Figure 5
Linkage disequilibrium plot of indel association with grain length (GL) on chromosome 3 in indica. Linkage disequilibrium analysis using indels (A) revealed so much variability in this 300 kb region. Eight LD blocks were formed most not exceeding 25 kb. The bar plots show that three of the five indels with the highest likelihood of association were within the vicinity of LOC_Os03g29710 and LOC_Os03g29730. The bar plots also show that indels within the vicinity of these two genes have contrasting effects to the phenotype (black implies positive additive effect, while red is the reverse). All the others decreased grain length. The widths of the bars indicated the relative effect of the alleles. INDEL_03_16927812 and INDEL_03_16930922 were outside the genic region of LOC_Os03g27910 (B). Grain length distribution for both raw and cooked grains showed that CA allele of the indel associates with GL > 6.0 mm and GLc > 11 mm. (C) Targeted association with GL and GLc using indels at the control region of LOC_Os03g29730 and an intronic indel (C) showed that CAGAT was able to discriminate 81 accessions that had ~6.3 mm and ~11mm GL and GLc, respectively, from the rest.
