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![PCA of rose varieties using RAPD and ISSR markers. [Numbers 1-32 represent the rose cultivars in the same sequence as in Table 1]](profile/Rupesh-Deshmukh/publication/301360794/figure/fig2/AS:613863015858183@1523367756785/PCA-of-rose-varieties-using-RAPD-and-ISSR-markers-Numbers-1-32-represent-the-rose.png)
PCA of rose varieties using RAPD and ISSR markers. [Numbers 1-32 represent the rose cultivars in the same sequence as in Table 1]
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Rose (Rosa × hybrida) is economically important floricultural crop and represents a major product for commercial floriculture market as well as oil industry. Understanding its genetic diversity is important for crop improvement programmes, while DNA fingerprinting for accurate identification of clones, cultivars and varieties. In the present invest...
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Context 1
... the PCA, all the rose cultivars were plotted on 3D graph. The principal components separated the rose cultivars in three major clusters and cultivars Suryodaya and Suryakiran were placed distinctly from all other cultivars (Fig. 4). The consensus tree made by bootstrapping was similar to the dendrogram generated by ...
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Characterization of genetic diversity of interspecific cotton genotypes has significant impact on interspecific breeding. Present investigation was carried out to assess the genetic diversity among 20 interspecific cross derivatives (GISV-17, GISV-33, GISV-39, GISV-95-4, GISV-105, GISV-114, GISV-185, GISV-197, GISV-201, GISV-208, GISV-248, GISV-252...
Citations
... In this study, even though it employed 10 RAPD primers, they recorded a mean of 88.63 % polymorphism among the investigated rose accessions. Such result is in agreement with previous studies on rose genotypes, which have also revealed higher level of polymorphisms (for example, 98.5% among the rose cultivars [14] and 87.5% among Indian rose cultivars and fragrant roses [15]. ...
Aims: Owing to its export value in flower trade elsewhere in the world, Rose is the key commercial flower crop and the area under rose cultivation is ever increasing and the end-users always prefer new color variations. Hence, evolving new cultivars with novel color characteristics is the need of the hour, for which understanding genetic variation in the available cultivars is very much needed. Study Design: This investigation was conducted to analyze the genetic diversity of 11 elite and commonly cultivated rose accessions in South India by using randomly amplified polymorphic DNA (RAPD) markers. Place and Duration of Study: Department of Floriculture and Landscape Architecture, Horticultural College and Research Institute, TNAU, Coimbatore. Methodology: A total of 10 RAPD primers were employed, which was sufficient to distinguish the investigated rose cultivars. 1306 Results: Among the 44 PCR products produced by these markers, 39 (88.64%) were found to be polymorphic bands. The number of amplified products per RAPD primer varied from 3 to 8 with a mean of 4.4 bands per primer. The Un weighted paired group of arithmetic means (UPGMA) dendrogram distinguished the rose accessions into two major clusters suggesting that the accessions were different from each other. The genetic similarity coefficients were determined with this RAPD data, and they were ranged from 0.59 to 0.89. Conclusion: Molecular profiling data of this study have contributed to characterize and catalogue the rose germplasm data, which will be useful to identify the diverse rose lines for further breeding program that have the potential to improve the color variations.
... Molecular markers have proven to be valuable tools for species identification, but also for the characterization and evaluation of genetic diversity within and between species [23,24], because the DNA polymorphism detected by these markers is not affected by the environment [25]. Inter Simple Repeated Sequence (ISSR) markers as well as Start Codon Targeted (SCoT) markers have been widely used in PCR techniques in recent years, providing valuable tools for the rapid genetic characterization of organisms and a relatively cost-effective method of determination [23,[26][27][28][29][30]. ...
... In addition, MI and PR, which show the ability of primers to distinguish genotypes, with their high values, indicated that the ISSR and SCoT markers were effective in discriminating the 16 genotypes. These findings are consistent with a number of reports Horticulturae 2023, 9, 946 9 of 20 using ISSR and ScoT primers [23,[28][29][30], although in the genetic analysis of R. damascena, markers such as RAPD, SSR, AFLP and microsatellites have been used [9,11,[55][56][57][58]. ...
