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.
Lee et al. (Tue,) studied this question.