Effectiveness of Single Nucleotide Polymorphism Markers in Genotyping Germplasm Collections of Coffea canephora Using KASP Assay

Akpertey, Abraham; Padi, Francis Kwame; Meinhardt, Lyndel W.; Zhang, Dapeng

doi:10.3389/fpls.2020.612593

Cited by 24 publications

(19 citation statements)

References 63 publications

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“…The development of SNP-based approaches to agri-food traceability is encouraged by the increasing number of SNP catalogs mostly derived by GBS analysis. These panels are available in different species of agri-food interest such as grapevine, olive, pulses, cacao, and coffee [ 76 , 77 , 78 , 79 , 80 ]. Most of the works using a SNP-based traceability approach have focused on olive oil analysis [ 40 , 41 ], however, SNPs have been efficiently employed in differentiating Arabica and Robusta coffee varieties [ 81 ], in the authentication of Portuguese wine [ 42 ], and in the identification of Nebbiolo variety in musts and wines [ 43 ].…”

Section: Molecular Approaches To Agri-food Analysismentioning

confidence: 99%

Molecular Approaches to Agri-Food Traceability and Authentication: An Updated Review

Fanelli

Mascio

Miazzi

et al. 2021

Foods

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In the last decades, the demand for molecular tools for authenticating and tracing agri-food products has significantly increased. Food safety and quality have gained an increased interest for consumers, producers, and retailers, therefore, the availability of analytical methods for the determination of food authenticity and the detection of major adulterations takes on a fundamental role. Among the different molecular approaches, some techniques such as the molecular markers-based methods are well established, while some innovative approaches such as isothermal amplification-based methods and DNA metabarcoding have only recently found application in the agri-food sector. In this review, we provide an overview of the most widely used molecular techniques for fresh and processed agri-food authentication and traceability, showing their recent advances and applications and discussing their main advantages and limitations. The application of these techniques to agri-food traceability and authentication can contribute a great deal to the reassurance of consumers in terms of transparency and food safety and may allow producers and retailers to adequately promote their products.

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Section: Molecular Approaches To Agri-food Analysismentioning

confidence: 99%

Molecular Approaches to Agri-Food Traceability and Authentication: An Updated Review

Fanelli

Mascio

Miazzi

et al. 2021

Foods

View full text Add to dashboard Cite

show abstract

“…4 d,e). Taken together, our results suggest PAP 400 may be a different species and a case of mislabelling, which can occur in seedbanks during plant cultivation and storage 36 . This is possible given that IPK holds seeds of other Papaver species in its collection.…”

Section: Resultsmentioning

confidence: 62%

Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis

Hong

Tamiru‐Oli

Hurgobin

et al. 2022

Sci Rep

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Opium poppy (Papaver somniferum) is one of the world’s oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the extent of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations using discriminate analysis of principal components and STRUCTURE analysis. Most accessions obtained from the same country were grouped together within subpopulations, likely a consequence of the restriction on movement of poppy germplasm. Alkaloid profiles of accessions were highly diverse, with morphine being dominant. Phylogenetic analysis identified genetic groups that were largely consistent with the subpopulations detected and that could be differentiated broadly based on traits such as number of branches and seed weight. These accessions and the associated genotypic data are valuable resources for further genetic diversity analysis, which could include definition of poppy core sets to facilitate genebank management and use of the diversity for genetic improvement of this valuable crop.

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“…4d,e ). Taken together, our results suggest PAP 400 may be a different species and a case of mislabelling, which can occur in seedbanks during plant cultivation and storage 36 . This is possible given that IPK holds seeds of other Papaver species in its collection.…”

Section: Resultsmentioning

confidence: 62%

Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis

Hong

Tamiru‐Oli

Hurgobin

et al. 2021

Preprint

View full text Add to dashboard Cite

Opium poppy (Papaver somniferum) is one of the world's oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the level of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations. Although the accessions were from geographically diverse regions, no strong association was detected between geographic origin and subpopulation at regional and sub-regional levels. However, most accessions obtained from the same country were grouped together as genetically distinct, likely a consequence of the restriction on movement of poppy germplasm. Phylogenetic analysis identified clades that were largely consistent with the subpopulations detected. Clades could be differentiated broadly based on capsule dehiscence, plant stature and seed weight, traits believed to be associated with poppy domestication. Our study determined that the genetically diverse collection was likely composed of both wild and cultivated forms. This has direct implications for germplasm management and utilization of the available diversity for genetic improvement of poppy.

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Effectiveness of Single Nucleotide Polymorphism Markers in Genotyping Germplasm Collections of Coffea canephora Using KASP Assay

Cited by 24 publications

References 63 publications

Molecular Approaches to Agri-Food Traceability and Authentication: An Updated Review

Molecular Approaches to Agri-Food Traceability and Authentication: An Updated Review

Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis

Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis

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