Rosa damascena Mill. is commercially the most important rose species used to produce essential oils. The plants of this species, cultivated in the district of Western Macedonia (Greece) for rose oil production, originatedfrom indigenous genotypes but also nurseries abroad, mainly from Bulgaria. The present study investigated the genetic relationship between nine genotypes of R. damascena from Greece, one genotype from Turkey, three genotypes from Bulgaria and three genotypes from France using the molecular markers ISSR and SCoT. Also, the rooting ability of shoot cuttings from these nine genotypes was investigated by applying 2 g/L of the rooting regulator K-IBA. In addition, petals were chemically analyzed using GC-MS and LC-MS to identify the compounds that are the main components of the rose oil. The nine rose genotypes of R. damascena, cultivated in Greece, one from Turkey and one of the three genotypes from Bulgaria were clustered in one clade in the dendrogram. The other two genotypes from Bulgaria were clustered in a separate clade that demonstrated the existence of genetic diversity among the three Bulgarian genotypes, while the French genotypes were clustered in a third clade. The shoot cuttings rooted relatively easily (55–70%) with the application of K-IBA, without any significant differences among the nine genotypes. Large variation was observed among the nine genotypes in the main volatile compounds of the flower petal extracts, which are related to rose oil components. For these compounds, the concentrations in μg/g of the fresh petal weight were 2-phenylethylalcohol (1148.35–2777.19), nerol (27.45–64.93), citronellol (88.45–206.59), geraniol (69.12–170.99) and nonadecane (209.27–533.15). Of the non-volatile compounds, gallic acid was the most abundant phenolic acid in the petal extracts of the nine genotypes (0.28–0.82 μg/g), while for the flavonoids, quercetin and kaempferol variations of 0.35–1.17 μg/g and 0.26–2.13 μg/g were recorded, respectively.
... In a similar report, genetic diversity in Jasmine sp. was evaluated with 90.64% polymorphism (Ghehsareh et al., 2015). Similar studies were carried out in gerbera (Bhatia et al., 2009) and in rose (Panwar et al., 2015). For ISSR markers, PIC value remained up to 0.49 thus, indicating the equal distribution of a marker in the population. ...
... During present investigations, PIC and Rp value was found to be better in ISSR than RAPD. Panwar et al. (2015), also recorded high PIC and Rp for ISSR as compared to RAPD markers in 32 rose cultivars. Among all the markers used in the study, highest EMR and MI value recorded for ISSR markers indicated the suitability of these markers in assessing diversity. ...
Carnation genotypes and mutants developed using gamma irradiations were characterized using PCR based DNA markers (RAPD, ISSR and SSR) for designing future breeding strategies. RAPD markers showed 70.00 to 94.74 percent polymorphism among the genotypes and mutants whereas, for ISSR and SSR markers 83.33 to 94.44 and 66.67 to 87.50 percent polymorphism was recorded, signifying variability among different genotypes tested. UPGMA based analysis of cluster separated carnation genotypes and mutants into two discrete groups. RAPD, ISSR and SSR markers were subjected for comparative analysis like effective multiplex ratio, marker index, polymorphic information content, resolving power and gene flow wherein, highest EMR (13.00), MI (5.33) and Rp (70) values were found for ISSRs and maximum PIC value (0.63), gene flow (3.33) were found for SSR. The results clearly indicated the reproducibility of SSRs and their ability to detect variability among the genotypes and mutants. Significant level of genetic variation was depicted by AMOVA which suggested the usefulness of studies in carnation breeding and unique bands obtained could be utilized for varietal identification.
... Molecular markers are considered to be the best method for genetic diversity analysis, genetic map construction and marker-assisted selection at DNA level (Agarwal et al. 2019;Uckele et al. 2021). In recent years, molecular markers such as AFLP (Pirseyedi et al. 2005), RAPD (Agaoglu et al. 2000), SCoT (Agarwal et al. 2019), SSR (Veluru et al. 2019) and ISSR (Panwar et al. 2015) have been widely used in the evaluation and genetic analysis of rose germplasm resources. Although these molecular markers enrich the genetic information of rose germplasm, they often have certain limitations because of low marker density and limited molecular markers. ...
