Figure 5.

Identification of OsML2 for mesocotyl length. (A) Genome-wide association signals (top) in the region 13.4–16.4 Mb on chromosome 7 and LD heatmap (bottom) of 10 non-synonymous SNPs above the threshold. A total of 10 red points show non-synonymous SNPs above threshold in qFML7-2, qFML7-3 and qFML7-4, and blue arrow indicates possible functional locus in OsML2 (LOC_Os07g24010). Triangular block (named Block 1) shows region with strong local LD (r² > 0.6). (B) Haplotype analysis (left) of 7 non-synonymous SNPs above threshold in Block 1 and comparison of ML (right) among haplotypes in indica and japonica. Different letters above the violins indicate significant differences (p < 0.05) when analyzed by Duncan's test. Red arrow indicates possible functional locus. (C) Independent-sample T-tests for ML differences between alleles of each of the 6 non-synonymous SNPs in Block 1 using accessions carrying allele (A) of the peak signal (Chr7_13611491). Data in parentheses show number of accessions. Manhattan plots for ML in Block 1 using (D) 373 accessions and (E) 222 indica accessions carrying allele (A) of the peak signal. Red points show 6 non-synonymous SNPs in Block 1. (F) Expression analysis of OsML2 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). (G) Haplotype analysis (left) of 12 non-synonymous SNPs in OsML2 and comparison of ML (right) among haplotypes of OsML2 in indica and japonica, respectively. Different letters above the violins indicate significant differences (p < 0.05) detected by Duncan's test.