Fig. 7

Haplotype analysis withinqPC1-7.1. A Local Manhattan plot and LD heat map for qPC1-7.1 on Chr 7. The red arrow (Top panel) indicates the position of LOC_Os07g02520/ Os07g0116300.B Structure and polymorphism of OsSAC1. Four haplotypes were detected in 147 aus accessions. In the rest of the accessions either of the SNPs were missing or in heterozygous condition. (C) Box plots show significant variation among the haplotypes for PC1 score and agronomic traits. Box edges represent the 0.25 and 0.75 quantiles, with the median values shown within boxes. Whiskers extend to the most extreme point, which is no more than 1.5 times the interquartile range. Differences between the haplotypes were statistically tested using Tukey’s test (*, **, ***, and **** represent P value < 0.05, < 0.01, < 0.001, and < 0.0001, respectively)