Molecular markers are important genetic tools that permit the detection and utilization of genetic variation in germplasm resources. To develop high-density single nucleotide polymorphisms (SNPs) markers for rose, specific length amplified fragment sequencing (SLAF-seq) was performed in 158 rose individuals using the Rosa chinensis Jacq. genome as a reference for enzyme digestion prediction. After high-throughput sequencing, SNP marker development, and evolutionary analysis, the phylogenetic trees of 158 rose individuals were constructed according to the SNPs. A total of 1,703,904 SLAF tags were developed, among which 277,749 were polymorphic SLAF tags. According to the obtained polymorphic SLAF tags, a total of 1,816,980 population SNP markers were obtained, and 17,233 highly consistent SNP markers. The cluster analysis revealed that 158 rose individuals could be grouped into two major clusters. The average observed heterozygosity and polymorphism information content were 0.1802 and 0.2306, respectively. The population structure analysis of 158 rose individuals (K = 12) indicated that most of the populations had different ancestors and showed signs of crossover. The obtained SNPs in the rose genome can aid variety identification and have important implications for the conservation and improvement of varieties.
... New innovations have given rise to new molecular markers that can be used in describing genetic characteristics of plants in the Rosa genus. Several molecular assays have been used in recent years to test the genetic variation of various rose plants [14][15][16][17][18][19][20][21][22]. In theory, these molecular approaches, operations, classes, polymorphic count, function, and time requirements are varied. ...
... Korkmaz and Dogan [21] observed 90.1% and 88.8% polymorphisms among twenty-seven Rosa spp. in Turkey, after using ISSR and RAPD markers, respectively. Panwar et al. [18] also reported 94% genetic polymorphism with ISSR markers. Carvalho et al. [48] found 93.7% polymorphism among a selection of rose genotypes based on ISSR markers. ...
Background
Rosa damascena Mill is a well-known species of the rose family. It is famous for its essential oil content. The aim of the present study was to assess the genetic diversity and population structure of a mini core collection of the Iranian Damask rose germplasm. This involved the use of universal rice primers (URP) and start codon targeted (SCoT) molecular markers.
Results
Fourteen URP and twelve SCoT primers amplified 268 and 216 loci, with an average of 19.21 and 18.18 polymorphic fragments per primer, respectively. The polymorphic information content for URR and SCoT primers ranged from 0.38 to 0.48 and 0.11 to 0.45, with the resolving power ranging from 8.75 to 13.05 and 9.9 to 14.59, respectively. Clustering was based on neighbor-joining (NJ). The mini core collection contained 40 accessions and was divided into three distinct clusters, centered on both markers and on the combination of data.
Conclusion
Cluster analysis and principal coordinate analysis were consistent with genetic relationships derived by STRUCTURE analysis. The findings showed that patterns of grouping did not correlate with geographical origin. Both molecular markers demonstrated that the accessions were not genetically diverse as expected, thereby highlighting the possibility that gene flow occurred between populations.
... . Talas Oğraş et al.[23] reported a high percentage of polymorphism (99.52%) in a study conducted to determine the genetic diversity among nineteen rose genotypes using a molecular fingerprinting method based on fifteen ISSR markers. In another study, Panwar et al.[24] also reported that ISSR markers with high genetic polymorphism are beneficial to discriminate rose cultivars. Carvalho et al.[25] also reported a high percentage of polymorphism (93.7%) with dinucleotide repeats using 9 ISSR primers on 33 distant rose genotypes. ...
