Weed presence altered biotic stress and light signaling in maize even when weeds were removed early in the critical weed-free period

Purpose: This study is designed to identify genes and processes that are differentially regulated in corn when it is grown with or without weeds through the entire critical weed free period (to V8) or when weeds were removed early in the critical weed free period (at V4) and the plants were allowed to recover until V8. Methods: Corn was grown as described above in field plots near Brookings SD in 2007 and 2008 and RNA was extracted from the top-most leaf tips from four plants per treatment plot. Unidirectional cDNA illumina sequencing libraries were constructed for each sample (pooled leaf tips from the given plot), and were sequenced (some samples were paired end sequenced and some were single end sequenced - all 100 bases for PE and SE reads), quality trimmed, and analyzed using the Tuxedo suite of programs for SE reads of the forward read libraries for each sample. Results: We identified a small number of genes that were differentially expressed in both years. More importantly, gene set enrichment analysis of the data determined that weeds, when present through the critical weed free period impacted phytochrome signaling, defense responses, photosynthetic processes, oxidative stress responses, and various hormone signaling processes. When weeds were removed at V4 and the plants allowed to recover until V8, the weeds still imprinted impacts on phytochrome signaling, oxidative stress, and defense responses. Thus, it appears that weeds presence through the early portion of the critical weed free period, even after removal, induced processes that reduce corn growth and yield that lasted at least through V8. Conclusions: This study represents the first investigation of the impact of the lasting effects of weeds during the early critical weed free period on the transcriptome of corn, and provides additional data on the impact of weeds through the critical weed free period that augments and confirms much of what was observed in similar microarray studies. Overall design: Experimental Design: Samples all collected at the same developmental stage (V8) from three treatments (control, weedy, and weeds removed followed by recovery), in each of two years (2007 and 2008), with two to three biological replicates of each treatment in each year.

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Horvath DP, Bruggeman S, Moriles-Miller J, Anderson JV, Dogramaci M, Scheffler BE, Hernandez AG, Foley ME, Clay S