Fig. 5. Haplotype analysis of the unknown candidate genes identified by GWAS. (a, c, e, g, i and k) haplotype analyses of LOC_Os11g12530 (a), LOC_Os02g42820 (c), LOC_Os11g17600 (e), LOC_Os02g16040 (g), LOC_Os07g11310 (i), and LOC_Os02g16940 (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 LOC_Os11g12530 (b), LOC_Os02g42820 (d), LOC_Os11g17600 (f), LOC_Os02g16040 (h), LOC_Os07g11310 (j), and LOC_Os02g16940 (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 LOC_Os11g12530 (m), LOC_Os02g42820 (n), LOC_Os11g17600 (o), LOC_Os02g16040 (p), LOC_Os07g11310 (q), and LOC_Os02g16940 (r). Different letters indicate significant differences according to Duncan's least significant range test (p<0.05).
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