The genetic architecture of photosynthesis and plant growth‐related traits in tomato

Franklin Magnum de Oliveira Silva, Gabriel Lichtenstein, Saleh Alseekh, Laise Rosado‐Souza, Mariana Conte, Vanessa Fuentes Suguiyama, Bruno Silvestre Lira, Dimitrios Fanourakis, Björn Usadel, Leonardo Lopes Bhering, Fábio M. DaMatta, Ronan Sulpice, Wagner L. Araújo, Magdalena Rossi, Nathalia de Setta, Alisdair R. Fernie, Fernando Carrari, Adriano Nunes‐Nesi

To identify genomic regions involved in the regulation of fundamental physiological processes such as photosynthesis and respiration, a population of Solanum pennellii introgression lines (ILs) was analyzed. We determined phenotypes for physiological, metabolic and growth related traits, including gas-exchange and chlorophyll fluorescence parameters. Data analysis allowed the identification of 208 physiological and metabolic QTL with 33 of these being associated to smaller intervals of the genomic regions, termed BINs. Eight BINs were identified that were associated with higher assimilation rates than the recurrent parent M82. Two and ten genomic regions were related to shoot and root dry matter accumulation, respectively. Nine genomic regions were associated with starch levels, whilst twelve BINs were associated with the levels of other metabolites. Additionally, a comprehensive and detailed annotation of the genomic regions spanning these QTL allowed us to identify a total of 87 candidate genes which putatively control the investigated traits. We confirmed eight of these at the level of variance in gene expression. Taken together, our results allowed the identification of candidate genes which most likely regulate photosynthesis, primary metabolism and plant growth, and as such provide new avenues for crop improvement.