Multi-Omics Analyses on Maya-Land Tomatoes Shed Light on Plant Strategies to Thrive in High Temperatures

Heat stress limits tomato yield and quality. Deciphering the key genes and metabolites related to heat tolerance is essential for selecting tolerant varieties. In this study, we profiled the transcriptomes and metabolomes of roots and shoots in response to heat stress from a Maya-land ecotype of heirloom tomato (Calkiní), which grows in lowlands and elevated temperatures. We compared them with those of another heirloom ecotype that grows in highlands and lower temperatures (Acaxochitlán). In our omics approach, several transcripts encode enzymes that participate in diverse biosynthetic pathways and produce differentially accumulated metabolites. Although both ecotypes display programs to deal with heat stress, the roots of the Calkiní ecotype showed an increased accumulation of diverse metabolites and the up-regulation of key genes involved in molecular and physiological strategies to cope with heat stress. One of the key findings of this study is the elevated accumulation of transcripts and metabolites associated with phenylpropanoid and suberin biosynthesis in the heat-resistant ecotype. Such increases correlate with substantial suberin deposition in the exodermis and endodermis of Calkiní roots, with enhanced gibberellin accumulation in the meristematic zone under heat stress. Additionally, we found differential expression and accumulation of metabolites and genes involved in the PA-GAPC-NFY heat stress tolerance pathway among both ecotypes. Our work strengthens the importance of studying Mexican native tomato varieties and ecotypes to identify traits that allow plants to cope with diverse biotic and abiotic stresses, specifically providing insights into the genetic and metabolic pathways linked to heat tolerance among ecotypes and tissues.