Extended Data Fig. 10: GWAS identification of TSH4 as a candidate gene for tassel branch number (TBN) variation.
From: Genome-wide selection and genetic improvement during modern maize breeding
a, Manhattan plot (upper left) and LD heat map (lower left) for GWAS signal TBN_7_133305039. SNP and indel based association analysis results are shown as blue and orange dots in the Manhattan plot, respectively. Peak markers and putative causal polymorphisms are circled and their positions in LD heat map are indicated by red lines. The candidate gene position in Manhattan plot is showed as red arrows. The significantly associated SNP (chr7_133305039, P = 6.83 × 10–8) and indel (chr7_133209283_C/CT, 1-bp deletion, P = 1.86 × 10–5) were strongly correlated (r2 = 0.53). b, Candidate gene structure and polymorphisms of chr7_133209283_C/CT. c, d, Phenotype of different haplotypes (c, box plot) and haplotype frequency changes during breeding (d, bar plot), for the association signal of chr7_133209283_C/CT.
