Hyeon Park

Domestication has profoundly shaped the phenotypic differentiation and genetic architecture of Perilla. However, analyses of the morphological difference between its cultivated and weedy forms across its varieties remains incomplete. This study analyzed morphological variation, genetic diversity, population structure, and marker–trait associations of 45 accessions representing the cultivated and weedy forms of two Perilla varieties (P. frutescens var. frutescens and var. crispa) collected from South Korea and Japan. Analyses of ten qualitative and quantitative agronomic traits revealed clear domestication-related differentiation. Cultivated var. frutescens showed larger and heavier seeds, whereas cultivated var. crispa and the weedy accessions were characterized by longer inflorescences and higher floret numbers but smaller seeds. Strong positive correlations were observed among seed-related traits, particularly between seed size and seed weight (r = 0.932), indicating coordinated selection of seed traits. Genetic diversity analysis using 70 SSR markers identified 330 alleles consistent with domestication bottlenecks in cultivated forms while higher diversity was generally retained in the weedy accessions. Population structure, UPGMA clustering, and principal coordinate analyses broadly differentiated the cultivated and weedy accessions, although partial admixture indicated shared ancestry and historical gene flow. Association mapping using Q-based GLM and Q + K MLM models identified 23 significant marker–trait associations involving 16 SSR markers consistently detected across both models. Several markers were associated with multiple traits, implying pleiotropy or tight genetic linkage. Notably, five SSR markers (KNUPF192, KNUPF202, KNUPF207, KNUPF230, and KNUPF238) may represent potential candidate loci for marker-assisted selection to improve seed-related traits in var. frutescens and leaf-related traits in var. crispa.

This study evaluated morphological variation in 45 accessions of cultivated Perilla frutescens var. frutescens (PFF) and var. crispa (PFC) collected from South Korea and Japan, together with their weedy counterparts, var. frutescens (WPFF) and var. crispa (WPFC) from South Korea, using ten quantitative and ten qualitative traits. Clear morphological differentiation was observed between cultivated and weedy forms in both varieties, particularly in pigmentation, plant fragrance, and seed-related traits. PFF cultivars were characterized by predominantly green pigmentation, a typical frutescens aroma, and significantly larger and heavier seeds, suggesting stronger phenotypic differentiation in leaf and seed utilization. In contrast, PFC cultivars showed substantial morphological overlap with WPFC and WPFF accessions, indicating comparatively weaker phenotypic differentiation. Principal component analysis showed that the first principal component (PC1) explained 25.7% of the total phenotypic variance and was strongly associated with five quantitative traits (plant height, inflorescence length, floret number, seed size, and 100-seed weight) and five qualitative traits (adaxial and abaxial leaf color, flower color, seed color, and seed hardness). Along PC1, PFF cultivars formed a well-defined cluster, whereas PFC cultivars and the weedy WPFF and WPFC accessions exhibited broader dispersion, reflecting greater morphological variability. These results provide morphological insights into the differentiation between cultivated and weedy Perilla accessions and indicate potential domestication-related patterns. However, these interpretations are based primarily on morphological observations, and further genetic and evolutionary studies will be necessary to clarify the domestication history of these taxa. The identified trait complexes provide a useful phenotypic foundation for marker-assisted breeding, informed cultivar selection, and effective germplasm conservation and management.

To identify SSR markers associated with both quantitative and qualitative traits in Perilla, we analyzed a total of 68 individuals from an F₂ population derived from a cross between WPC06-339 (weedy var. crispa) and WPF17-049 (weedy var. frutescens) using 40 SSR primer sets. The genetic diversity of these markers ranged from 0.464 to 0.676, with a mean value of 0.607. Correlation analysis of 13 morphological traits (4 qualitative, 9 quantitative) revealed significant positive correlations among three leaf-related traits and two inflorescence-related traits. Association analysis involving 40 SSR markers and the 13 morphological traits identified 39 significant marker–trait associations, comprising 18 SSR markers associated with 11 morphological traits. Among these SSR markers, 12 were associated with two to five quantitative or qualitative traits. Additionally, 10 SSR markers were significantly associated with three qualitative traits, while 15 SSR markers were associated with eight quantitative traits. Notably, GBPFM179, KNUPF59, and KNUPF167 were significantly associated with multiple quantitative or qualitative traits. GBPFM179 and KNUPF182 exhibited the highest R² values, of 0.38, for stem color and days to maturity, respectively. These SSR markers demonstrate the potential for use in marker-assisted selection in Perilla breeding programs aimed at enhancing leaf or seed productivity through the selection of both quantitative and qualitative traits.

