Background Pyramiding different resistance genes into one plant genotype confers enhanced resistance at the phenotypic level, but the molecular mechanisms underlying this effect are not well-understood. In soybean, aphid resistance is conferred by Rag genes. We compared the transcriptional response of four soybean genotypes to aphid feeding to assess how the combination of Rag genes enhanced the soybean resistance to aphid infestation. Results A strong synergistic interaction between Rag1 and Rag2, defined as genes differentially expressed only in the pyramid genotype, was identified. This synergistic effect in the Rag1/2 phenotype was very evident early (6 h after infestation) and involved unique biological processes. However, the response of susceptible and resistant genotypes had a large overlap 12 h after aphid infestation. Transcription factor (TF) analyses identified a network of interacting TF that potentially integrates signaling from Rag1 and Rag2 to produce the unique Rag1/2 response. Pyramiding resulted in rapid induction of phytochemicals production and deposition of lignin to strengthen the secondary cell wall, while repressing photosynthesis. We also identified Glyma.07G063700 as a novel, strong candidate for the Rag1 gene. Conclusions The synergistic interaction between Rag1 and Rag2 in the Rag1/2 genotype can explain its enhanced resistance phenotype. Understanding molecular mechanisms that support enhanced resistance in pyramid genotypes could facilitate more directed approaches for crop improvement.

Objectives The objective was to evaluate the prebiotic effects of a milled whole cranberry beverage on modulating the gut microbiota in young adults. Methods Adults (n = 17; ages 18–42 y; BMI 30.5 ± 3.1 kg/m2) were enrolled in a 60-d, two-period, randomized, placebo-controlled, crossover clinical study. Throughout the study, participants were fed a standardized 10-d cycle menu on site. During each 20-d treatment period, participants consumed twice daily a whole cranberry or placebo beverage (240 mL per serving). Treatment periods were separated by an 11-wk washout period and preceded by 10-d run-in periods on the controlled study diet. Fecal samples were collected before and after the dietary intervention for bacterial compositional analysis and short-chain fatty acid analysis by LC-MS/MS. The V5-V6 region of the 16S rRNA gene in fecal DNA was amplified and sequenced. Taxonomy was assigned using the q2-feature-classifier in QIIME2 and matched against the Greengenes 13_8 database. Differential abundance was analyzed using ANCOM2 in R. Alpha-diversity was assessed using Faith's PD, Shannon diversity, and observed OTU richness generated by QIIME 2 and compared between treatments using Mann-Whitney U test. Beta-diversity was compared between treatments using PERMANOVA of the weighted and unweighted UniFrac distances between samples generated by QIIME 2. Results Coriobacteriaceae was significantly more abundant after participants consumed the cranberry as compared with the placebo beverage (ANCOM W > 0.7). The clinically-important pathogen Clostridium perfringens was present after consumption of the placebo beverage, but was a structural zero (not present) after consumption of the cranberry beverage. Alpha-diversity, beta-diversity, and fecal short-chain fatty acid concentrations did not differ between treatments. Conclusions Daily consumption of a whole cranberry beverage resulted in favorable change in the composition of the gut microbiota and thus showed prebiotic potential. Funding Sources Ocean Spray Cranberries, Inc.

Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly influenced the root-associated bacterial communities and root metabolite composition of sorghum. Sorghum NUE was positively correlated with the bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to N stress and indicate that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our study provides new insight into the links between host genetic regulation of root metabolites and root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.