Genetic diversity is inevitable in making any crop improvement program successful. DNA fingerprinting technology to assess the genetic relationship among the selected genotypes for identification and cataloging of different species and cultivars of roses is a promising tool for Rosa genomes. The inter-simple sequence repeats markers (ISSRs) were used to investigate the genetic diversity among twenty-one diverse Rosa genotypes belonging to two different species, Rosa hybrida and R. damascena, and three distinct groups of rose varieties, namely Hybrid Tea, Floribunda, and Damask roses. Twenty-four ISSR primers yielded a total of 280 scorable amplified fragments from 250-1800 bp in length, from which 244 were polymorphic, resulting in an average of 86.4% polymorphism. UPGMA cluster analysis based on Jaccard’s pairwise similarity coefficient values ranged from 0.264 to 0.818, clearly distinguished different species and genotypes, grouping them into three distinct clusters. The results confirmed a high degree of variation in the rose germplasm studied highlighting the potential of improvement in roses for the ornamental and perfume industry.
... The majority of wild rose species are found in Asia, which is one of the major gene centers of these species (Broertjes and van Harten 1978). Various species of Rosa have adapted to the conditions found between 500 and 4700 m a.s.l. in the Indian Himalayan Region (Hooker 1879;Duthie 1971;Bamber 1976;Ambasta 1986;Pal 1991;Tejaswini and Prakash 2005). During the adaption process, these species are likely to have evolved into distinct taxa with the potential to develop into varieties and potential strains that can play a key role in the development of future roses. ...
... In this study we found wild roses to be distributed from the subtropical areas of Kathua, J&K (accession A-1, 792 m a.s.l.) to the higher arid regions of Nyoma, Leh, Ladakh (accession B-14, 4504 m a.s.l.), indicating the robustness and adaptability of these species to this wide range of climatic conditions. The altitudinal range of wild Rosa species in the Indian Himalaya Region has also been recorded in earlier studies (Hooker 1879;Gupta 1979;Collet 1984;Sharma and Jamwal 1988;Pal 1991). ...
The aim of this study was to assess morphological variation in wild Rosa L. germplasm from the Western Himalayan Region that includes the geographical area of two Union territories (Jammu and Kashmir [J&K] and Ladakh) and one state (Himachal Pradesh [HP]) of India. Field trips in different locations of J&K, Ladakh, and HP from 2014 to 2018 were undertaken in different seasons to collect accessions of wild Rosa species. A total of 59 accessions belonging to six wild Rosa species (Rosa canina L., R. foetida var. persiana [Lem.] Rehder, R. macrophylla Lindl., R. moschata Herrm., R. multiflora Thunb. and R. webbiana Wall ex. Royle) were collected. Fifty-five vegetative and reproductive characters (39 qualitative and 16 quantitative characters) were recorded for all of the accessions to determine the most significant morphological differences among the six species and among accessions of the same species. Phenotypic variability among the studied accessions was evaluated using descriptive statistics, principal component analysis (PCA), and cluster analysis. Among the quantitative characters analyzed, the coefficient of variation (CV) was highest for the number of rose hips per inflorescence and lowest for petal length; for the qualitative characters, the CV was highest for rose hip shape and lowest for sepal prickles. Results of the PCA indicated that the first six components accounted for 65.44% of the total variation. Leaflet length displayed a significant positive correlation with leaflet width, petiole length and pedicel length. Petal length, petal breadth, and flower diameter were positively correlated with each other. Hip length showed a positive correlation with hip width and a negative correlation with pedicel length, and hip color. Hip number per inflorescence showed a positive correlation with leaflet length, leaflet breadth, petiole length, pedicel length, and a strong negative correlation with prickle length. Clustering analysis categorized the Rosa accessions into two clusters and several groups and subgroups, indicating a high level of morphological variation in the germplasm. The key traits among the species identified to have a high discriminating value were leaflet length, leaflet breadth, prickle shape and size, stipule margin, style nature, sepal margin, flower color, and size and shape of hips. These results indicate that there is a high potential for obtaining desirable trait combinations from wild Rosa germplasm of the Western Himalaya Region.
