Transferability of ISSR, SCoT and SSR Markers for Chrysanthemum × morifolium Ramat and Genetic Relationships among Commercial Russian Cultivars

Characterization of genetic diversity in germplasm collections requires an efficient set of molecular markers. We assessed the efficiency of 36 new SCoT markers, 10 new ISSR markers, and 5 microsatellites for the characterization of genetic diversity in chrysanthemum core collection of 95 accessions (Russian and foreign cultivars). Seven new SCoT (SCoT12, 20, 21, 23, 29, 31, 34) and six new ISSR markers ((GA)8T, (CT)8G, (CTTCA)3, (GGAGA)3, (TC)8C, (CT)8TG) were efficient for the genetic diversity analysis in Chrysanthemum × morifolium collection. After STRUCTURE analysis, most Russian cultivars showed 20–50% of genetic admixtures of the foreign cultivars. Neighbor joining analysis based on the combination of SSR, ISSR, and SCoT data showed the best accordance with phenotype and origin compared to the separate analysis by each marker type. The position of the accessions within the phylogenetic tree corresponded with the origin and with some important traits, namely, plant height, stem and peduncle thickness, inflorescence type, composite flower and floret types, flower color, and disc color. In addition, several SCoT markers were suitable to separate the groups distinctly by the phenotypical traits such as plant height (SCoT29, SCoT34), thickness of the stem and peduncle (SCoT31, SCoT34), and leaf size and the floret type (SCoT31). These results provide new findings for the selection of markers associated with important traits in Chrysanthemum for trait-oriented breeding and germplasm characterization.

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ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

10.21203/rs.3.rs-666059/v1 ◽

2021 ◽

Author(s):

Lalit Arya ◽

Ramya Kossery Narayanan ◽

Anjali Kak ◽

Chitra Devi Pandey ◽

Manjusha Verma ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Morinda Citrifolia ◽

Species Differentiation ◽

Information Index ◽

Upgma Cluster Analysis ◽

Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

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Analysis of genetic relationships of genotypes of the genus Rosa L. from the collection of Nikita Botanical Gardens using ISSR and IRAP DNA markers

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj20.639 ◽

2020 ◽

Vol 24 (5) ◽

pp. 474-480

Author(s):

I. I. Suprun ◽

S. A. Plugatar ◽

I. V. Stepanov ◽

T. S. Naumenko

Keyword(s):

Genetic Diversity ◽

Bayesian Methods ◽

Dna Markers ◽

Wild Species ◽

Genetic Similarity ◽

Genetic Relationships ◽

Issr Markers ◽

The Other ◽

Clustering Methods ◽

Botanical Gardens

In connection with the development of breeding and the creation of new plant varieties, the problem of their genotyping and identification is becoming increasingly important, therefore the use of molecular methods to identify genetic originality and assess plant genetic diversity appears to be relevant. As part of the work performed, informative ISSR and IRAP DNA markers promising for the study of genetic diversity of the Rosa L. genus were sought and applied to analysis of genetic relationships among 26 accessions of the genus Rosa L. from the gene pool collection of Nikita Botanical Gardens. They included 18 cultivated varieties and 8 accessions of wild species. The species sample included representatives of two subgenera, Rosa and Platyrhodon. The subgenus Platyrhodon was represented by one accession of the species R. roxburghii Tratt. Cultivated roses were represented by varieties of garden groups hybrid tea, floribunda, and grandiflora. The tested markers included 32 ISSRs and 13 IRAPs. Five ISSR markers (UBC 824, ASSR29, 3A21, UBC 864, and UBC 843) and three IRAPs (TDK 2R, Сass1, and Сass2) were chosen as the most promising. They were used for genotyping the studied sample of genotypes. In general, they appeared to be suitable for further use in studying the genetic diversity of the genus Rosa L. The numbers of polymorphic fragments ranged from 12 to 31, averaging 19.25 fragments per marker. For markers UBC 864 and UBC 843, unique fingerprints were identified in each accession studied. The genetic relationships of the studied species and varieties of roses analyzed by the UPGMA, PCoA, and Bayesian methods performed on the basis of IRAP and ISSR genotyping are consistent with their taxonomic positions. The genotype of the species R. roxburghii of the subgenus Platyrhodon was determined genetically as the most distant. According to clustering methods, the representative of the species R. bengalensis did not stand out from the group of cultivated varieties. When assessing the level of genetic similarity among the cultivated varieties of garden roses, the most genetically isolated varieties were ‘Flamingo’, ‘Queen Elizabeth’, and ‘Kordes Sondermeldung’; for most of the other varieties, groups of the greatest genetic similarity were identified. This assessment reflects general trends in phylogenetic relationships, both among the studied species of the genus and among cultivated varieties.

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Characterization of Natural Isolates of Bipolaris maydis Associated with Mating Types, Genetic Diversity, and Pathogenicity in Fujian Province, China

Plant Disease ◽

10.1094/pdis-03-19-0650-re ◽

2020 ◽

Vol 104 (2) ◽

pp. 323-329

Author(s):

Yuli Dai ◽

Lin Gan ◽

Hongchun Ruan ◽

Niuniu Shi ◽

Yixin Du ◽

...

