2Engineering C 4 photosynthesis into C 3 crops such as rice or wheat could substantially 25 increase their yield by alleviating photorespiratory losses 1,2 . This objective is challenging 26 because the C 4 pathway involves complex modifications to the biochemistry, cell biology and 27 anatomy of leaves 3 . Forward genetics has provided limited insight into the mechanistic basis 28 of these characteristics and there have been no reports of significant quantitative intra-29 specific variation of C 4 attributes that would allow trait-mapping 4,5 . Here we show that 30 accessions of C 4 Gynandropsis gynandra collected from locations across Africa and Asia 31 exhibit natural variation in key characteristics of C 4 photosynthesis. Variable traits include 32 bundle sheath size and vein density, gas exchange parameters and carbon-isotope 33 discrimination associated with the C 4 state, but also abundance of transcripts encoding core 34 enzymes of the C 4 cycle. Traits relating to water use showed more quantitative variation than 35 those associated with carbon assimilation. We propose variation in these traits likely adapted 36 the hydraulic system for increased water use efficiency rather than improving carbon fixation, 37 indicating that selection pressure may drive C 4 diversity in G. gynandra by acting to modify 38 water use rather than photosynthesis. As these accessions can be easily crossed and 39 produce fertile offspring, our findings indicate that natural variation within a C 4 species is 40 sufficiently large to allow genetic-mapping of key anatomical C 4 traits and regulators. 41Plants that use C 4 photosynthesis can effectively abolish photorespiratory losses caused when 42 Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (RuBisCO) fixes oxygen rather than CO 2 6,7 . In 43 The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/253211 doi: bioRxiv preprint first posted online Jan. 25, 2018;
3Despite the complex modifications associated with C 4 photosynthesis, current estimates are that 53 the C 4 pathway has evolved independently more than sixty times in angiosperms 11 , which suggests 54 a relatively straightforward route must allow the transition from the ancestral C 3 to the derived C 4 55 state. Genome-wide analysis of transcript abundance in multiple C 3 and C 4 species has provided 56 unbiased insight into processes that likely change in C 4 compared with C 3 leaves [12][13][14] . Furthermore, 57 cis-elements that control expression of genes encoding the C 4 cycle have been documented. To 58 date however, the regulators that recognize these motifs have not been isolated 15 . Despite progress 59 in our understanding of C 4 photosynthesis, it is currently not possible to rationally design a C 4 60 pathway in a C 3 leaf. 61When natural variation is present, it enables quantitative methods such as Genome-Wide 62Association Studies (GWAS) and/or the development of a mapping population. Molecular marker-63 trait associations on the population allow identification of the causal genes...