Molecular characterization, haplotype analysis and development of markers specific to gene regulating methionine accumulation in kernels of subtropical maize.

Unlabelled: Maize kernel protein is deficient in sulfur-containing essential amino acid such as methionine. The gene encodes methionine-rich 18-kDa δ-zein in maize kernels. In this study, we sequenced full-length of gene (820 bp) among 10 maize inbreds, revealing 43 SNPs and 22 (average length-7.58 bp). Three s (4 bp at 113th, 15 bp at 463rd and 3 bp at 615th position) distinguished the wild-type (functional) from the mutant (non-functional) allele of . The 4 bp (TTAT) insertion caused a frameshift mutation, resulting in truncated DZS18 protein. The 15 bp insertion (ATG-TCT-TCG-ATG-ATA) added methionine-serine-serine-methionine-isoleucine, while the 3 bp deletion (CAA) led to loss of a glutamine residue in the mutant allele. Three gene-based PCR markers were developed for diversity analysis of gene among 48 inbreds, which had an average methionine content of 0.136 %. (range: 0.031-0.340 %). Eight haplotypes were identified with methionine content varying from 0.066 % (Hap7) to 0.262 % (Hap3). Haplotypes with 4 bp deletion accumulated more methionine (0.174 %) than haplotypes with 4 bp insertion (0.082 %). The average methionine in 15 bp deletion and insertion haplotypes was 0.106 % and 0.150 %, respectively. The 3 bp insertion had 0.140 % methionine, while the deletion possessed 0.117 % methionine. Protein-protein association analysis predicted that DZS18 protein interacts with 19-kDa α-zein, 27- and 16-kDa γ-zeins, WAXY and O2 protein. A paralogue of gene with 74 % sequence identity was identified. The functional markers reported here could facilitate the development of high methionine maize cultivars, which holds great significance to combat malnutrition, especially in developing countries.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-024-04088-2.