Keyword(s):

Genetic Diversity ◽

Mating Type ◽

Dna Polymorphism ◽

Sweet Corn ◽

Issr Markers ◽

Bipolaris Maydis ◽

Fujian Province ◽

Field Isolates ◽

Rational Distribution

Due to the natural destructiveness and persistence of the southern corn leaf blight (SCLB) fungus Bipolaris maydis (Nisikado et Miyake) Shoem, the characterization of B. maydis field isolates is essential to guide the rational distribution of resistant materials in corn-growing regions. In the present study, 102 field isolates collected from seven locations covering the entire region of Fujian Province, China, were assessed for mating type distribution, genetic diversity, and pathogenicity toward local sweet corn cultivars. Mating type detection via polymerase chain reaction indicated that 36.3 and 63.7% of isolates were MAT1-1 and MAT1-2, respectively; more than 80% of these isolates were confirmed using cross assays with known mating type isolates. Thirteen intersimple sequence repeat (ISSR) markers within and among two mating type populations revealed a high level of DNA polymorphism for all combined isolates and between MAT1-1 and MAT1-2 populations. The MAT1-2 population was more diverse based on DNA polymorphism than the MAT1-1 population. The value of GST was 0.0070, ranging from 0.0399 to 0.3044 based on analysis of combined isolates and individual regional populations, respectively, suggesting the presence of genetic differentiation in the two mating type populations from different locations. Pathogenicity assays revealed that both MAT1-1 and MAT1-2 populations were pathogenic to all 11 local sweet corn cultivars tested in this study. The potential of sexual reproduction, existence of genetic diversity in the two mating type populations, and pathogenicity suggest that B. maydis populations have independently clonally adapted under natural field conditions during corn cultivation.

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Structure and Genetic Diversity of Nine Important Landraces of Capsicum Species Cultivated in the Yucatan Peninsula, Mexico

Agronomy ◽

10.3390/agronomy9070376 ◽

2019 ◽

Vol 9 (7) ◽

pp. 376 ◽

Cited By ~ 3

Author(s):

Lucero del C. López Castilla ◽

René Garruña Hernández ◽

Crescencio de la Cruz Castillo Aguilar ◽

Aida Martínez-Hernández ◽

Matilde Margarita Ortiz-García ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Yucatan Peninsula ◽

Conservation Status ◽

Sustainable Use ◽

Issr Markers ◽

Southern Mexico ◽

Yucatán Peninsula ◽

Capsicum Spp ◽

Capsicum Species

Mexico has a wealth of Capsicum species, which has led to the development of a large number of chili pepper landraces. A great wealth of Capsicum germplasm can be found in southern Mexico in the Yucatan Peninsula, an important area of diversification of Capsicum annuum. Specifically, in the western Yucatan Peninsula, three of the five domesticated species of Capsicum (C. annuum, C. chinense and C. frutescens) have been reported. However, information on their genetic diversity, conservation status and potential use is lacking. To generate useful information toward the sustainable use, management and conservation of these species, we evaluated the structure, diversity and genetic relationships of nine accessions of Capsicum spp., of major importance cultivated in the western Yucatan Peninsula using 42 ISSR loci. The results indicated that these accessions consisted of three genetic groups that were defined by the respective species of each accession. The level of genetic diversity was moderate and distributed mainly among accessions. The ISSR markers detected a high level of polymorphism and allowed the genetic differentiation of the C. annuum complex. The results indicated that the accessions collected in the western Yucatan Peninsula constitute a valuable genetic resource that can be used in genetic improvement and conservation programs.

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Genetic Characterization of Cleveland Bay Horse Breed

Diversity ◽

10.3390/d11100174 ◽

2019 ◽

Vol 11 (10) ◽

pp. 174 ◽

Cited By ~ 2

Author(s):

Khanshour ◽

Hempsey ◽

Juras ◽

Cothran

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Genetic Similarity ◽

Genetic Resource ◽

Genetic Characterization ◽

Genetic Relationships ◽

Similarity Measures ◽

Horse Breed ◽

The Usa

The Cleveland Bay (CB) is the United Kingdom’s oldest established horse breed. In this study we analyzed the genetic variability in CB horses and investigated its genetic relationships with other horse breeds. We examined the genetic variability among 90 CB horses sampled in the USA compared to a total of 3447 horses from 59 other breeds. Analysis of the genetic diversity and population structure was carried out using 15 microsatellite loci. We found that genetic diversity in CB horses was less than that for the majority of other tested breeds. The genetic similarity measures showed no direct relationship between the CB and Thoroughbred but suggested the Turkman horses (likely in the lineage of ancestors of the Thoroughbred) as a possible ancestor. Our findings reveal the genetic uniqueness of the CB breed and indicate its need to be preserved as a genetic resource.

