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.

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

Assessment of molecular genetic diversity and population structure of sesame (Sesamum indicum L.) core collection accessions using simple sequence repeat markers

2013 ◽  
Vol 12 (1) ◽  
pp. 112-119 ◽  
Author(s):  
Jong-Hyun Park ◽  
Sundan Suresh ◽  
Gyu-Taek Cho ◽  
Nag-Gor Choi ◽  
Hyung-Jin Baek ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Simple Sequence Repeat ◽  
Core Collection ◽  
Sesamum Indicum ◽  
Group Method ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
The Core ◽  
Simple Sequence

Sesame (Sesamum indicum L.) is one of the oldest oil crops and is widely cultivated in Asia and Africa. The aim of this study was to assess the genetic diversity, phylogenetic relationships and population structure of 277 sesame core collection accessions collected from 15 countries in four different continents. A total of 158 alleles were detected among the sesame accessions, with the number varying from 3 to 25 alleles per locus and an average of 11.3. Polymorphism information content values ranged from 0.34 to 0.84, with an average of 0.568. These values indicated a high genetic diversity at 14 loci both among and within the populations. Of these, 44 genotype-specific alleles were identified in 12 of the 14 polymorphic simple sequence repeat markers. The core collection preserved a much higher level of genetic variation. Therefore, 10.1% was selected as the best sampling percentage from the whole collection when constructing the core collection. The 277 core collection accessions formed four robust clusters in the unweighted pair group method and the arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the sesame accessions based on their geographical locations. Similar patterns were obtained using model-based structure analysis and country-based dendrograms, as some accessions situated geographically far apart were grouped together in the same cluster. The results of these analyses will increase our understanding of the genotype-specific alleles, genetic diversity and population structure of core collections, and the information can be used for the development of a future breeding strategy to improve sesame yield.

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.

scholarly journals Genetic Diversity of Carpetgrass Germplasm Based on Simple Sequence Repeat Markers

HortScience ◽  
2015 ◽  
Vol 50 (6) ◽  
pp. 797-800
Author(s):  
Xiaoli Wang ◽  
Zhiyong Wang ◽  
Li Liao ◽  
Xinyi Zhang ◽  
Changjun Bai
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Warm Season ◽  
Group Method ◽  
Sequence Repeat ◽  
Marker Assisted Breeding ◽  
Arithmetic Means ◽  
Pair Group ◽  
Simple Sequence

Carpetgrass [Axonopus compressus (Sw.) Beauv.] is an important warm-season perennial turfgrass that is widely used in tropical and subtropical areas. The genetic diversity of 63 carpetgrass accessions in China was studied using simple sequence repeat (SSR) markers. Fourteen SSR primer combinations generated a total of 49 distinct bands, 48 (97.96%) of which were polymorphic. The number of observed alleles ranged from 2 to 6, with an average of 3.5. Coefficients of genetic similarity among the accessions ranged from 0.24 to 0.98. Unweighted pair-group method with arithmetic means (UPGMA) clustered the 63 accessions into three groups, and not all samples from the same region belonged to the same group. SSR markers will promote marker-assisted breeding and the assessment of genetic diversity in wild germplasm resources of carpetgrass.

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 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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