Fig. 4

Characterization of natural alleles of YS1. a Schematic representation of the five most abundant YS1 allelic haplotypes present in the GWAS panel and their frequencies (%) (www.arabidopsis.org). NB gene orientation is 3′ to 5′ as indicated with an arrow on the left; two splice variants are known (purple and green), exons are indicated with purple or green boxes and introns with lines connecting them. SNPs differing from the Col-0 reference genome sequence (YS1 allele 1; YS1-1) are marked; two SNPs referred to in the text are indicated by arrows, chromosome 3 positions are indicated at the bottom (picture from http://signal.salk.edu/atg1001/3.0/gebrowser.php). b Average photosynthesis efficiencies (Ф_PSII) (±s.e.m.) of accessions carrying one of five YS1 alleles before (LL) and after an increase in irradiance (HL), the inset shows small but significant differences (*p < 0.05, T-test series) between allelic groups. c Ф_PSII (±s.e.m.; N = 16) of F1 progeny of crosses between Col-0 wild type (WT; YS1-1) or ys1-1 mutants with either Ll-0 carrying a YS1-3 allele, or Ga-0 carrying a YS1-4 allele, confirming that natural genetic variation at the YS1 gene explains the phenotypic variation identified by QTL23; * indicates a significant difference (p < 0.05; T-test) in allelic effect on the Ф_PSII difference at indicated time points between the different WT × accession and ys1 × accession F1 progenies. d–g Fold changes in mRNA expression of YS1 (d), RpoB encoding the β-subunit of the Plastid-Encoded Polymerase (PEP) protein (e), and the chloroplast-encoded tRNA genes TrnD (f) and TrnW (g), two transcriptional targets of PEP, transcription of which is affected by YS1. Expression at HL is compared with expression at LL in F1 progeny of crosses between either Col-0 WT or the Col-0 ys1-1 mutant and natural accessions Kin-0 and Mt-0 (carrying the YS1-3 allele, dashed lines) or Ga-0 and Old-1 (carrying the YS1-4 allele, continuous lines)