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Basmati rice is the largest selling type of rice on the UK market because it is valued for its aroma and cooking properties. Although the geographic origin of Basmati is protected, the definition of Basmati is not protected in law in the UK, and its protection has been achieved through an industry and enforcement authority Code of Practice. When the first Code was published in 2005, there were 15 rice varieties mainly landrace varieties, which could be labelled as Basmati. A DNA  assay using single sequence repeats (SSRs or microsatellites) was developed to authenticate Basmati varieties and distinguish them from non-Basmati rice on a qualitative and quantitative basis. However, since 2005 both India and Pakistan have been plant breeding Basmati for disease resistance, salt tolerance and better yield such that the Code of Practice was amended to include an extra 25 varieties of Basmati rice in 2017. As the genetic diversity of these new varieties is greater than the original set of Basmati varieties, the SSR assay originally developed could no longer be used, and a project was commissioned to develop a more appropriate set of DNA markers.  

Using the results of a previous project to select markers from new information from whole genome sequencing of Basmati and non-Basmati varieties, a new approach using a PCR based genotyping technology called KASP (Kompetitive Alelle Specific PCR) was developed. A sub-set of 69 DNA KASP markers (out of an original 327) was successfully found to be able to distinguish between most of the 60 varieties tested, including some pairs of varieties that could not be distinguished using previous technique. The project has demonstrated that KASP assays are a feasible approach to distinguish between Basmati and non-Basmati varieties. The report suggests further work that would be needed to optimise and improve the reliability of the KASP assay technique (e.g. more replications and better samples of DNA to find more markers), this could then be used to design and develop a cost effective, fit for purpose method that can be applied by enforcement labs to verify labelling of Basmati rice.

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Basmati rice is a high value popular type of rice based on its distinctive organoleptic properties. Approval of varieties meeting the specification laid down for Basmati rice is undertaken by the Indian and Pakistani Export Authorities, and these have been accepted in a UK industry/enforcement Code of Practice (COP). Originally 15 varieties were approved to be marketed as Basmati, 9 of which are allowed to be imported tariff free into the EU as brown rice. New varieties have been bred for higher yield, disease and pest resistance, as well as salt tolerance, and 25 new varieties have been added to the COP. This has resulted in the need for new DNA markers to be investigated as the original DNA microsatellite method cannot identify the new varieties effectively. This study details whether single nucleotide polymorphisms (SNP) and insertion/deletion (InDel) variations developed into KASP™ (Kompetitive Allele Specific PCR; LGC Biosearch Technologies) were more effective DNA markers for all the approved varieties of Basmati rice. The results provide a method that distinguishes 37 Basmati varieties from all others using between 3 and 8 KASP markers out of a pool of 98 informative markers. A reduced set of 24 KASP markers could determine whether a sample belongs to one of eight family groups.

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