scholarly journals Genetic variability in sugarcane (Saccharum spp. hybrid) genotypes through inter simple sequence repeats (ISSR) markers

2016 ◽  
Vol 8 (3) ◽  
pp. 1404-1409 ◽  
Author(s):  
Vivekanand P. Rao ◽  
Sanjay Singh ◽  
R. Chaudhary ◽  
M. K. Sharma ◽  
R.S. Sengar ◽  
...  
Keyword(s):  
Polymorphic Information Content ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Genomic Diversity ◽  
Group Method ◽  
Saccharum Spp ◽  
Arithmetic Average ◽  
Sugarcane Varieties ◽  
Pair Group ◽  
Simple Sequence

In the present study, 14 sugarcane (Saccharum spp. hybrid) genotypes were used for genomic diversity analysis based on nineteen inter simple sequence repeat (ISSR). These nineteen sets of ISSR markers generated a total of 164 discernible and reproducible bands including 109 polymorphic and 55 monomorphic bands. The unweighted pair group method with arithmetic average (UPGMA) analysis revealed three distinct clusters: I, II and III within the 14 genotypes. The polymorphic information content (PIC) value per locus ranged from 0.14 (UBC811) to 0.53 (ISSR1) locus with an average of 0.42 for all loci. The range of genetic distance or coefficient of similarity among sugarcane genotypes varied 0.14 - 0.78. The analysis of these similarities matrix revealed that greater similarity between CoS03234 and CoSe1424 (0.78), and lowest similarity between CoS03234 and Co0118 (0.14). The knowledge gained in this study would be useful to future breeding programs for increasing genetic diversity of sugarcane varieties and cultivars to meet the increasing demand of sugarcane cultivation for sugar and bio energy uses.

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

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 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.

EST-PCR, EST-SSR and ISSR markers to identify a set of wild cranberries and evaluate their relationships

2015 ◽  
Vol 95 (6) ◽  
pp. 1155-1165 ◽  
Author(s):  
Dong An ◽  
Natalia V. Bykova ◽  
Samir C. Debnath
Keyword(s):  
Molecular Markers ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Polymorphic Information Content ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Breeding Program ◽  
Group Method ◽  
Sequence Repeat ◽  
Simple Sequence

An, D., Bykova, N. V. and Debnath, S. C. 2015. EST-PCR, EST-SSR and ISSR markers to identify a set of wild cranberries and evaluate their relationships. Can. J. Plant Sci. 95: 1155–1165. The cranberry (Vaccinium marcrocarpon Ait.) is a woody, evergreen, perennial vine with great potential for economic and health benefits. Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. One hundred and two wild cranberry clones collected from four Canadian provinces and five cultivars were screened with inter simple sequence repeat (ISSR), expressed sequence tag–simple sequence repeat (EST-SSR) and EST–polymerase chain reaction (PCR) markers to validate the genetic diversity and relationships among them. EST-PCRs (0.54) and EST-SSRs (0.35) generated higher frequency of major alleles than ISSRs (0.08), but ISSRs presented a higher level of polymorphism and greater polymorphic information content and expected heterozygosity than EST-SSRs and EST-PCRs. Combined cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) separated the wild clones and cultivars into four main clusters, which was in agreement with the principal coordinate (PCo) analysis. Analysis of molecular variation detected sufficient variations among genotypes within communities and among communities within provinces with ISSR (66 and 36%, respectively), EST-PCR (72 and 34%, respectively) and EST-SSR (72 and 34%, respectively) markers. These values were 71 and 35%, respectively, for combined analysis. Combined use of three types of molecular markers, for the first time in Vaccinium species, detected a sufficient degree of variation among cranberry genotypes, allowing for differentiation and rendering these technologies valuable for genotype identification in a diverse cranberry germplasm and for more efficient parental choice in the current cranberry breeding program.

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)-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 Phylogenetic Relationships among Selected Citrus Germplasm Accessions Revealed by Inter-simple Sequence Repeat (ISSR) Markers

1998 ◽  
Vol 123 (4) ◽  
pp. 612-617 ◽  
Author(s):  
Deqiu Fang ◽  
Robert R. Krueger ◽  
Mikeal L. Roose
Keyword(s):  
Phylogenetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Genetic Distances ◽  
Group Method ◽  
Sour Orange ◽  
Arithmetic Average ◽  
Pair Group ◽  
Citrus Germplasm ◽  
Group 5

ISSR markers were analyzed to study phylogenetic relationships among 46 Citrus L. accessions representing 35 species. A dendrogram based on the unweighted pair-group method, arithmetic average cluster analysis was constructed using a similarity matrix derived from 642 polymorphic ISSR fragments generated by 10 primers. These 46 accessions could be classified into five major groups: 1) C. indica Tan.; 2) C. maxima (Burm.) Merrill; 3) lemon [C. limon (L.) Burm.] or lime [C. aurantifolia (Christm.) Swingle] type accessions; 4) C. halimii B. C. Stone; and 5) sour orange (C. aurantium L.), mandarins and their hybrids. Group 5 was further divided into three subgroups. Although some previous work had grouped it with mandarins, C. indica appeared to be a distinct genotype or species that was not close to mandarins. C. tachibana Tan. grouped closely to mandarins. C. vulgaris Risso was not related to sour orange but was similar to accessions usually classified in the lime or lemon group. Sour orange and its hybrids, C. nippokoreana Tan., C. hanayu Hort. ex Shirai, C. sudachi Hort. ex Shirai, and C. yuko Hort. ex Tan. had close phylogenetic relationships with mandarins. Although the mandarin accessions studied were divergent in morphology, the genetic distances among them were relatively small. Relationships among these Citrus accessions revealed by ISSR markers were generally in agreement with previous taxonomic classifications.

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

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