... Qi et al. (2018) developed organ-specific microsatellite markers (3245 genomic SSR primers and 33 EST-SSRs) in rose and tested them for diversity analysis in 48 rose genotypes. But very few studies were available for diversity analysis in Indian origin modern rose cultivars (Panwar et al. 2015;Prasad et al. 2006) and these were conducted in the limited number of Indian genotypes using RAPD and ISSRs markers. Considering the superiority of SSR markers in terms of robustness, amenability to comparison across laboratories etc. the present study was undertaken using morphological and molecular markers (SSRs) with an aim to characterize 109 Indian bred rose cultivars belonging to Hybrid Tea and Floribunda groups to ascertain the genetic diversity and presence of population sub-structure. ...
... This result is in agreement with earlier studies on rose genotypes that reported 98.5% polymorphism among the rose cultivars for RAPDs (Rai et al. 2015). Panwar et al. (2015) and Prasad et al. (2006) had also reported 94% and 87.5% polymorphism with ISSR and RAPD markers in Indian rose cultivars and fragrant roses. However, RAPDs and ISSRs being random markers are considered to have low repeatability and comparability across laboratories, hence, SSRs are considered more suitable due to their robust nature. ...
Rose (Rosa × hybrid L.) is one of the most important commercial ornamental crops cultivated worldwide for its beauty, fragrance and nutraceutical values. Characterization of rose germplasm provides precise information about the extent of diversity present among the cultivars. It also helps in cultivar identification, intellectual property right protection, variety improvement and genetic diversity conservation. In the present study, 109 Indian bred rose cultivars were characterized using 59 morphological and 48 SSR markers. Out of 48 SSRs used, 31 markers exhibited polymorphism and 96 alleles were identified with an average of 3.9 alleles per locus. Nei’s expected heterozygosity value of each locus ranged from 0.08 (with SSR ABRII/RPU32) to 0.78 (SSR Rh58). The similarity coefficient values ranged from 0.42 to 0.90 which indicated presence of moderated diversity among Indian cultivars. The neighbor-joining tree based on morphological data grouped the cultivars into two major clusters and several minor clusters based on their morphological resemblance. However, UPGMA dendrogram constructed using matching coefficient values grouped the cultivars into eight different clusters. Interpopulation analysis revealed higher genetic similarities between Hybrid Tea and Floribunda cultivars. An analysis for presence of population sub-structure grouped the Indian cultivars into eight different genetic groups. Analysis of molecular variance revealed apportioning of 97.59% of the variation to within subgroup diversity and 3.07% to between the cultivar groups. We have demonstrated here successful utilization of robust SSR to distinguish cultivars and assess genetic diversity among Indian bred rose cultivars. The information provided here is useful for cultivar identification and protection, cultivar improvement and genetic diversity conservation.
... Previous authors had used different marker systems such as Random Amplified Polymorphic (RAPD), Amplified Fragment Length Polymorphism (AFLP), Restricted Fragment Length Polymorphism (RFLP), Inter Simple Sequence Repeats-ISSR, Simple Sequence Repeats (SSR) and Sequence Tagged Microsatellite Site (STMS) for analyzing genetic diversity and characterization of cultivated and wild rose genotypes belongs to particular geographical origin (Wu et al. 2000;De Cock et al. 2008;Samiei et al. 2010;Azeem et al. 2012;Yang et al. 2017) or specific group or subclass of roses (Gardes et al. 2005;Scariot et al. 2006;Kiani et al. 2010;Alsemaan et al. 2011;Akond et al. 2012;Jiang and Zang, 2017). Very few studies have been conducted to examine the genetic diversity in Indian roses (Rai et al. 2015;Panwar et al. 2015;Prasad et al. 2006;Mohapatra and Rout 2005) and investigations comparing the cultivated Indian rose population with native wild roses and exotic cultivated types are rather scarce. The present experiment was therefore, planned to analyse the diversity, genetic structure and level of population differentiation in a large number of Indian cultivated types with respect to the exotic cultivars and wild native species. ...
