Extended Data Fig. 3: V and parchmentless pods.
a, Manhattan plot of GWAS analysis based on the ZW6 genome reference for a subset of accessions carrying only the R79* allele (haplotype 3 in Extended Data Fig. 2e) of gene Psat01G0420500 and wild type accessions (i.e. no v/v mutants), showing the P GWAS signal but not the V GWAS signal. b, Manhattan plot of GWAS analysis from a subset of accessions excluding those with haplotype 3 (Extended Data Fig. 2e) of gene Psat01G0420500 (i.e. no p/p but only the v/v mutants). This analysis shows only the V GWAS signal but not the P GWAS signal. c, Close-up view of the local details of the chromosome 5 GWAS peak corresponding to V. d, Genetic mapping of V vs v from previous studies36. e, Candidate genes (19) within the V genetic interval, with Psat05G0804500 (PsMYB26) highlighted in orange. f, Gene expression level in the pod tissues (8 days post flowering, three biological replicates for each sample) compared between the wild-type line (P/P V/V, JI1995) and the mutant line (P/P v/v, JI0074), across the 19 candidate genes under the interval. g, Allelic and haplotype variation in Psat05G0804500 (PsMYB26) across the diversity panel. All parchmentless accessions, except those carrying the R79* allele of P, are associated with a 23 kb Ogre retrotransposon element insertion. h, Gene expression patterns for the 19 candidate genes in various organs and developmental stages (three biological replicates for each sample) of Caméor, showing that Psat05G0804500 (PsMYB26) is expressed exclusively in pod and endocarp (red box). The normalization and statistical approach is the same as described in Extended Data Fig. 2h.
