Sequence variations associated with novel purple-pericarp super-sweetcorn compared to its purple-pericarp maize and white super-sweetcorn parents

• Published in: Molecular genetics and genomics : MGG Vol. 298; no. 6; pp. 1395 - 1405
• Main Authors: Anirban, Apurba, Masouleh, Ardashir Kharabian, Henry, Robert J., O’Hare, Tim J.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-11-2023; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Anthocyanins; Anthocyanins - genetics; B1 gene; Biochemistry; Biomedical and Life Sciences; Biosynthesis; Corn; Gene Expression Regulation, Plant; Genes; Genomes; Human Genetics; Life Sciences; Microbial Genetics and Genomics; Nucleotide sequence; Original Article; Pericarp; Phenotype; Phenotypes; Pigmentation; Pigmentation - genetics; Plant Genetics and Genomics; Plant Proteins - genetics; Plant Proteins - metabolism; Sweet taste; Sweetness; Zea mays - genetics; Zea mays - metabolism; Costa Rica; InDel; Maize; Purple sweetcorn; SNP; shrunken2
• ISSN: 1617-4615; 1617-4623
• DOI: 10.1007/s00438-023-02060-y

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.