Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds

Abstract

Sweet corn has become a popular food worldwide. It possesses six-times more sugar than field corn due to the presence of recessive shrunken2 (sh2) gene. Despite availability of diverse sweet corn germplasm, comprehensive characterization of sh2 has not been undertaken so far. Here, entire Sh2 gene (7320 bp) among five field corn-(Sh2Sh2) and six sweet corn-(sh2sh2) inbreds was sequenced. A total of 686 SNPs and 372 InDels were identified, of which three SNPs differentiated the wild-(Sh2) and mutant-(sh2) allele. Ten InDel markers were developed to assess sh2 gene-based diversity among 23 sweet corn and 25 field corn lines. Twenty-five alleles and 47 haplotypes of sh2 were identified among 48 inbreds. Among markers, MGU-InDel-2, MGU-InDel-3, MGU-InDel-5 and MGU-InDel-8 had PIC>0.5. Major allele frequency varied from 0.458–0.958. The gene sequence of these maize inbreds was compared with 25 orthologues of monocots. Sh2 gene possessed 15–18 exons with 6-225bp among maize, while it was 6–21 exons with 30-441bp among orthologues. While intron length across maize genotypes varied between 67-2069bp, the same among orthologues was 57–2713 bp. Sh2-encoded AGPase domain was more conserved than NTP transferase domain. Nucleotide and protein sequences of sh2 in maize and orthologues revealed that rice orthologue was closer to maize than other monocots. The study also provided details of motifs and domains present in sh2 gene, physicochemical properties and secondary structure of SH2 protein in maize inbreds and orthologues. This study reports detailed characterization and diversity analysis in sh2 gene of maize and related orthologues in various monocots.

Provitamin A, lysine and tryptophan enrichment in shrunken2-based sweet corn genotypes through genomics-assisted breeding for crtRB1 and opaque2 genes

“…Globally, the preference and demand of sweet corn has increased steadily in the last decade [17]. Sweet corn consumed as fresh at milky stage possesses nutritional bene ts for human health [13].…”

“…Mutant sh2-based sweet corn possesses six-fold higher sucrose and suitable for prolonged storage and transportation [16]. Large number of sh2-based sweet corn hybrids have been released for commercial cultivation worldwide [17].…”

Molecular Characterization and Haplotype Analysis of Low Phytic Acid-1 (lpa1) Gene Governing Accumulation of Kernel Phytic Acid in Subtropically-Adapted Maize

“…Of the 48 genotypes examined in the study formed 42 haplotypes. Chhabra et al [49] identified 44 haplotypes, Katral et al [52] identified 41 haplotypes and Chhabra et al [55] identified 47 haplotypes of 48 maize genotypes based on su1, Zmfatb and sh2 gene-based markers, respectively and Shin et al [56] identified 14 haplotypes of 15 sweet corn accessions using SNP based markers. Sequencing technologies has made it simpler to generate haplotype information, which aids in determining ancestry and demographic history [57].…”

Diversity of twenty-three sweet corn (Zea mays L. saccharata) varieties in Indonesia

“…However, only four genes are commonly used in sweet corn breeding: sh2 and bt2, which are categorized as 'super sweet' corn, and sugary-1 (su1) and sugary enhancer (se), which are categorized as general sweet corn (Santos et al 2014;Ojo et al 2020). Recessive sh2-based sweet corn genotypes, also known as 'extra sweet corn' or 'super sweet,' accumulate six times more sugar than normal corn at the milky ripe stage (Chhabra et al 2022) Sweet corn is one of the most famous vegetables in Asian countries like Indonesia (Dermail et al 2022), as it can be consumed fresh or processed as an ingredient for the food industry (Alan et al 2013). Sweet corn has the thirdlargest planted area of a vegetable in Indonesia, after chili peppers and shallots.…”