European Journal of Sustainable Agroecosystems

Early growth vigor is vital agronomic quality in rice (Oryza sativa L.) that relates directly to seedling establishment, competitive abilities, and total output of crop production, in various environmental conditions. Grasping genetic architecture of early vigor is vital in creation of better rice varieties through genomic selection and marker-assisted breeding approach. The present genome-wide association study (GWAS) assessed genetic reasons for multiple early vigor qualities in 312 rice varieties that underwent genotyping with 35,847 high-quality SNPs. Field studies executed in two planting periods aimed to record seedling emergence, germination rate, shoot and root length, seedling weight, leaf area, initial height of plant, and seedling vigor index. Analysis of population structure specified three major genetic population, implying sufficient genetic differentiation. LD analysis presented rapid LD decay of about 200 kb, enough for accurate marker-trait association mapping. GWAS identified 47 significant loci for early vigor traits (P < 5 × 10⁻⁸, FDR corrected) using a mixed linear model approach correcting for population structure and kinship. Annotation of candidate genes revealed 92 genes with putative functions in pathways of seedling development, root morphogenesis, carbohydrate metabolism and stress response. Consistent effects of candidate genes across environments were found for OsJAZ1 (jasmonic acid signaling), OsLEA3 (drought stress response) and OsNAC4 (transcriptional regulation). Functional genomic data integration, network analysis and comparative mapping confirmed biological relevance of the identified loci. This large-scale GWAS study provides valuable genomic resources and validated markers for genomic selection in rice breeding programs to develop climate-resilient varieties with improved early establishment and higher grain yield potential.