Fig. 1. Salt stress-induced phenotypic and molecular variation in Pokkali, Kaituodao, and Giza 176. A, Phenotypic characteristics of three rice varieties (Pokkali, Kaituodao, and Giza 176) grown under control (CK) and salt stress (ST, 100 mmol/L NaCl) conditions for one week and two weeks. Scale bars, 10 cm. B, Hierarchical clustering of the top 50 differentially expressed genes (DEGs) related to salt stress. Clustering was based on Fragments Per Kilobase of transcript per Million mapped reads (FPKM)-normalized, log2-transformed expression values. The heatmap shows global expression patterns across genotypes, treatments, and time points. CK, Control; ST, Salt stress; p1, k1, and g1 represent Pokkali, Kaituodao, and Giza 176 after one-week salt stress; p2, k2, and g2 represent Pokkali, Kaituodao, and Giza 176 after two-week salt stress. C, Venn diagrams showing the overlap of DEGs among varieties at one week and two weeks. Comparisons include P1 (CKp1 vs STp1), K1 (CKk1 vs STk1), G1 (CKg1 vs STg1), and P2 (CKp2 vs STp2), K2 (CKk2 vs STk2), G2 (CKg2 vs STg2). D, Relative expression of five salt-responsive genes in the three varieties under CK and ST conditions, validated by qRT-PCR. Leaf tissues were collected from plants after one-week (1W) and two-week (2W) stress, with Actin used as the internal reference gene for data normalization. Treatments include 1W CK, 2W CK, 1W ST, and 2W ST. Data are mean ± SD (n = 3). Different lowercase letters represent significant differences at the 0.05 level by the Duncan’s multiple range test (DMRT). E, Haplotype (HAP) analysis of OsMKK4 and OsIPK, showing single nucleotide polymorphisms and Insertions/Deletions between Hap.1 (Reference, 9311) and Hap.2 (Giza 176 allele).