RNA-Seq Identifies Genes and Processes That Are Differentially Expressed in Soybean Due to Weed Stress.

Recent studies have brought into question the mechanisms through which weeds cause reduced crop yield. In modern agricultural systems, it is rare that nutrients, light, or even water are limiting- yet weed presence still causes significant yield loss. Thus, understanding how weeds are sensed by crop plants and the physiological and developmental processes that are negatively affected by weed presence could provide new insights needed to develop novel weed resistance in crops. In order to gain an enhanced understanding of crop- weed interactions, we have undertaken a transcriptomics approach to identify weed-responsive genes in soybean under field conditions. Over three years, and with 6 biological replicates per treatment, young leaf material was collected in weed- free or weed infested plots from soybean at the V3 stage of growth,  the beginning of the critical weed- free period in soybean..  RNA was extracted from the leaf and subjected to RNAseq analysis. Numerous weed-responsive genes were identified in this effort.  Processes that appear to be affected by weeds include Gibberellic acid  and auxin responses, and down-regulation of numerous small heat-shock genes. Several genes involved in meristem development were also differentially expressed in response to weeds. These results should provide an indication of the signaling processes through which soybean senses weed presence and alters its growth and development  responses.