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Maize (Zea mays) is the third major cereal crop in the Indian subcontinent, but the crop yields per hectare of Indian maize cultivars are less than half of the global average due to the impurity of seed lots supplied to farmers. In this study, we discovered high-quality Single Nucleotide Polymorphic markers (SNPs) in two widely cultivated maize hybrids and their parental inbreds. Paired-end double digest restriction site-associated DNA sequencing was used to discover SNPs and a total of 30,764,454 reads with a read length of 151 bp per sample were generated. Genotyping of SNPs for maize hybrids 'MAH 14-5' and 'Hema' revealed a total of 47,812 and 15,815 Genetic Purity Analysis markers, respectively, of which 44,388 and 12,391 were unique with 3,424 being common to both hybrids. Identified SNPs were used to develop primers for Kompetitive Allele-Specific PCR genotyping assays to determine the genetic purity of 10 seed lots and the results were found to correlate with Grow-out-Tests. Thus, the SNPs discovered in this study proved reliable to test the genetic purity of commercial seed lots. Advances in plant molecular breeding tools especially ddRADseq for SNP discovery offer new opportunities to genotype existing cultivars and accelerate the production of genetically pure seeds.

Summary Identification of rice genotypes is of prime importance to ensure quality seed, which is required for achieving global food demand. Three rice hybrids and their parental lines were identified on the basis of seed colour, seed size and 1000 seed weight, response to different chemicals (Phenol, Modified phenol with Copper sulphate or Ferrous sulphate, NaOH, GA3 and 2,4-D) and electrophoresis of soluble seed proteins (SDS-PAGE). All the genotypes were identified by using key based on seed colour, 1000 seed weight and seed size except for the female lines and their maintainers. No individual chemical test was able to distinguish all the genotypes. However, the combinations of different rapid chemical tests were useful in identification of individual genotypes. While all the cultivars were identified successfully by using electrophoresis of seed protein (SDS-PAGE) and hence it could be used as a powerful tool to identify every genotype in a short period of time.