Genome-wide association studies were conducted using the QTL library procedures from Genstat software. Only the nonderived photosynthesis-related traits with comparable error variances (A, E, gs, Ca, Cb, and Ccx) were used for the analysis. Adjusted means (BLUEs) of those traits were tested for association with 9,825 SNP markers using the 144 common bean accessions obtained using the Illumina Infinium BARCBean6K_3 BeadChipTM assay and DArTseqTM analysis, and retrieved from a previous study after quality control56. SNP markers and accessions with >25% missing data were removed, as well as SNPs with a minor-allele frequency <0.01. SNPs called as heterozygous were set as missing data.

GWAS was performed separately for WW and WD in the mixed-model framework of Genstat software, using kinship matrix with coefficients of co-ancestry between accessions, and fitting markers as fixed and accessions as random terms on REML. Using a threshold level of –log10 (P value) = 3, the significant marker-trait associations were highlighted. This threshold was set to discard the background noise observed in the Manhattan plots without compromising the identification of potentially interesting regions, which would be missed, for instance, by the too stringent and conservative Bonferroni-corrected threshold of significance. For every SNP significantly associated with a trait, the effect of the minor-frequency SNP variant was calculated.

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