Identification of Crowding Stress Tolerance Co-Expression Networks Involved in Sweet Corn Yield

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.

Fig 1. Venn diagrams to identify common DEGs from pairwise comparisons.

^a Up- and down- regulated DEGs in the first hybrid from listed pairwise comparison identified at FDR p-value<0.05 and |FC|>1.5 were labeled + and -, respectively.

Fig 2. Hierarchical clustering of phenotypic traits and module eigengene values (ME).

Phenotypic traits were labeled as ‘Height.V6’, height at V6; ‘Ear.No.plant’, number of ears per plant; ‘Ear.No.ha’, number of ears per hectare; ‘Kernel.mass.plant’, kernel mass per plant; ‘Kernel.mass.ha’, kernel mass per hectare; ‘SPAD.R1’, SPAD at R1; ‘Leaf.N’, leaf nitrogen; ‘Fill.percentage’, fill percentage; ‘SPAD.V6’, SPAD at V6; ‘LAI’, leaf area index; ‘Kernel.moisture’, kernel moisture; ‘Height.R1’, height at R1; ‘GDD.silk’, GDD to silk; ‘Ear.length’, ear length; ‘Fill.length’, fill length.

Fig 3. Visualization of GO terms in biological functions of module 13 and 36.

Significance (FDR p-values) of GO term is color labeled from red to white. Similar GO terms are linked by edges, where the degree of similarity represented by the line width. (A) Module 13, (B) Module 36.