Fig. 6

Haplotype analysis withinqPC2-1.1. A Local Manhattan plot and LD heat map for qPC2-1.1 on Chr 1. The red arrow (Top panel) indicates the position of OsGLT1.B LD heat map of LOC_Os01g48960. C Structure and DNA polymorphism of OsGLT1. D Box plots of PC2 score and agro-morphological traits for three haplotypes Hap-1 (n = 9), Hap-2 (n = 126) and Hap-3 (n = 6) of OsGLT1. E Box plots of PC2 score and agro-morphological traits for three haplotypes Hap-1 (n = 116), Hap-2 (n = 11) and Hap-3 (n = 7) of OsPUP4. 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 multiple comparisons with Tukey’s t test (ns, not significant, *, **, ***, and **** represent P value < 0.05, < 0.01, < 0.001, and < 0.0001, respectively)