Identification of Gene Associated with Sweetness in Corn (<i>Zea mays</i> L.) by Genome-Wide Association Study (GWAS) and Development of a Functional SNP Marker for Predicting Sweet Corn
Vinitchan Ruanjaichon | Kanogporn Khammona | Burin Thunnom | Khundej Suriharn | Chalong Kerdsri | Wanchana Aesomnuk | Arweewut Yongsuwan | Naraporn Chaomueang | Paradee Thammapichai | Siwaret Arikit | Samart Wanchana | Theerayut Toojinda
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 <i>p</i>-value of ≤1.53 × 10<sup>−14</sup>. The candidate gene identified within the linkage disequilibrium (LD) of this marker was <i>shrunken2</i> (Zm00001d044129; <i>sh2</i>), 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 <i>sh2</i> 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 <i>sh2</i>-based sweet corn from other types of corn. This functional marker is extremely useful for marker-assisted breeding in <i>sh2</i>-sweet corn improvement and marketable seed production.
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