closer relatedness with apricot than with plum; 2) P. simonii should be a variant of P. salicina while P. ussuriensis an independent species; 3) P. domestica was more closely related to P. spinosa than to P. cerasifera. Two accessions of European plum (‘89-7-3’ and ‘Wanhei’) were clustered into outgroups in the dendrogram with all 104 accessions, which could been grouped within Group III in the PCoA plot. The distribution of both European plum and Chinese plum-types across respective groups did not reflect the geographic origins. The present study also further confirmed that the wild plants found in Xinjiang of China were P. domestica.

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