Identification of genetic loci associated with flavonoid content in sweet corn across different populations and environments

Flavonoids are crucial for plant growth and development and serve as key indicators of high-quality sweet corn. To understand the genetic basis of flavonoid content variation in sweet corn, we conducted quantitative trait locus (QTL) mapping for six flavonoids (dihydrokaempferol, quercetin, apigenin, kaempferol, isoquercitrin, and naringenin) in two environments. Two linkage maps were used: one was constructed from the introgression line (IL) population developed from sweet corn inbred lines “HZ11” and “ZX127,” with 167 pairs of polymorphic simple repeat sequence (SSR) markers and a total length of 3264.08 cM; another linkage map was constructed from a recombinant inbred line (RIL) population derived from a cross between K44 and F22, with 175 pairs of SSR markers and a length of 4322.37 cM. In this study, 145 flavonoid-related QTLs were detected. The proportion of phenotypic variance explained by individual QTLs ranged from 0.24 to 16.03%. Notably, six QTLs (qQUE2.1a, qAPI2.1a, qAPI4.1a, qISO2a, qNAR7.2a, and qNAR8a) were detected in the IL population across both environments. Only one QTL in the RIL population, namely, qKAE1d, was the main QTL controlling KAE, with explaining 16.03% phenotypic variation. Seven stable QTL clusters were detected on Chr 2, Chr 4, Chr 7, Chr 8, and Chr 9, respectively. This suggested that these clusters are responsible for controlling flavonoid QTLs in sweet corn. These findings provided a basis for nutritional quality improvement of sweet corn using marker-assisted selection breeding.