Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management

Nunziata, Angelina; Ruggieri, Valentino; Petriccione, Milena; Masi, Luigi De

doi:10.3390/ijms21134805

Cited by 15 publications

(23 citation statements)

References 42 publications

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“…More in depth investigations are also required to better understand the nature of processes leading to the endophyte/pathogen conversion, also with reference to genetic diversity in Castanea [ 107 ]. Besides the above-mentioned role by mycoviruses, this biological phenomenon may also derive by the ability to produce phytotoxins or other compounds involved in disease induction.…”

Section: Discussionmentioning

confidence: 99%

Endophytic Fungi and Ecological Fitness of Chestnuts

Nicoletti

Beccaro

Sękara

et al. 2021

Plants

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Chestnuts (Castanea spp.) are plants of relevant economic interest in the agro-sylvicultural contexts of mountain regions throughout the temperate zone, particularly in the northern hemisphere. In recent years, several biological adversities have repeatedly endangered species belonging to this genus, calling for coordinated actions addressed to contrast their decline. These actions have mainly focused on the control of key pests/pathogens and the improvement of resistance/tolerance by the plant host, while the role of microorganisms as mediators of interactions between plants and the noxious agents has been less considered, essentially by reason of a limited knowledge on their ecological impact. In line with the increasing awareness of the basic importance of microbial symbionts in regulating plant fitness in both natural and crop contexts, this paper offers an overview on the occurrence and effects of endophytic fungi of chestnuts.

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Section: Discussionmentioning

confidence: 99%

Endophytic Fungi and Ecological Fitness of Chestnuts

Nicoletti

Beccaro

Sękara

et al. 2021

Plants

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“…In this work, it was discovered that 22 new development markers can be used to advance genetic research in the genus Carya. According to Nunziata et al (2020), a group of cultivars were initially defined to assess the extent of genetic variation using random amplified polymorphic DNA (RAPD) markers for the purpose of varietal identification in European chestnut (Castanea sativa Mill.). Also, high-resolution melting (HRM) was employed for SNP mining inside 64 expressed sequence tags (EST) that involved all linkage groups and was validated by target resequencing.…”

Section: Genetic Diversity Assessmentmentioning

confidence: 99%

Advances in genomics for diversity studies and trait improvement in temperate fruit and nut crops under changing climatic scenarios

et al. 2023

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Genetic improvement of temperate fruit and nut crops through conventional breeding methods is not sufficient alone due to its extreme time-consuming, cost-intensive, and hard-to-handle approach. Again, few other constraints that are associated with these species, viz., their long juvenile period, high heterozygosity, sterility, presence of sexual incompatibility, polyploidy, etc., make their selection and improvement process more complicated. Therefore, to promote precise and accurate selection of plants based on their genotypes, supplement of advanced biotechnological tools, viz., molecular marker approaches along with traditional breeding methods, is highly required in these species. Different markers, especially the molecular ones, enable direct selection of genomic regions governing the trait of interest such as high quality, yield, and resistance to abiotic and biotic stresses instead of the trait itself, thus saving the overall time and space and helping screen fruit quality and other related desired traits at early stages. The availability of molecular markers like SNP (single-nucleotide polymorphism), DArT (Diversity Arrays Technology) markers, and dense molecular genetic maps in crop plants, including fruit and nut crops, led to a revelation of facts from genetic markers, thus assisting in precise line selection. This review highlighted several aspects of the molecular marker approach that opens up tremendous possibilities to reveal valuable information about genetic diversity and phylogeny to boost the efficacy of selection in temperate fruit crops through genome sequencing and thus cultivar improvement with respect to adaptability and biotic and abiotic stress resistance in temperate fruit and nut species.

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“…The genetic diversity of cucumbers has been evaluated based on the following types of molecular markers: isozyme [ 16 , 17 , 18 ], restriction fragment length polymorphism (RFLP) [ 19 ], random amplified polymorphic DNA (RAPD) [ 20 ], amplified fragment length polymorphism (AFLP) [ 21 ], and simple sequence repeat (SSR) [ 22 ]. Among these, RAPD has limitations owing to low interlaboratory reproducibility [ 23 ], while RFLP and AFLP are expensive [ 11 ]. SSR has the advantage of being codominant and multiallelic, but it has limited application in an automated genotyping system [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

“…Sufficient numbers of genome-wide SNPs can be obtained from Genotyping-by-sequencing (GBS), which is a next generation sequencing-based genotyping method using relatively inexpensive and straightforward protocols [ 27 ]. In particular, these SNPs can be utilized in an automated genotyping platform [ 23 , 28 ] using a wide range of technologies such as the Fluidigm SNP assay [ 29 ], high-resolution melting (HRM) [ 30 ], and kompetitive allele-specific polymerase chain reaction (KASP) [ 31 ]. The Fluidigm SNP assay uses a nanofluidic integrated fluidic circuit-based genotyping system.…”

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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Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management

Cited by 15 publications

References 42 publications

Endophytic Fungi and Ecological Fitness of Chestnuts

Endophytic Fungi and Ecological Fitness of Chestnuts

Advances in genomics for diversity studies and trait improvement in temperate fruit and nut crops under changing climatic scenarios

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

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