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) was derived from the purple-pericarp maize 'Costa Rica' (A1Sh2.A1Sh2) and white shrunken2 (sh2) super-sweetcorn 'Tims-white' (a1sh2.a1sh2), however, information regarding anthocyanin biosynthesis genes controlling purple colour and sweetness 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 the report of a previous study. In the case of the Pr1 gene, in contrast to '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' rather than purple in 'Costa Rica') of the recessive pr1 allele. In sweetcorn, the structural gene (sh2), sequence showed similarity 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 to the reference yellow-nonsweet line in both the anthocyanin biosynthesis and sweetcorn genes.

Keywords: InDel; Maize; Purple sweetcorn; SNP; shrunken2.

Fig. 1

Seeds and plants of ‘Costa Rica’, ‘Tims-white’, and ‘Tim1’ used in field experiments and DNA re-sequencing: A ‘Costa Rica’ cob with purple-pericarp starchy (non-sweet) round kernels, B ‘Costa Rica’ plant, C ‘Tims-white’ cob with white-pericarp non-starchy (sweet) kernels, D ‘Tims-white’ plant, E ‘Tim1’ cob with purple-pericarp non-starchy (sweet) kernels, F ‘Tim1’ plant, G Flow chart showing the purple-pericarp super-sweetcorn development scheme, from the initial cross to the development of the F6 progeny; H DNA re-sequencing by Illumina NovaSeq

Fig. 2

SNPs in the structural genes: A A single homozygous non-synonymous SNP common in ‘Tim1’ and ‘Costa Rica’ in the structural gene A1 (anthocyanin1), and B A single homozygous non-synonymous SNP common between ‘Tim1’ and ‘Tims-white’ in the structural gene sh2 (shrunken2)

Fig. 3

SNPs in the regulatory genes: A A single homozygous nonsynonymous SNP common between ‘Tim1’ and ‘Costa Rica’ in the regulatory gene Pl1 (purple plant1); B Three common heterozygous nonsynonymous SNPs between ‘Tim1’ and ‘Costa Rica’ in the regulatory gene Pl1; C A six bp deletion in the CDS region of both in ‘Tim1’ and ‘Costa Rica’ in the regulatory gene Pl1, Deletion is indicated by a red circle; D A single heterozygous nonsynonymous SNP common between ‘Tim1’ and ‘Costa Rica’ in the regulatory gene R1 (coloured1); and E Two common homozygous nonsynonymous SNPs between ‘Tim1’ and ‘Tims-white’ in the regulatory gene B1 (plant colour1)

Fig. 4

Dinucleotide (TA) repeats in the pr1 gene present in ‘Tim1’ and ‘Tims-white’ lines. Red boxes indicate TA repeats in ‘Tim1’, and green box indicates TA repeats in ‘Tims-white’