Identification of SNP core primer and establishment of high throughput detection scheme for purity identification in maize hybrids

Abstract

Purity is one of the most important indexes of maize seed quality, especially for inbred seedlings in hybrids which is a key factor affecting field yield. A new high-throughput and economical technology named KASP (Kompetitive allele specific PCR) is suitable for seed purity detection. This study was based on 12 sets of triplet samples of hybrids with their parents and 335 SNP fingerprint data which was nationally approved as standard samples of maize hybrids. Sixty candidate loci were selected from 384 SNP basic loci, and the success rate of transformation from chip to KASP primers was 95%. Considering comprehensive elements including parental complementary rate, polymorphism and other indicators such as stability and genotyping effect of primers, 20 core primers were finally determined for purity identification of maize hybrids. The results showed these core primers were able to effectively identify the purity of 99.7% of tested samples. The purity of tested sample Jingke 968 was identified by searching SNP-DNA fingerprint database and selecting parental complementary primers. One inbred seedling and two off-types were detected in 110 individuals, and the purity value was 97.3%. Meanwhile, a high-throughput purity detection scheme was established based on the core primers of purity identification for batch samples, which is fast, accurate, high-throughput and low-cost, providing more options of purity identification for government regulatory agencies and enterprises.