Abstract
Authentication of Basmati rice has relied on microsatellite markers since 2004, but microsatellites cannot distinguish between all of the forty-one Basmati varieties approved in 2017. This study investigated whether single nucleotide polymorphisms (SNP) and insertion/deletion (InDel) variations developed into KASP™ (Kompetitive Allele Specific PCR; LGC Biosearch Technologies) could be used to distinguish between commercial Basmati varieties. Suitable loci were identified by comparing whole genome sequences of 120 diverse rice accessions. Sequences flanking these loci were standardized across a wide range of rice genomes to produce optimal KASP designs. We selected 364 KASP designs to use for genotyping; they were either near to informative microsatellite markers, within the Badh2 and Waxy genes, or distributed throughout the rice genome. Genotypes for 327 KASP were obtained with 255 loci revealing polymorphism in up to 41 samples of approved Basmati varieties and 20 non-Basmati varieties. The varieties genotyped had not been used in the KASP design process. KASP were able to distinguish between commercial Basmati varieties that could not be distinguished with currently available microsatellites. Thirty-seven Basmati varieties could be distinguished from all others with 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. All of the KASP markers used in this study can be purchased from LGC Biosearch Technologies. These markers have potential to be used by industry for routine testing and regulation.
Highlights
Basmati is a type of long-grained fragrant rice, and only certain named varieties grown in specified regions of India and Pakistan are permitted to carry the name Basmati (Singh et al 2000)
Only samples that were both clearly visible on the gel and had measured concentrations of > 50 ng/ul were considered suitable for genotyping with KASP technology, and these were selected for use in the first KASP screen
This study used KASP markers to test 41 of the approved Basmati varieties listed in the 2017 Code of Practice (CoP) and demonstrated that they distinguish between more pairs of the approved Basmati varieties than has been previously possible with microsatellites (Nader et al 2019)
Summary
Basmati is a type of long-grained fragrant rice, and only certain named varieties grown in specified regions of India and Pakistan are permitted to carry the name Basmati (Singh et al 2000). Authorities in India and Pakistan have recently approved specific modern varieties derived from crosses with Basmati landraces to be sold labeled as Basmati if they conform to certain physical and aromatic characteristics (Mahajan et al 2018; Roy et al 2018).
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