RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean.

Weeds reduce yield in soybeans (Glycine max) through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate growing seasons. RNASeq data were collected from six biological samples of soybeans growing with or without weeds. Weed species and the methods to maintain weed-free controls varied between years to mitigate treatment effects, and to allow detection of general soybean weed responses. Soybean plants were not visibly nutrient- or water-stressed. We identified 55 consistently downregulated genes in weedy plots. Many of the downregulated genes were heat shock genes. Fourteen genes were consistently upregulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the upregulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in Arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest that the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean.

Tillage and corn residue harvesting impact surface and subsurface carbon sequestration.

Corn stover harvesting is a common practice in the western U.S. Corn Belt. This 5-yr study used isotopic source tracking to quantify the influence of two tillage systems, two corn ( L.) surface residue removal rates, and two yield zones on soil organic C (SOC) gains and losses at three soil depths. Soil samples collected in 2008 and 2012 were used to determine C enrichment during SOC mineralization, the amount of initial SOC mineralized (SOC), and plant C retained in the soil (PCR) and sequestered C (PCR - SOC). The 30% residue soil cover after planting was achieved by the no-till and residue returned treatments and was not achieved by the chisel plow, residue removed treatment. In the 0- to 15-cm soil depth, the high yield zone had lower SOC (1.49 Mg ha) than the moderate yield zone (2.18 Mg ha), whereas in the 15- to 30-cm soil depth, SOC was higher in the 60% (1.38 Mg ha) than the 0% (0.82 Mg ha) residue removal treatment. When the 0- to 15- and 15- to 30-cm soil depths were combined, (i) 0.91 and 3.62 Mg SOC ha were sequestered in the 60 and 0% residue removal treatments; (ii) 2.51 and 0.36 Mg SOC ha were sequestered in the no-till and chisel plow treatments, and (iii) 1.16 and 1.65 Mg SOC ha were sequestered in the moderate and high yield zone treatments, respectively. The surface treatments influenced C cycling in the 0- to 15- and 15- to 30-cm depths but did not influence SOC turnover in the 30- to 60-cm depth.

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

Weed presence early in the life cycle of maize (typically, from emergence through the 8 to 12 leaf growth stage) can reduce crop growth and yield and is known as the critical weed-free period (CWFP). Even if weeds are removed during or just after the CWFP, crop growth and yield often are not recoverable. We compared transcriptome responses of field-grown hybrid maize at V8 in two consecutive years among plants grown under weed-free and two weed-stressed conditions (weeds removed at V4 or present through V8) using RNAseq analysis techniques. Compared with weed-free plant responses, physiological differences at V8 were identified in all weed-stressed plants and were most often associated with altered photosynthetic processes, hormone signaling, nitrogen use and transport, and biotic stress responses. Even when weeds were removed at V4 and tissues sampled at V8, carbon: nitrogen supply imbalance, salicylic acid signals, and growth responses differed between the weed-stressed and weed-free plants. These underlying processes and a small number of developmentally important genes are potential targets for decreasing the maize response to weed pressure. Expression differences of several novel, long noncoding RNAs resulting from exposure of maize to weeds during the CWFP were also observed and could open new avenues for investigation into the function of these transcription units.