Fig. 7

Genome-wide association study using antibacterial activities of rice seed crude extracts from 107 accessions of landraces from WRC and JRC as phenotype data. a–c Manhattan and Quantile–quantile plots of SNPs associated with antibacterial activity in 80% Methanol extracts from husk (a), acetone extracts from brown rice (b), and 80% Methanol extracts from husk (c). d–g Upper panels show box plot of relative growth rate of E. coli for acetone extracts from brown rice of WRC and JRC accessions with different haplotypes. Lower panels show the LD blocks which carry highly associated SNPs. The accessions were clasified into two haplotypes according to the highest associated SNP in each LD block at chr. 3 (d), chr. 4 (e), chr. 7 (f), and chr. 9 (g). In the upper panels, x axis indicates haplotype and y axis indicates relative growth rate of E. coli, which represents the antibacterial activity of the sample extracts. ***p < 0.001 (Student’s t-test)