Extended Data Fig. 2: Gene identity and functional variation underlying parchmentless pods (P vs. p).
a, Manhattan plot from GWAS analysis for the parchmentless pod trait, based on the ZW6 genome reference. b, Close-up view of the Manhattan plot in the most significant region identified in panel a. c, F2 genetic mapping interval derived from the cross JI2822 x JI0816, showing the mapped locus between markers AX-183563747 and AX-183563750 (chr1: 380,049,894-380,967,975) (Supplementary Tables 18–20). d, Map of gene positions within the P interval with Psat01G0420500 encoding a tracheary element differentiation inhibition factor CLE41 indicated in yellow. e, Allelic and haplotype variations for Psat01G0420500. Note that Hap1 carries a silent A-to-C transversion at chr1_380699321, close to chr1_380699320 of Hap3, where the T-to-A transversion is responsible for the Arg79* nonsense mutation. f, Haplotypes of Psat01G0420500 corresponding to accessions with ‘parchmentless’ phenotypes. g, Predicted amino acid sequence of Psat01G0420500 indicating the position of the Arg79* mutation in relation to the TDIF84 motif. h, Gene expression patterns for the 10 candidate genes from the genomic interval, in various organs and developmental stages of Caméor, showing that Psat01G0420500 (PsCLE41) is expressed exclusively in pod. Three biological replicates were used for each sample. The Min-Max scaling (normalization) approach was used to calculate the expression level for each gene across stages and organs by the formula: X_scaled = (X - X_min)/(X_max - X_min), where X is the original gene expression value, X_scaled is the scaled value, X_min is the minimum value of X, and X_max is the maximum value of X.
