Molecular genetic diversity assessment of Citrus species grown in Iran revealed by SSR, ISSR and CAPS molecular markers

Sharafi, Ata Allah; Abkenar, Asad Asadi; Sharafi, Ali

doi:10.26910/issn.2528-8083vol2iss8.2017pp22-27

Cited by 3 publications

(4 citation statements)

References 24 publications

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“…Unlike many other marker systems, ISSR-PCR reaction is a single-primer PCR amplification ( Sharafi et al., 2017 ). Some molecules of the primer serve as forward primers and copies of the same primer orient and anneal to the template DNA in the opposite direction as reverse primers.…”

Section: The Concept Of Molecular or Dna Markersmentioning

confidence: 99%

“…In ISSR analysis, the primers used may be unanchored primers or primers anchored at either the 3′ or 5′ end. The primer anchor is normally made up of 1–4 degenerate nucleotides that overlap the flanking microsatellite sequences ( Sharafi et al., 2017 ). Usually, anchored primers are preferred for ISSR-PCR.…”

Section: The Concept Of Molecular or Dna Markersmentioning

confidence: 99%

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Basic concepts and methodologies of DNA marker systems in plant molecular breeding

Amiteye

2021

Heliyon

104

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The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR-or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.

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Section: The Concept Of Molecular or Dna Markersmentioning

confidence: 99%

Section: The Concept Of Molecular or Dna Markersmentioning

confidence: 99%

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

Amiteye

2021

Heliyon

104

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“…In terms of genetic relationships, [15] mentioned the level of genetic relationship of varieties that derived from Citrus maxima Merr, Citrus reticulata Blanco, and Citrus sinensis L. Osbeck was only 68, 54, and 47%, respectively. [16] also stated that there was no difference between 'Eureka' and 'Lisbon' lemons, and between 'Frost Valencia' and 'Washington Navel' sweet oranges that based on SSR and ISSR markers. The aim of this research was to determine morphological and physiochemical characteristics, fruit set periods, and the genetic relationship of four citrus species.…”

Section: Introductionmentioning

confidence: 99%

Identification of Morphological and Physiochemical Characteristics, Flowering Periods, and Genetic Relationship of Citrus Species

Hardiyanto¹,

Devy²,

Sugiyatno³

2023

IOP Conf. Ser.: Earth Environ. Sci.

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Variety improvement program of citrus in Indonesia has still been prioritized, therefore, characterization and identification of varieties within and/or among citrus species are absolutely required in order to obtain desired varieties based on market demand needs. The aim of this research was to determine morphological characteristics, flowering periods, and the genetic relationship of four citrus species. This study was carried out at Indonesia Citrus and Subtropical Fruit Research Institute (ICISFRI). A total of 12 varieties derived from Citrus reticulata Blanco, Citrus sinensis L. Osbeck, Citrus aurantifolia (Christm.) Swingle), and Citrus lemon (L.) Burm. F was used for morphological description. The genetic relationship was evaluated by morphological and molecular analyses using Inter-simple Sequence Repeat (ISSR). The result showed that variations of morphological characters were identified either within or among four citrus species. Citrus reticulata Blanco had the highest physiochemical contents. In terms of flowering periods, varieties that belong to Citrus reticulata Blanco, and Ortaji (Citrus sinensis L. Osbeck) required 9 to 11 days for fully blooming after flower bud; whereas Montaji (Citrus limon (L.) Burm. F) and Nimas (Citrus aurantifolia (Christm.) Swingle) needed 16 days. In both morphological and molecular analyses, 12 varieties were classified into two main clusters, however, some differences were found between the two dendrograms. The genetic relationship of four citrus species based on similarity coefficient ranged from 1 to 25 (morphological analyses) and 0.62 to 0.90 (ISSR marker), respectively. The highest genetic relationship derived from both analyses was performed by Krisma versus Monita, and Krisma versus Orlinda Kuning, respectively. Morphological analyses are still needed to complement molecular analyses in citrus classification in order to produce desired new citrus varieties in order to create sustained citrus agribusiness in Indonesia.

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“…In order to identify citrus species, various molecular techniques have been reported such as random amplified polymorphic DNA (RAPD, [ 13 , 14 , 17 , 26 ]), restriction fragment length polymorphisms (RFLP, [ 6 ]), amplified fragment length polymorphism (AFLP, [ 12 , 25 ]), sequence-related amplified polymorphism (SRAP, [ 3 ]), start codon targeted (SCoT) polymorphisms [ 9 ], inter-simple sequence repeats (ISSRs, [ 28 – 30 ]), LTR-IRAP, LTR-REMAP [ 5 ], and SSR [ 3 , 4 , 7 , 8 , 12 , 16 , 20 , 30 , 32 ].…”

Section: Introductionmentioning

confidence: 99%

A new insight on genetic diversity of sweet oranges: CAPs-SSR and SSR markers

Shahnazari

Noormohammadi

Sheidai

et al. 2022

Journal of Genetic Engineering and Biotechnology

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Background Citrus species are among the most important and widely consumed fruit trees in the world and are subjected to increasing global cultivation. Sweet orange (Citrus sinensis L. Osbeck) is one of 30 species of citrus which is cultivated in different regions of Iran. In this study, 80 trees of 13 sweet orange cultivars of Mazandaran province were studied for genetic diversity and fingerprinting by five short simple repeat (SSR) marker. Results The studied cultivars showed a high degree of genetic variability with an average genetic polymorphism of 98.46%. Behshahr and Jadeh Ghadim2 genotypes had the highest and lowest values in Nei genetic diversity, number of effective alleles, and Shannon index, respectively. Based on k-means clustering, the studied genotypes were divided into two main different groups. The high magnitude of genetic similarity between replicates of different cultivars indicated a potential case of homonymy or synonymy. DAPC analysis showed genetic admixture among some of the cultivars. The heatmap plot illustrated the alleles involved in cultivar differentiation. The CAPs analysis of monomorphic alleles of SSR loci indicated that these alleles differ in their sequences which add up to the genetic variability of citrus germplasm. Conclusion In general, SSR markers, due to their codominant nature and abundance in genome, are a good indicator for cultivar fingerprinting and hybrid prediction in orange cultivars. The present results showed the high diversity of sweet orange trees in different cultivars in the north of the country.

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Molecular genetic diversity assessment of Citrus species grown in Iran revealed by SSR, ISSR and CAPS molecular markers

Cited by 3 publications

References 24 publications

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

Identification of Morphological and Physiochemical Characteristics, Flowering Periods, and Genetic Relationship of Citrus Species

A new insight on genetic diversity of sweet oranges: CAPs-SSR and SSR markers

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