SEQUENCE VARIATIONS ASSOCIATED WITH NOVEL PURPLE-PERICARP SUPER-SWEETCORN COMPARED TO ITS PURPLE-PERICARP MAIZE AND WHITE SUPER-SWEETCORN PARENTS

Abstract

Recently, a novel purple-pericarp super-sweetcorn line, Tim1 (A1A1.sh2sh2) is derived from the purple-pericarp maize Costa Rica (A1Sh2.A1Sh2) and white shrunken2 (sh2) super-sweetcorn Tims-white (a1sh2.a1sh2), however information regarding purple colour controlling anthocyanin biosynthesis genes and sweetcorn gene is lacking. Specific sequence differences in the CDS (coding DNA sequence) and promoter regions of the anthocyanin biosynthesis structural genes, anthocyanin1 (A1), purple aleurone1 (Pr1) and regulatory genes, purple plant1 (Pl1), plant colour1 (B1), coloured1 (R1), and the sweetcorn structural gene, shrunken2 (sh2) were investigated using the publicly available annotated yellow starchy maize, B73 (NAM5.0) as a reference genome. In the CDS region, the A1, Pl1 and R1 gene sequence differences of Tim1 and Costa Rica were similar, as they control purple-pericarp pigmentation, however the B1 gene showed similarity between the Tim1 and Tims-white lines, which may indicate that it does not have a role in controlling pericarp colour, unlike a previous study. In case of Pr1 gene, unlike Costa Rica, 6- and 8-bp dinucleotide (TA) repeats were observed in the promoter region of the Tims-white and Tim1 lines, respectively, indicating the defective functionality (redder colour in Tim1 than purple in Costa Rica) of the recessive pr1 allele. In the sweetcorn structural gene (sh2), sequence similarity was observed between purple-sweet Tim1 and its white-sweet parent Tims-white, as both display a shrunken phenotype in their mature kernels. These findings revealed that the developed purple-sweet line is different than the reference yellow-nonsweet line regarding both the anthocyanin biosynthesis and sweetcorn genes.