SNP genotyping of maize (Zea mays) hybrids and parental inbred lines for genetic purity testing using double digest restriction site-associated DNA sequencing

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.