Genetic diversity and population structure of Cucumis sativus L. by using SSR markers

Dar, Aejaz Ahmad; Mahajan, Reetika; Lay, Padma; Sharma, Susheel

doi:10.1007/s13205-017-0944-x

Cited by 27 publications

(21 citation statements)

References 45 publications

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“…High RP values, with positive correlations with PIC and MI, indicate high descriptive potential of diversity between cucumber genotypes. Although the RP value is less than the one reported by Payel et al [40], it is higher than the one reported by Dar et al [41], who Table 3. Oligonucleotide primer sequences and real-time PCR amplification parameters.…”

Section: Issr Analysiscontrasting

confidence: 61%

“…This result is comparable with the results of Mohammed et al [42], who reported that genetic similarity coefficients ranged between 0.15 and 0.62 in 10 cucurbit species using 13 RAPD primers. Dar et al [41] stated that Jaccard's similarity coefficient ranged from 0.07 to 0.89 for 104 genotypes of cucumber using 23 SSR primer pairs. Considering the percent of total genetic diversity, the results may not be statistically appropriate for PCA but genetically they indicate the desirable sampling of ISSR markers of the 38 cucumber genotypes.…”

Section: Clustering and Principal Component Analysismentioning

confidence: 99%

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Correlation between cucumber genotype and resistance to damping-off disease caused by Phytophthora melonis

Hashemi

Golparvar

Esfahani

et al. 2019

Biotechnology & Biotechnological Equipment

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Cucumber (Cucumis sativus L.) damping-off disease caused by Phytophthora melonis is a limiting factor affecting cucurbit production. This study assessed a collection of 38 domestic and exotic commercial cucumber genotypes for damping-off resistance at transplanting and 50% flowering. Plants were classified using a four-score scale, the average damping-off percentage ranging from 7.92% (resistant) to 88.01% [highly susceptible (HS)]. Most of the genotypes were susceptible and HS to P. melonis. These genotypes were analyzed with 15 inter-simple sequence repeat (ISSR) markers. A total of 317 bands were produced, of which 297 bands (93.69%) were polymorphic. The primer ISSR29 possessed the highest resolving power, polymorphic information content and marker index value, which could be the most informative primer for distinguishing cucumber genotypes. Cluster analysis and principal component analysis were carried out and there was a probable connection between cucumber genotypes and resistance level against P. melonis, indicating possible application for ISSR in studying disease resistance of cucumber and producing cultivars that resist damping-off. The expression of three candidate genes probably involved in the defence against P. melonis was quantified by quantitative real-time polymerase chain reaction in five cucumber genotypes showing different susceptibility to the pathogen. CsWRKY20, CsLecRK6.1 and LOX1 genes were differentially expressed depending on genotype in early stages of infection. LOX1 was the most expressed gene across experiments and the one that best discriminated between susceptible and resistant genotypes. These results are a valuable resource for future functional genomics studies to unravel the molecular mechanisms of C. sativus/P. melonis interaction.

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Section: Issr Analysiscontrasting

confidence: 61%

Section: Clustering and Principal Component Analysismentioning

confidence: 99%

Correlation between cucumber genotype and resistance to damping-off disease caused by Phytophthora melonis

Hashemi

Golparvar

Esfahani

et al. 2019

Biotechnology & Biotechnological Equipment

View full text Add to dashboard Cite

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“…Our results showed average of PIC value (0.384), was similar when compared with previous findings in Indian cucumber (0.333) (DAR et al, 2017) and Chinese cucumber (0.388) (HUA et al, 2010). A wide range of genetic distance was found among the genotypes ranging from 0.03 to 0.70 which indicated a large diversity among the genotypes selected in the present study.…”

Section: Ssr Based Genetic Diversitysupporting

confidence: 92%

“…Simple sequence repeat (SSR) or microsatellite markers occur frequently in most eukaryotic genomes and can be very informative, reliable (reproducible), codominant, multiallelic and highly polymorphic, making them well suited for detecting variation among closely relative varieties (FORMISANO et al, 2012;GARCIA et al, 2004). Genetic diversity was assessed previously by using 23 SSR primer pairs in cucumber (DAR et al, 2017). Although, the degree of genetic diversity in cucumber has been assessed with a number of DNA markers (STAUB et al, 2005;ZHUANG et al, 2008;SIKDAR et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of cucumber genotypes revealed by SSR markers and agronomic traits