Waxy maize is mainly cultivated in South Korea for the production of food and snacks, and colored maize with increased anthocyanin content is used in the production of functional foods and medicinal products. Association mapping analysis (AMA) is supported as the preferred method for identifying genetic markers associated with complex traits. Our study aimed to identify molecular markers associated with two anthocyanin content and six seed coat color traits in near-isogenic lines (NILs) of colored waxy maize assessed through AMA. We performed AMA for 285 SSR loci and two anthocyanin content and six seed coat color traits in 10 NILs of colored waxy maize. In the analysis of population structure and cluster formation, the two parental lines (HW3, HW9) of “Mibaek 2ho” variety waxy maize and the 10 NILs were clearly divided into two groups, with each group containing one of the two parental inbred lines. In the AMA, 62 SSR markers were associated with two seed anthocyanin content and six seed coat color traits in the 10 NILs. All the anthocyanin content and seed coat color traits were associated with SSR markers, ranging from 2 to 12 SSR markers per characteristic. The 12 SSR markers were together associated with both of the two anthocyanin content (kuromanin and peonidin) traits. Our current results demonstrate the effectiveness of SSR analysis for the examination of genetic diversity, relationships, and population structure and AMA in 10 NILs of colored waxy maize and the two parental lines of the “Mibaek 2ho” variety waxy maize.

Globally, maize is one of the most consumed crops along with rice and wheat. However, maize is sensitive to different abiotic stress factors, such as drought, which have a significant impact on its production. The aims of this study were to investigate (1) genetic variation among 41 maize-inbred lines and the relationships among them and (2) significant marker–trait associations (SMTAs) between 7 selected physiochemical traits and 200 simple sequence repeat (SSR) markers to examine the genetics of these traits. A total of 1023 alleles were identified among the 41 maize-inbred lines using the 200 SSR loci, with a mean of 5.1 alleles per locus. The average major allele frequency, gene diversity, and polymorphism information content were 0.498, 0.627, and 0.579, respectively. The population structure analysis based on the 200 SSR loci divided the maize germplasm into two primary groups with an admixed group. Moreover, this study identified, respectively, 85 SMTAs and 31 SMTAs using a general linear model (Q GLM) and a mixed linear model (Q + K MLM) with statistically significant (p < 0.05 and <0.01) associations with the seven physiochemical traits (caffeic acid content, chlorogenic acid content, gallic acid content, ferulic acid content, 2,2-diphenyl-1-picrylhydrazyl free radical scavenging activity, leaf relative moisture content, total phenolic content). These SSR markers were highly correlated with one or more of the seven physiochemical traits. This study provides insights into the genetics of the 41 maize-inbred lines and their seven physiochemical traits and will be of assistance to breeders in the marker-assisted selection of maize for breeding programs.

Despite being the third most-consumed crop, maize (Zea mays L.) is highly vulnerable to drought stress. The predominant secondary metabolite in plants is phenolic acids, which scavenge reactive oxygen species to minimize oxidative stress under drought stress. Herein, the effect of carbon nanodots (CND) and manganese ferrite (MnFe₂O₄) nanoparticles (NP) on the drought stress tolerance of maize has been studied. The experimental results revealed that the highest leaf blade length (54.0 cm) and width (3.9 cm), root length (45.2 cm), stem diameter (11.1 mm), root fresh weight (7.0 g), leaf relative water content (84.8%) and chlorogenic (8.7 µg/mL), caffeic (3.0 µg/mL) and syringic acid (1.0 µg/mL) contents were demonstrated by CND-treated (10 mg L⁻¹) inbred lines (GP5, HW19, HCW2, 17YS6032, HCW3, HCW4, HW7, HCW2, and 16S8068-9, respectively). However, the highest shoot length (71.5 cm), leaf moisture content (83.9%), shoot fresh weight (12.5 g), chlorophyll content (47.3), and DPPH free radical scavenging activity (34.1%) were observed in MnFe₂O₄ NP-treated (300 mg L⁻¹) HF12, HW15, 11BS8016-7, HW15, HW12, and KW7 lines, respectively. The results indicate that CND and MnFe₂O₄ NP can mitigate drought stress effects on different accessions of the given population, as corroborated by improvements in growth and physio-biochemical traits among several inbred lines of maize.