Fig. 6
Contributions of TraesCS1A02G064800 alleles to the length of the peduncle and the main shoot in RILs. a The associated signals on chromosome 1A. Red dots indicate the SNPs of the marker-trait associations above the significance threshold (− Log10[P-value] = 5.0). b Pairwise LD analysis. Local Manhattan plot (top) and LD heat map (bottom) surrounding the peak on chromosome 1A. Red color highlights the strong LD with the significant variants. Arrows indicate the four SNPs that were significantly (− Log10[P-value] > 5.0) associated with the traits and located in the exonic region of this gene TraesCS1A02G064800. c Gene structure and the haplotypes of TraesCS1A02G064800. Green rectangles and black lines indicate exons and introns, respectively. The gene is located on the reverse strand. The haplotypes were determined based on 306 worldwide wheat accessions. The SNPs of the haplotypes were indicated in c. d, e The differences of the length of the peduncle (d) and the main shoot (e) and among the four haplotypes (n = 59 accessions (Hap1), 93 accessions (Hap2), 88 accessions (Hap3), 53 accessions (Hap4) of TraesCS1A02G064800. Data are means ± SD (n = 5). Significant differences were determined by ANOVA. Different lowercase letters indicate significant differences (P < 0.05). f, g Contrast between original Zhongmai175 alleles (AA, long plants, RILlong) and Yanzhan4110 alleles (GG, short plants, RILshort) with respect to the length of the peduncle (f) and the main shoot (g). Data are shown as mean ± SD (n = 5). Significant differences were determined by Student’s t test (two sided)