Fig. 3

PAV-GWAS for agronomic traits. a PAV-GWAS for Verticillium wilt resistance, and the threshold of P value was set as 0.01. b VIGS assay on GhNAC083. c Genomic annotation for trait-related PAVs. d Concept illustration for consistent and conflict SV-Gene expression-Phenotype triplets. e Display of Parent#1_DEL_2442 and Parent#2_DEL_5283. The alignment of long reads from Parent#1 and Parent#2 were displayed in IGV toolkit. f Fiber length divergence of 2 genotypes compared to CRI12-like genotypes in Wang_2017 cohort (n = 169). Boxplot center, median; bounds of box, lower quartile (Q1) and upper quartile (Q3); minima, Q1 − 1.5 (Q1–Q3); maxima, Q1 + 1.5 (Q1–Q3). The dots represent for original values. P values were calculated by t-test and “**” represent for P ≤ 0.01. g Gene expression of GhKCR1A and GhKCR1D in wang_2017 cohort (n = 169). X-axis was the rank of fiber length (from short to long; divided into quartiles). Y-axes are TPM (transcripts per million mapped reads) of GhKCR1A and GhKCR1D, respectively. The description of boxes is the same as that in f, and “***” represents for P ≤ 0.001 in t-test. h Illustration for prediction of agronomic trait based on functional variations by support vector regression. i Pearson correlation between predicted phenotype and real phenotype