Integrative physiological and transcriptome analyses elucidate the effect of shading during the grain-filling stage of wheat () cv. ZY96-3.

Shading plays an important role in determining nutrient content and yield fo wheat (Triticum aestivum ). However, the genetic mechanism underlying the effects of shading treatment on grain filling remains unclear. Therefore, we performed phenotypic and transcriptome analyses on wheat cv. ZY96-3 during grain development under normal and shaded conditions. Shading resulted in a significant decrease in grain size and 1000-grain weight. Correlation analysis revealed the strong effect of shading on the mean and maximum grain-filling rate and secondary grain-filling parameters R 2 and R 3 . And shading reduced starch content and starch-related enzyme activity (including granule-bound starch synthase and soluble starch synthase). Transcriptomic analyses showed that shading mainly affected pathways related to photosynthetic antenna proteins, carbon fixation in photosynthetic organisms, and starch and sucrose metabolism. Sixteen genes related to photosynthetic antenna protein and carbon fixation pathways were first upregulated and then downregulated; whereas all differentially expressed genes (PetC , Fd , LFNR1 , LFNR2 , PC , PsbO , PsaG , and PSB28 ) in the photosynthetic antenna protein pathway belonged to electron transport chain proteins. We found that shading treatment affects the physiological and molecular properties of grain development during the grain-filling stage. This study reveals new candidate genes (such as TaLFNR1-7A and TaFd-7A ) for breeding wheat varieties with high photosynthetic efficiency in regions with insufficient light intensity.