DNA-Based Tools to Certify Authenticity of Rice Varieties-An Overview

Abstract

Rice (Oryza sativa L.) is one of the most cultivated and consumed crops worldwide. It is mainly produced in Asia but, due to its large genetic pool, it has expanded to several ecosystems, latitudes and climatic conditions. Europe is a rice producing region, especially in the Mediterranean countries, that grow mostly typical japonica varieties. The European consumer interest in rice has increased over the last decades towards more exotic types, often more expensive (e.g., aromatic rice) and Europe is a net importer of this commodity. This has increased food fraud opportunities in the rice supply chain, which may deliver mixtures with lower quality rice, a problem that is now global. The development of tools to clearly identify undesirable mixtures thus became urgent. Among the various tools available, DNA-based markers are considered particularly reliable and stable for discrimination of rice varieties. This review covers aspects ranging from rice diversity and fraud issues to the DNA-based methods used to distinguish varieties and detect unwanted mixtures. Although not exhaustive, the review covers the diversity of strategies and ongoing improvements already tested, highlighting important advantages and disadvantages in terms of costs, reliability, labor-effort and potential scalability for routine fraud detection.

Keywords: DNA barcoding; DNA-markers; PCR; SNPs; SSRs; adulteration; fraud; high-resolution melting; isothermal amplification; multiplex.

Figure 4

Number of publications per biennium, in the last 20 years, focusing on rice authentication through DNA-based methods. The data were obtained by searching in the SCOPUS database (www.scopus.com; accessed on 18 November 2021) articles published in 2001–2021 using the following terms: (Rice) AND (Authentication), (Rice) AND (Fraud), (Rice) AND (Molecular markers), (Rice) AND (Adulteration) and (Identification) AND (Rice) AND (Varieties). 2001–02: [67,83,87,127]; 2003–04: [128]; 2007–08: [57,60,129,130,131]; 2009–10: [54,78,130,132,133,134,135,136]; 2011–12: [59,86,116,123,137,138,139,140,141,142]; 2013–14: [55,58,81,143,144,145]; 2015–16: [89,111,146,147,148,149]; 2017–18: [53,103,108,150,151,152,153]; 2019–20: [52,154,155]; 2021: [51,104,112,114,156,157].

Figure 1

Identification of the 10 larger consuming, producing and exporting countries of the world (A) Production of milled rice in 2019/2020, and rice consumption in 2020/2021 in each of the 10 top producing/consuming countries. (B) The 10 main rice exporting countries worldwide with values of exportation in million metric tons. (Graphs were built based on data in [2]).

Figure 1

Identification of the 10 larger consuming, producing and exporting countries of the world (A) Production of milled rice in 2019/2020, and rice consumption in 2020/2021 in each of the 10 top producing/consuming countries. (B) The 10 main rice exporting countries worldwide with values of exportation in million metric tons. (Graphs were built based on data in [2]).

Figure 2

Schematic representation of some of the most common types of rice fraud and the preferred type of strategy (DNA or non-DNA-based) for their detection. Whenever the rice has features that result from the interaction of plant genetics and the environment (including agricultural practices, rice processing, long-term or inadequate storage, contamination with toxic compounds, pollutants etc.), DNA-based techniques are not appropriate to detect fraud, and other methods must be employed.

Figure 3

Schematic representation of the most common types of DNA markers used in rice authentication, indicating the key methods that characterize each one (legend in the bottom), and some of the methodologies used to improve marker detection.