Carotenoids, a subfamily of the isoprenoids, are one of the most diverse classes of secondary metabolites distributed throughout nature. They are lipophilic in nature, and include over 600 tetraterpenoid compounds synthesized by plants, bacteria, and fungi. Carotenoids, as the major pigment responsible for the red, yellow, and orange colors of fruits and vegetable, help promote human health and wellness by serving as antioxidants and precursors to vitamin A. Climate changes that threaten plant reproduction, negatively impact crop production worldwide. Little is understood about the chemistry of carotenoids in plant reproductive structures. Insight into the metabolic roles and functions of carotenoids in plant reproduction and, the effects of abiotic stresses on carotenoid biosynthesis in these structures would globally impact agriculture production by reducing yield loss. The potential for these metabolites to protect the reproductive structures under elevated temperature stress was assessed using biochemical analysis, genomics, and genetic studies. Fourteen candidate genes involved in carotenoid biosynthesis were identified, revealing three small gene families. Quantitative real-time polymerase chain reaction (qPCR) expression analysis of these genes and targeted metabolic profiling using liquid chromatography-high resolution mass spectrometry (LC-HRMS) throughout plant development under control and moderately elevated temperature stress showed that gene expression and metabolite accumulation are tissue specific and differentially responsive to elevated temperature stress. Three phytoene synthase genes were identified and characterized. Genomic analyses revealed that the PSY gene family exhibits functional diversity in plant tissues, both with respect to location and stage of development, as well as in response to abiotic stress.