Fig. 1
From: Native alleles at lhcb6 shape photosynthetic efficiency and early growth in maize
Marker-trait associations from a genome-wide association study (GWAS) for maximum potential quantum yield of photosystem II (Fv/Fm) in growth stage V6. (A) Marker-trait associations across chromosomes. Phenotypic data were assessed on 211 DH lines derived from the landrace Kemater during early development in growth stage V6 in field experiments in two locations. The x-axis shows the ten chromosomes of maize and the y-axis the -log10 of the p-value of associations of SNPs with Fv/Fm. The significance threshold (false discovery rate FDR < 15%) is indicated by a dashed horizontal line. Marker-trait associations are color-coded: orange (significant); grey and black (not significant, ns). (B) Marker-trait associations for the QTL on chromosome 10. The x-axis indicates the physical position of SNPs on chromosome 10 in the reference sequence B73v5 and the y-axis the -log10 of the p-value of associations of SNPs with Fv/Fm. Significance of associations of SNPs with Fv/Fm (FDR < 15%) is indicated by symbols: empty circles (no significant association, ns); filled circles (significant association); triangle (SNP with highest significance, lead SNP, AX-90599221). Linkage disequilibrium (r2) between the lead SNP and SNPs in the target region is color-coded. QTL boundaries are given by vertical lines.
