|DRNEVICH, JENNY - University Of Illinois|
Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/1/2015
Publication Date: 1/21/2016
Citation: Choe, E., Drnevich, J., Williams II, M.M. 2016. Identification of crowding stress tolerance co-expression networks involved in sweet corn yield. PLoS One. doi: org/10.1371/journal.pone.0147418.
Interpretive Summary: Crop stress tolerance to high plant population density is one of major factors to modern yield improvement. Yet, sweet corn hybrids greatly varies tolerance to high plant population density. Research was conducted to explore plant density tolerance difference among sweet corn hyrbids and to identify candidate tolerance mechanisms influencing yield. Phenotypic and transcriptional analyses were performed on high- and low-yielding groups of sweet corn hybrids under high plant density. Yield traits were significantly different between high- and low-yielding hybrid groups. Transcriptional profiling identified a strong hybrid differences. Biological functions of differentially expressed genes idenified on each hybrid, indicating each hybrid has a unique tolerance mechanisms to high plant density. By clustering the genes into modules and correlating the modules with phenotypic data, modules associated with yield were idenified. Collectivley, candidate tolerant processes were identified in photosynthesis, glycolysis, cell wall, carbohydrate/nitrogen metabolic process, chromatin, and transcription regulation. The impact of this research is that it identified stress tolerance mechanisms influencing yield therefore these mechanisms can be utilized for improving U.S. sweet corn production.
Technical Abstract: Tolerance to crowding stress has played a crucial role in improving agronomic productivity in field corn; however, commercial sweet corn hybrids vary greatly in crowding stress tolerance. The objectives were to 1) explore transcriptional changes among sweet corn hybrids with differential yield under crowding stress, 2) identify relationships between phenotypic responses and gene expression patterns, and 3) identify groups of genes associated with yield and crowding stress tolerance. Under conditions of crowding stress, three high-yielding and three low-yielding sweet corn hybrids were grouped for transcriptional and phenotypic analyses. Transcriptional analyses identified from 372 to 859 common differentially expressed genes (DEGs) for each hybrid. Large gene expression pattern variation among hybrids and only 26 common DEGs across all hybrid comparisons were identified, suggesting each hybrid has a unique response to crowding stress. Over-represented biological functions of DEGs also differed among hybrids. Strong correlation was observed between: 1) modules with up-regulation in high-yielding hybrids and yield traits, and 2) modules with up-regulation in low-yielding hybrids and plant/ear traits. Modules linked with yield traits may be important crowding stress response mechanisms influencing crop yield. Functional analysis of the modules and common DEGs identified candidate crowding stress tolerant processes in photosynthesis, glycolysis, cell wall, carbohydrate/nitrogen metabolic process, chromatin, and transcription regulation. Moreover, these biological functions were greatly inter-connected, indicating the importance of improving the mechanisms as a network.