Fig. 3.

Analysis of DNA polymorphisms in the OsSAP16 gene. (A) The genome-wide association signal and the candidate gene LOC_Os07g38240 (OsSAP16) identified for LTGP on chromosome 7. (B) Protein structure of OsSAP16. OsSAP16 contains two AN1 and two C2H2 zinc finger domains. (C) Gene structure and haplotype analysis of OsSAP16 according to the three linked (r²>0.6) SNPs shown. Positions of SNPs were defined relative to the transcription start site of the gene. (D, E) Boxplots of LTGP based on haplotypes of OsSAP16. n, number of the accessions with a specific haplotype. The black horizontal lines represent the median values, the boxes represent the middle quartiles, and the whiskers are the range of data. Differences of haplotypes compared with Hap B (D) and Hap 1 (E) were analyzed by Welch’s t-test. *P<0.05; ns, not significant.