scholarly journals Molecular characterization of wild grapes from northeastern part of Turkey

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 93-102
Author(s):  
Muhammed Kupe ◽  
Sezai Ercisli ◽  
Tatjana Jovanovic-Cvetkovic ◽  
Sadiye Eyduran ◽  
Rayda Ayed
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Simple Sequence Repeat ◽  
Group Method ◽  
Gene Pools ◽  
Sequence Repeat ◽  
Natural Habitats ◽  
Wild Grape ◽  
Wild Grapevine ◽  
Simple Sequence

Progress in grape breeding requires the exploitation of genetic variation among market classes, races and gene pools. Wild grapevines (Vitis vinifera ssp. sylvestris) are being endangered in their natural habitats and high priorities should be given to the wild germplasm. Turkey is one of the richest sources of wild grapevine and they mostly grown on forest trees on river basin. The present study was carried out to determine the amount of genetic variation and the degree of relatedness among 23 wild grape genotypes using 17 simple-sequence-repeat markers (SSR). Two international grape cultivars, Cabernet Sauvignon and Merlot are also included study. Number of alleles per locus of the 17 Simple Sequence Repeat (SSR) markers ranged from 3.0 to 14.0 and a total of 162 alleles with an average of 9.53 alleles per locus. The average expected and observed heterozygosity values were 0.773 and 0.781, respectively, which exhibited high level of genetic diversity in the wild grape germplasm. The unweighted pair group method with arithmetic mean analysis revealed three main genetic clusters that partially separated wild grape genotypes each other and. The international cultivars formed a out group. The high genetic diversity among native wild grapes from Coruh valley is suggesting that this area could be one of the centre of diversity of the specie. The results indicate a substantial genetic diversity in V. vinifera ssp. sylvestris and the need of exploring a wider area to increase the chance of finding a particular genotype.

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 802-810 ◽  
Author(s):  
Muwang Li ◽  
Li Shen ◽  
Anying Xu ◽  
Xuexia Miao ◽  
Chengxiang Hou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bombyx Mori ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Group Method ◽  
Sequence Repeat ◽  
Bombyx Mori L ◽  
Simple Sequence ◽  
Silkworm Bombyx Mori

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2–17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12–0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.Key words: silkworm, Bombyx mori L., microsatellites, simple sequence repeat (SSR), genetic diversity.

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)

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 Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6419 ◽  
Author(s):  
Lei Hao ◽  
Guosheng Zhang ◽  
Dongye Lu ◽  
Jianjun Hu ◽  
Huixia Jia
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Simple Sequence Repeat ◽  
Phylogenetic Analyses ◽  
Group Method ◽  
Phenotypic Traits ◽  
Germplasm Management ◽  
Sequence Repeat ◽  
Marginal Populations ◽  
Simple Sequence

Salix psammophila (desert willow) is a shrub endemic to the Kubuqi Desert and the Mu Us Desert, China, that plays an important role in maintaining local ecosystems and can be used as a biomass feedstock for biofuels and bioenergy. However, the lack of information on phenotypic traits and molecular markers for this species limits the study of genetic diversity and population structure. In this study, nine phenotypic traits were analyzed to assess the morphological diversity and variation. The mean coefficient of variation of 17 populations ranged from 18.35% (branch angle (BA)) to 38.52% (leaf area (LA)). Unweighted pair-group method with arithmetic mean analysis of nine phenotypic traits of S. psammophila showed the same results, with the 17 populations clustering into five groups. We selected 491 genets of the 17 populations to analyze genetic diversity and population structure based on simple sequence repeat (SSR) markers. Analysis of molecular variance (AMOVA) revealed that most of the genetic variance (95%) was within populations, whereas only a small portion (5%) was among populations. Moreover, using the animal model with SSR-based relatedness estimated of S. psammophila, we found relatively moderate heritability values for phenotypic traits, suggesting that most of trait variation were caused by environmental or developmental variation. Principal coordinate and phylogenetic analyses based on SSR data revealed that populations P1, P2, P9, P16, and P17 were separated from the others. The results showed that the marginal populations located in the northeastern and southwestern had lower genetic diversity, which may be related to the direction of wind. These results provide a theoretical basis for germplasm management and genetic improvement of desert willow.

Genetic diversity of Canadian elite summer rape (Brassica napus L.) cultivars from the pre- to post-canola quality era

2010 ◽  
Vol 90 (1) ◽  
pp. 23-33 ◽  
Author(s):  
Y -B. Fu ◽  
R K Gugel
Keyword(s):  
Genetic Diversity ◽  
Brassica Napus ◽  
Erucic Acid ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Gene Pools ◽  
Sequence Repeat ◽  
Low Erucic Acid ◽  
Simple Sequence ◽  
Canola Quality

The development of canola quality Brassica napus oilseed cultivars was a major achievement of Canadian public oilseed breeding programs. Simple sequence repeat (SSR) markers were applied to assess the genetic diversity of 300 plants representing one landrace introduced from Argentina in 1943, seven Canadian elite cultivars developed and released by Agriculture and Agri-Food Canada since 1954, and two European cultivars that were the source of the low erucic acid and low glucosinolate traits that define canola quality. Application of 22 SSR primer pairs from eight linkage groups detected 88 polymorphic alleles from 33 likely loci. The allelic frequencies in 300 samples ranged from 0.003 to 0.993 and averaged 0.388. The estimates of mean heterozygosity for these cultivars ranged from 0.055 to 0.203 and averaged 0.139. The most SSR variation was detected in the cultivars Argentine, Golden and Oro. A trend of decline in SSR variation was observed over the years of breeding effort. The proportion of total SSR variation residing among the cultivars was 51.4%; between high vs. low erucic acid cultivars 15% and between high vs. low glucosinolate cultivars 21.2%. Pairwise genetic differentiations among these cultivars ranged from 0.140 to 0.819 and averaged 0.500. Cluster analysis revealed that the genetic relationships of these cultivars were consistent with their known pedigrees. These findings are useful for broadening the genetic base of improved B. napus gene pools, selecting genetically diverse genotypes for hybrid combinations, and conserving summer rape germplasm.Key words: Simple sequence repeat, summer rape, Brassica napus, genetic diversity, genetic relationship, genetic structure

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 Diversity of Arabica Coffee (Coffea arabicaL.) in Nicaragua as Estimated by Simple Sequence Repeat Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Mulatu Geleta ◽  
Isabel Herrera ◽  
Arnulfo Monzón ◽  
Tomas Bryngelsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Simple Sequence Repeat ◽  
Significant Contribution ◽  
Gene Diversity ◽  
Ex Situ ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Arabica Coffee ◽  
Simple Sequence

Coffea arabicaL. (arabica coffee), the only tetraploid species in the genusCoffea, represents the majority of the world’s coffee production and has a significant contribution to Nicaragua’s economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR) markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei’s gene diversity (HT) and the within-population gene diversity (HS) were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA) revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST=0.13;P<0.001). The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved throughex situconservation of a low number of populations from each variety.

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.

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.

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