Haplotype analyses of five QTL genes for root length.

Gene structures (left) and root lengths of different haplotypes (right) of (A) OsRL3.3 (LOC_Os03g50350) for qRL3-3, (B) OsSIZ2 (LOC_Os03g50980) for qRL3-3, (C) OsRL7.1 (LOC_Os07g03160) for qRL7-1, (D) OsRL11.1 (LOC_Os11g43320) for qRL11-1, (E) OsRL8.2 (LOC_Os08g43040) for qRL8-2, where red colored numbers show the key positions where amino acid substitutions occurred among major haplotypes, that resulted in significant differences in root length; among violin maps of different haplotypes in subpopulations japonica (upper right) and indica (lower right), different letters above the violins indicate significant differences (P < 0.05) when analyzed by Duncan’s test or independent-sample t-tests.