Sweetness is an economically important eating quality trait for sweet-corn breeding. To investigate the genetic control of the sweetness trait, we conducted a genome-wide association study (GWAS) in an association panel consisting of 250 sweet corn and waxy corn inbred and recombinant inbred lines (RILs), together with the genotypes obtained from the high-density 600K maize genotyping single-nucleotide polymorphism (SNP) array. GWAS results identified 12 significantly associated SNPs on chromosomes 3, 4, 5, and 7. The most associated SNP, AX_91849634, was found on chromosome 3 with a highly significant p-value of ≤1.53 × 10⁻¹⁴. The candidate gene identified within the linkage disequilibrium (LD) of this marker was shrunken2 (Zm00001d044129; sh2), which encodes ADP-glucose pyrophosphorylase (AGPase), a 60 kDa subunit enzyme that affects starch metabolism in the maize endosperm. Several SNP markers specific to variants in sh2 were developed and validated. According to the validation in a set of 81 inbred, RIL, and popular corn varieties, marker Sh2_rs844805326, which was developed on the basis of the SNP at the position 154 of exon 1, was highly efficient in classifying sh2-based sweet corn from other types of corn. This functional marker is extremely useful for marker-assisted breeding in sh2-sweet corn improvement and marketable seed production.

Waxy maize (Zea mays L. var. ceratina) is a special type of maize characterized by a sticky texture when cooked, due to high amylopectin content in the endosperm. Waxy maize is popular in China and Southeast Asia for fresh consumption. Breeding strategies have been used to improve the quality of waxy maize, including hybrid breeding by crossing super sweet maize and waxy maize. However, the lack of a marker has limited the efficiency of breeding for the waxy trait, especially because the waxy allele is recessive. In this study, we conducted a genome-wide association study (GWAS) in an association panel consisting of 213 inbred lines and recombinant inbred lines (RILs) of field maize and waxy maize to identify loci associated with the waxy kernel phenotype. The genotypic data were 155,768 SNPs derived from the high-density 600 K maize genotyping array for single-nucleotide polymorphisms (SNPs). The GWAS results identified the qWx9 locus on chromosome 9 (25.06–25.18 Mb) associated with the trait. Based on the most significantly associated SNP (AX-90613979, −log10(P) = 6.8)), which was located on Wx1, a MassArray marker was developed and validated in a panel of 139 maize lines containing waxy maize and sweet maize with different amylose content. The newly developed marker had a significant association with amylose content (R² value of 0.81, p < 0.001) and clearly distinguished between waxy maize and sweet maize lines that had different amylose content. This marker will be useful for maize breeding programs for the waxy trait, as well as for breeding programs for hybrid maize combining the sweetness and waxy traits. The gene-based SNP markers could aid breeders by eliminating the costs and time required to perform lengthy field trials and help to accelerate sweet maize and waxy maize breeding programs.