Fig. 4. Haplotype analysis of six known candidate genes identified by GWAS. (a, c, e, g, i and k) haplotype analyses of OsTre6P (a), OsGH3.12 (c), OsPT10 (e), OsWRKY74 (g), OsCPK30 (i) and OsPT3 (k). A schematic diagram of each gene is shown on the top. Gray boxes indicate exons. (b, d, f, h, j and l) LD plots show association loci for OsTre6P (b), OsGH3.12 (d), OsPT10 (f), OsWRKY74 (h), OsCPK30 (j) and OsPT3 (l). The color of each SNP indicates the r2 value for the correlation with the lead SNP. Red and green color intensities indicate stronger and weaker LD (0 to 1). (m-r) Phenotypic variation of the haplotypes for OsTre6P (m), OsGH3.12 (n), OsPT10 (o), OsWRKY74 (p), OsCPK30 (q) and OsPT3 (r). Different letters indicate significant differences according to Duncan's least significant range test (p<0.05).
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