Development of model web-server for crop variety identification using throughput SNP genotyping data

Singh, Rajender; Iquebal, Mir Asif; Mishra, C. N.; Jaiswal, Sarika; Kumar, Dhiraj; Raghav, Nishu; Paul, Surinder; Sheoran, Sonia; Sharma, Pradeep; Gupta, A.; Tiwari, Vinod; Angadi, U. B.; Kumar, Neeraj; Rai, Anil; Singh, Gurdeep; Kumar, Dinesh; Tiwari, Ruchi

doi:10.1038/s41598-019-41204-2

Cited by 19 publications

(17 citation statements)

References 30 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

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“…These correlations are consistent with Canadian breeding program histories. Although breeding within related germplasm decreases diversity because of drift and selection (Singh et al., 2019), crossing between elite, adapted entries increases the frequency of identifying better genotypes relative to crossing between dissimilar entries.…”

Section: Discussionmentioning

confidence: 99%

The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation

Hargreaves

N’Daiye

Walkowiak³

et al. 2021

The Plant Genome

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Cultivated germplasm provides an opportunity to investigate how crop agronomic traits, selection for major genes, and differences in crossing-over rates drive patterns of allelic variation. To identify how these factors correlated with allelic variation within a collection of cultivated bread wheat (Triticum aestivum L.), we generated genotypes for 388 accessions grown in Canada over the past 170 yr using filtered single nucleotide polymorphism (SNP) calls from an Illumina Wheat iSelect 90K SNP-array. Entries' breeding program, era of release, grain texture, kernel color, and growth habit contributed to allelic differentiation. Allelic diversity and linkage disequilibrium (LD) of markers flanking some major loci known to affect traits such as gluten strength, growth habit, and grain color were consistent with selective sweeps. Nonetheless, some flanking markers of major loci had low LD and high allelic diversity. Positive selection may have acted upon homoeologous genes that had significant enrichment for the gene ontology terms 'response-to-auxin' and 'response-to-wounding.' Long regions of LD, spanning approximately one-third the length of entire chromosomes, were associated with many pericentromeric regions. These regions were also characterized by low diversity. Enhancing recombination across these regions could generate novel allele combinations to accelerate Canadian wheat improvement.

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“…Epimutations can be observed after in vitro fecundation (fertilisation) but not in in vivo-conceived children (Peters et al, 2015;Song et al, 2015). Similarly, the somaclonal variations caused in plant cell cultures vary according to the species' reproductive biology, the cultivar and the number of individuals used, and the culture protocol, which does not promise any in vivo-in vitro continuity (Martínez, 2018;Skirvin et al, 1994).…”

Section: The Mutagenesis Exemptionmentioning

confidence: 99%

Advances in identifying GM plants: current frame of the detection of transgenic GMOs

Bertheau¹

2021

Burleigh Dodds Series in Agricultural Science

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Transgenic GMOs were welcomed in the 1990s due to the difficulties distinguishing genetic and epigenetic modifications from random mutagenesis and their ability to insert new nucleic sequences more rapidly but still randomly. Their marketing in Europe has been accompanied by health and environmental risk assessments, specific monitoring and traceability procedures to preserve the free choice of consumers and allow the coexistence of different supply chains. This chapter reviews the regulations, detection techniques, strategies and standards that have been put in place in the European Union since 1996 to ensure the analytical traceability of these GMOs. The capacity of the matrix approach, initially targeted at transgenic GMOs, to trace other types of GMOs is discussed in an accompanying chapter.

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Development of model web-server for crop variety identification using throughput SNP genotyping data

Cited by 19 publications

References 30 publications

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

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

The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation

Advances in identifying GM plants: current frame of the detection of transgenic GMOs

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