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Molecular characterization of genetic diversity and similarity centers of safflower accessions with ISSR markers

Revista Brasileira de Botânica ◽

10.1007/s40415-019-00574-7 ◽

2020 ◽

Vol 43 (1) ◽

pp. 109-121 ◽

Cited By ~ 1

Author(s):

Fawad Ali ◽

Muhammad Azhar Nadeem ◽

Ephrem Habyarimana ◽

Abdurrahim Yılmaz ◽

Muhammad Amjad Nawaz ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

Issr Markers

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Genetic Diversity Based on ISSR Markers of Apple Genotypes in Ardahan/Turkey

Notulae Scientia Biologicae ◽

10.15835/nsb10410347 ◽

2018 ◽

Vol 10 (4) ◽

pp. 554-558

Author(s):

Emre SEVİNDİK ◽

Hüseyin UYSAL ◽

Zehra Tuğba MURATHAN

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Genetic Distance ◽

Uv Light ◽

Genetic Relationships ◽

Issr Markers ◽

Genetic Distances ◽

The Matrix ◽

Commercial Kits ◽

Issr Primers

Within the present study, it was conducted a genetic diversity analysis using ISSR markers for some apple genotypes grown in Ardahan region, Turkey. Total genomic DNA (gDNA) isolation from apple leaves was performed using commercial kits. Five ISSR primers were used to determine the genetic diversity among the genotypes studied. Polymerase Chain Reaction (PCR) was performed with all gDNA samples to produce bands to score. PCR products were run in agarose gel and visualized under UV light. Bands on the gels were scored as “1”, while no bands at the corresponding positions were scored as “0”, to generate the matrix file. Five ISSR primers produced a total of 35 bands, and 20 of them were polymorphic. The polymorphic bands rated approximately 57%. Phylogenetic relationships and genetic distances between the genotypes were calculated by using the PAUP [Phylogenetic Analysis Using Parsimony (and Other Methods)] program. According to the PAUP data, the closest genetic distance was 0.03704 between ‘Kaburga’ and ‘Japon Apple’ genotypes, while the furthest genetic distance was 0.48148 between ‘Karanfil Apple’ and ‘Sisli Uruset’. The phylogenetic analysis obtained using UPGMA algorithm produced a phylogenetic tree with two clades. The results suggest that ISSR markers are useful tools for determining genetic relationships among apple genotypes.

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Assessment of the genetic diversity and genetic relationships of Lilium in China using ISSR markers

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2014.03.024 ◽

2014 ◽

Vol 55 ◽

pp. 184-189 ◽

Cited By ~ 7

Author(s):

Lihua Zhao ◽

Huamin Liu ◽

Guangze Cai ◽

Mingzhong Xia

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Issr Markers

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Genetic Diversity of an Alien Invasive Plant Mexican Sunflower (Tithonia diversifolia) in China

Weed Science ◽

10.1614/ws-d-11-00175.1 ◽

2012 ◽

Vol 60 (4) ◽

pp. 552-557 ◽

Cited By ~ 13

Author(s):

Jing Yang ◽

Ling Tang ◽

Ya-Li Guan ◽

Wei-Bang Sun

Keyword(s):

Genetic Diversity ◽

Native Species ◽

Invasive Plant ◽

Genetic Relationships ◽

Geographic Distance ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Chromosome Count ◽

Group Method ◽

Arithmetic Means

Mexican sunflower is a native species of North and Central America that was introduced into China early last century, but it has widely naturalized and become a harmful invasive plant in tropical and subtropical regions in South China. Inter-simple sequence repeat (ISSR) markers were employed to assess genetic diversity and variation in Mexican sunflower populations from China and neighboring regions. The karyotypes of populations were also studied. Our research showed high levels of genetic diversity in all populations. The lowest genetic diversity estimates were represented in two populations in Laos, suggesting prevention of new introductions into Laos is critical. Partitioning of genetic variance revealed that genetic variation was mostly found within populations, and unweighted pair group method with arithmetic means (UPGMA) analysis showed that the introductions into China and Laos were independent. There were no obvious correlations between genetic relationships and geographic distance of populations in China, consistent with the human associated dispersal history of Mexican sunflower. Previous cytological data and our chromosome count (2n = 34) and karyotype analysis showed chromosome stability among populations. The high levels of genetic diversity within invasive Mexican sunflower populations could be challenging for its management in China, and further expansion and potential negative effects on ecological systems of this plant should be monitored.

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Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

Plant Breeding and Seed Science ◽

10.1515/plass-2015-0024 ◽

2015 ◽

Vol 71 (1) ◽

pp. 81-95 ◽

Cited By ~ 7

Author(s):

Hoda Moradkhani ◽

Ali Ashraf Mehrabi ◽

Alireza Etminan ◽

Alireza Pour-Aboughadareh

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Genetic Relationships ◽

Issr Markers ◽

Issr Marker ◽

D Genome ◽

Ploidy Levels ◽

Marker Data ◽

Geographical Regions ◽

High Level

AbstractThe aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions ofAegilopsandTriticumspecies with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA) revealed that 81% (ISSR) and 84% (SSR) of variability was partitioned among individuals within populations. Comparing the genetic diversity ofAegilopsandTriticumaccessions, based on genetic parameters, shows that genetic variation ofAe. crassaandAe. tauschiispecies are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA) for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA), also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

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