Functional markers (FMs) are derived from polymorphisms that confer phenotypic trait variation, making them powerful tools in plant breeding. Unlike random markers, for which trait associations are unknown, or at best established via linkage or quantitative trait locus (QTL) analysis, FMs are associated with causative polymorphisms, providing precise and reliable information for trait selection. Since the concept of FMs was first proposed in 2003, the emergence and adoption of technologies that were not available at the time have significantly advanced FM discovery and application by enhancing the ability to precisely identify causal variants underlying complex traits, which is a critical prerequisite for FM development. Novel technologies such as high-throughput sequencing, multi-omics, gene editing, and advanced computational tools have enabled the precise identification and functional validation of DNA polymorphisms associated with trait variation. FMs can be used in genomic selection (GS) and modern plant breeding programs by improving selection efficiency and accuracy. While FMs provide numerous benefits, challenges still remain regarding their stability and transferability, and innovative approaches to overcome these limitations are continually being explored. The role of FMs in plant breeding is expected to grow as functional annotation of genomes improves and technologies like genome editing become more accessible. These developments will enable breeders to effectively integrate FMs into breeding pipelines for accelerating genetic gains and addressing global agricultural challenges.

Breeding for stress-tolerant hybrids begins with screening germplasm for tolerant genotypes. We employed a non-destructive and objective method to evaluate the low-temperature response of sweet corns at the seedling stage, using a digital image analysis. It was estimated using summed leaf area, a new parameter defined as the sum of the leaf area measured from images taken at different angles. The summed leaf area, SPAD, shoot and root fresh weight, and total root length were significantly different among hybrids. The group mean of sugary endosperm type was significantly higher than that of shrunken type for all traits but SPAD. For the summed leaf area, the top three ranked hybrids were from the sugary type, but the area for the following three hybrids from the shrunken type did not differ from that for the first three hybrids. The summed leaf area was correlated with SPAD (r = 0.49 **), shoot (r = 0.99 **) and root (r = 0.93 **) fresh weight, and total root length (r = 0.76 **). Phytoglycogen in seeds only had a significant correlation (r = 0.46 **) with the area. The summed leaf area of only one hybrid differed between normal- and low-temperature conditions. The low-temperature response based on the summed leaf area was reflected in the field condition, with a few exceptions. The results suggest that the summed leaf area via digital image analysis can be used to evaluate low-temperature response in sweet corns.