Roses are the most important commercial ornamental plants
grown for flowers, perfumery and nutraceutical
compounds. Commercially cultivated roses (Rosa × hybrida
L.) are complex interspecific hybrids probably derived from
8-10 wild species among the large diversity of 130-200
species in genus Rosa. Wild germplasm is a primary source
of variability and plays a major role in improving existing
varieties by broadening their genetic base. In the present
investigation, we have utilized the previously identified SSR
primers for studying the diversity among 148 selected rose
genotypes, including wild species and cultivated varieties
of Indian and exotic origin. A total of 88 alleles was scored
using 30 polymorphic loci; they produced average 2.9±1
alleles per locus. Polymorphism information content (PIC)
values for different SSR loci ranged from 0.08 to 0.8 with a
mean value of 0.5±0.2. The neighbor-joining tree generated
based on Nei’s (1978) genetic distance values grouped the
population into three major clusters. Cluster-I & II consists
of all modern rose cultivars (Rosa × hybrida L.) originated
from India and cluster-III consists of all exotic cultivars,
wild species and a few cultivars from India. STRUCTURE
analysis based on microsatellite allelic data, partitioned
the total rose genotypes into four different sub-populations
with some individual genotypes having genomic admixture.
Population subdivision estimates, FST between different
subpopulations ranged from 0.01-0.15 indicates low to
moderate level of divergence existing among the rose
cultivars and germplasm. Population differentiation in rose
cultivars and wild species corresponds to their geographical
origin and lineages. Analysis of molecular variance (AMOVA)
results revealed that 83.12 % of the variance was accounted
for by within sub-groups followed by significant levels of
variation among the populations (10.42%) and least variance
(6.46%) was noticed among individuals within groups.
... Several molecular marker systems have been developed for effective, accurate and fast identification of roses. Various DNA markers such as Restriction Fragment Length Polymorphism (RFLP), Random Amplified Polymorphic DNA (RAPD), Amplified Fragment Length Polymorphism (AFLP), Inter Simple Sequence Repeats (ISSR) and Simple Sequence Repeats (SSR) have been successfully used in roses for effective characterization and diversity analysis of various rose types (Esselink et al. 2003, Zhang et al. 2006, Panwar et al. 2015. Present study was undertaken for characterization and diversity analysis of fragrant rose cultivars of Indian and exotic origin using SSR markers. ...
... ity among selected cultivars. Highest and lowest similarity values were found in cultivar sets, Jawahar and Double Delight (0.86) and Century Two Seedling and Brandy (0.55). SimilarlyAkond et al. (2012) noticed average similarity coefficient values of 0.66 (0.47-0.98) and 0.73 (0.57-0.83) in domesticated miniature roses and hybrid lines using SSRs.Panwar et al. (2015) also reported an average similarity coefficient of 0.67 polymorphic marker were noted as either present ...
Rose (Rosa × hybrida L.) is a commercially important ornamental crop which represents major share in world
floriculture market and essential oil industry. In the present investigation, genetic diversity among 25 fragrant rose
cultivars belonging to exotic and Indian origin was studied during 2016–17 at New Delhi. Thirty one SSR markers
were used for characterization. A total of 96 alleles were identified among the genotypes with an average of 3.9 alleles
per loci. Diversity among populations of different origins was analysed and it revealed that, cultivars from Indian
origin exhibited higher diversity as compared to the selected cultivars from American and European origin. Effective
number of alleles (Ne) and expected heterozygosity (He) values were more in Indian population (Ne=1.93, He=0.49) as
compared to selected populations of American (Ne=1.45, He=0.45 and European (Ne=1.29, He=0.29) origin. Matching
coefficient values ranged from 0.55– 0.86 indicated the existence of moderate variability among fragrant roses of
different origin. Unweighted Pair Group Method using Arithmetic Mean (UPGMA) dendrogram clearly separated all
the 25 genotypes into 7 different clusters. Cultivars, Rose Sherbet, Century Two Seedling and Brandy showed distant
relationship with other cultivars and were found in three different individual clusters V, VI and VII respectively. The
highest and lowest similarity values were noticed between the cultivar sets, Jawahar and Double Delight (86%) and
Century Two Seedling and Brandy (55%). The molecular data generated in present investigation would be highly
helpful for cultivar identification, conservation and for breeding fragrant roses
