Extended Data Fig. 7: GWAS for coumarins and identification of the candidate gene GhF6’H1. | Nature Genetics

Extended Data Fig. 7: GWAS for coumarins and identification of the candidate gene GhF6’H1.

From: Integrated metabolomic and transcriptomic analyses identify MYB genes regulating key metabolites and agronomic traits in upland cotton Gossypium hirsutum

Extended Data Fig. 7: GWAS for coumarins and identification of the candidate gene GhF6’H1.

a, Manhattan plots showing the SV-GWAS and SNP-GWAS results for scopoline (mws1077_P), scopoletin (pme2993), and scoparone (pme3569). The red rectangle denotes the genomic location of the trait locus on chromosome D08. Comparison of the relative content of three metabolites between two haplotypes. b, Local Manhattan plot (top) and LD heat map (bottom) between 65,705,310 and 65,723,000 bp. The statistical analysis was performed with Bonferroni correction. c, Haplotypes of coumarin locus in the 403 panel. d, Comparison of GhF6’H1 expression between the two haplotypes. n represents the sample size in each haplotype. Box limits and center lines indicate quartiles and medians, respectively, whiskers denote 1.5× interquartile range and points show outliers (a, d). Significances are tested by the two-tailed Student’s t-test (a, d). e, Association between D08 haplotypes and genotypes of the 9.3 kb deletion (DEL) and SNP in the GWAS population. The mapping reads were analyzed using both manual observation (IGV) and software (DELLY).

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