Pati¹,

Anilabh²,

Verma³

et al. 2019

Genetika

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Understanding the level of genetic diversity and structure of landraces is essential for economical use of genetic resources. In the present study, we investigated the genetic diversity of 36 representative sample of cucumber genotypes based on 10 quantitative traits and 17 polymorphic simple sequence repeat (SSR) markers. Our result revealed variability in flowering behavior, growth habit and fruit characters. We found that the traits, days to opening of first female flower varied from 39.03 to 51.94, fruit length 6.09 to 30.01(cm), fruit weight 104.39 to 277.05(g) and yield per plant 699.38 to 1670.93(g). Genetic distance based on 17 SSR markers among 36 genotypes was quantified ranging from 0.03 to 0.70 indicated a wide diversity among the genotypes selected for evaluation in the present study. These primers produced 2-4 number of alleles with an average 2.76. Polymorphism information content varied from 0.005 to 0.550 with an average of 0.348. The observed heterozygosity mean was 0.098, while gene diversity or expected heterozygosity was 0.625 to 0.057. The distinct genotypes found in this study based on 406

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“…After early domestication in India, China, and Western Asia, cucumber was introduced to Europe and the Americas [ 7 ]. Because of climatic and cultivation conditions or dietary preference during domestication, modern cultivars have diversified into the following four major types: Huánan-type (southern China), Huábei-type (northern China), European-type, and a crossbreed of Huánan × Huábei.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity Assessment and Cultivar Identification of Cucumber (Cucumis sativus L.) Using the Fluidigm Single Nucleotide Polymorphism Assay

Park

Choi

Jung³

et al. 2021

Plants

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Genetic diversity analysis and cultivar identification were performed using a core set of single nucleotide polymorphisms (SNPs) in cucumber (Cucumis sativus L.). For the genetic diversity study, 280 cucumber accessions collected from four continents (Asia, Europe, America, and Africa) by the National Agrobiodiversity Center of the Rural Development Administration in South Korea and 20 Korean commercial F1 hybrids were genotyped using 151 Fluidigm SNP assay sets. The heterozygosity of the SNP loci per accession ranged from 4.76 to 82.76%, with an average of 32.1%. Population genetics analysis was performed using population structure analysis and hierarchical clustering (HC), which indicated that these accessions were classified mainly into four subpopulations or clusters according to their geographical origins. The subpopulations for Asian and European accessions were clearly distinguished from each other (FST value = 0.47), while the subpopulations for Korean F1 hybrids and Asian accessions were closely related (FST = 0.34). The highest differentiation was observed between American and European accessions (FST = 0.41). Nei’s genetic distance among the 280 accessions was 0.414 on average. In addition, 95 commercial F1 hybrids of three cultivar groups (Baekdadagi-, Gasi-, and Nakhap-types) were genotyped using 82 Fluidigm SNP assay sets for cultivar identification. These 82 SNPs differentiated all cultivars, except seven. The heterozygosity of the SNP loci per cultivar ranged from 12.20 to 69.14%, with an average of 34.2%. Principal component analysis and HC demonstrated that most cultivars were clustered based on their cultivar groups. The Baekdadagi- and Gasi-types were clearly distinguished, while the Nakhap-type was closely related to the Baekdadagi-type. Our results obtained using core Fluidigm SNP assay sets provide useful information for germplasm assessment and cultivar identification, which are essential for breeding and intellectual right protection in cucumber.

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Genetic diversity and population structure of Cucumis sativus L. by using SSR markers

Cited by 27 publications

References 45 publications

Correlation between cucumber genotype and resistance to damping-off disease caused by Phytophthora melonis

Correlation between cucumber genotype and resistance to damping-off disease caused by Phytophthora melonis

Genetic diversity of cucumber genotypes revealed by SSR markers and agronomic traits

Genetic Diversity Assessment and Cultivar Identification of Cucumber (Cucumis sativus L.) Using the Fluidigm Single Nucleotide Polymorphism Assay

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