Figure 4.

Identification of OsML1 for mesocotyl length in qFML3-2. (A) Genome-wide association signals in the region at 30.3–30.9 Mb on chromosome 3 and LD heatmap (bottom) for 28 non-synonymous SNPs (colored red) with different alleles between parents of known bi-parental maps. Blue arrow indicates possible functional locus in OsML1 (LOC_Os03g53320). Triangular block shows region with strong local LD (r² > 0.6). (B) Expression analysis of OsML1 in the mesocotyls from 6 accessions with long- and short-mesocotyls. Names and ML of accessions are plotted on the X-axis. Red and blue bars show long- and short-mesocotyl accessions, respectively. Data represent means ±s.d (n = 3). Asterisks represent significant differences between accessions with long- and short-mesocotyls (^**p < 0.01, Student's t test). (C) Structure of OsML1 showing non-synonymous SNPs and amino acid polymorphisms. (D) Haplotype analysis of two non-synonymous SNPs in OsML1. Red arrow indicates possible functional locus. (E) Comparison of ML among haplotypes of OsML1 in indica and japonica. Accessions with haplotype colored red had significantly longer mesocotyls than members of haplotypes colored green.