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The atypical IκB family member Bcl3 associates with p50/NF-κB1 or p52/NF-κB2 homodimers in the nucleus, and positively or negatively modulates transcription in a context-dependent manner. In mice lacking Bcl3 globally or specifically in CD11c+cells,Toxoplasma gondiiinfection is uniformly fatal and is associated with an impaired Th1 immune response. Since Bcl3 expression in dendritic cells (DC) is pivotal for antigen presentation and since classical DCs (cDC) are major antigen presenting cells, we investigated the role of Bcl3 specifically in cDCs inT. gondiiinfectionin vivoby crossing Zbtb46 cre mice withBcl3flx/flxmice. The conditional cDC Bcl3 KO was as susceptible to lethalT. gondiiinfection as the total Bcl3 KO and generated poor Th1 responses. Splenocyte single cell RNA seq in the model revealed defective Bcl3-dependent expression of genes involved in antigen processing. Consistent with this, soluble toxoplasma antigen presentation was impaired in Bcl3-deficient cDCs, and tetramer staining demonstrated defectiveT. gondiiantigen-specific splenic CD4+and CD8+T cell responses in infected cDCBcl3-/-mice.In vitrodifferentiation of bone marrow progenitors from wildtype and cDCBcl3-/-mice using Flt3L, NOTCH and IFN-γ stimulation recapitulated the defective Bcl3-dependent cDC antigen-presentation activity observed in vivo. Splenocyte single cell RNA seq also revealed the existence of a unique subpopulation of Zbtb46+LysM+DC which exhibited Bcl3-dependent expansion after infection. We also detected cDCs coexpressing the monocytic markers CD64 and Ly6C (designated icDC1 and icDC2) mainly in infected spleen, which were less abundant inBcl3flx/flxZbtb46 cremice. Together, our results indicate that Bcl3 in classical DCs is a major determinant of protective T cell responses and survival inT. gondii-infected mice, and shapes DC ontogeny.Author SummaryDendritic cells initiate immune responses against invading pathogens. As professional antigen presenting cells they process and present antigen via the major histocompatibility complex to T cells and thus activate them. Bcl3, an atypical member of the IκB family regulates the APC function of dendritic cells. In this study we show that expression of Bcl3 specifically in classical DCs is critical for host protection against a protozoan parasite,Toxoplasma gondii. Host protective proinflammatory mechanisms are compromised in mice deficient in Bcl3 in classical DCs leading to an elevated organ parasite load and eventually death of the infected animals. We also found the emergence of Bcl3-dependent hybrid DCs uponT. gondiiinfection, which have mixed phenotypic markers from DCs and monocytes. Antigen processing genes are significantly downregulated in Bcl3-deficient cDCs, which may account for defective cross presentation ofT. gondiiantigens. In an in vitro differentiation model, we showed that development of XCR1+cross presenting cDC1s is critically regulated by Bcl3. Overall, this study reveals the complexity of dendritic cell ontogeny and the role of Bcl3 in classical DC function in the context ofToxoplasmainfection.

Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of "required" and "desirable" metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for describing agricultural microbiome studies. We begin by briefly reviewing existing metadata standards relevant to agricultural microbiome research, and describe ongoing efforts to enhance the potential for integration of data across research studies. Our goal is not to delineate a fixed list of metadata requirements. Instead, we hope to advance the field by providing a starting point for discussion, and inspire researchers to adopt standardized procedures for collecting and reporting consistent and well-annotated metadata for agricultural microbiome research. National Science FoundationNational Science Foundation (NSF) [1714276] This material was supported in part by the National Science Foundation under grant number 1714276. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. Public domain – authored by a U.S. government employee

Resistance genes are an effective means for disease control in plants. They predominantly function by inducing a hypersensitive reaction, which results in localized cell death restricting pathogen spread. Some resistance genes elicit an atypical response, termed extreme resistance, where resistance is not associated with a hypersensitive reaction and its standard defense responses. Unlike hypersensitive reaction, the molecular regulatory mechanism(s) underlying extreme resistance is largely unexplored. One of the few known, naturally occurring, instances of extreme resistance is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent Soybean mosaic virus strains. To discern the regulatory mechanism underlying Rsv3-mediated extreme resistance, we generated a gene regulatory network using transcriptomic data from time course comparisons of Soybean mosaic virus-G7-inoculated resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. Our results show Rsv3 begins mounting a defense by 6 hpi via a complex phytohormone network, where abscisic acid, cytokinin, jasmonic acid, and salicylic acid pathways are suppressed. We identified putative regulatory interactions between transcription factors and genes in phytohormone regulatory pathways, which is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. One such transcription factor identified as a putative transcriptional regulator was MYC2 encoded by Glyma.07G051500. Known as a master regulator of abscisic acid and jasmonic acid signaling, MYC2 specifically recognizes the G-box motif (“CACGTG”), which was significantly enriched in our data among differentially expressed genes implicated in abscisic acidand jasmonic acid-related activities. This suggests an important role for Glyma.07G051500 in abscisic acid- and jasmonic acid-derived defense signaling in Rsv3. Resultantly, the findings from our network offer insights into genes and biological pathways underlying the molecular defense mechanism of Rsv3-mediated extreme resistance against Soybean mosaic virus. The computational pipeline used to reconstruct the gene regulatory network in this study is freely available at https://github.com/LiLabAtVT/rsv3-network. This project was funded in part by the Virginia Soybean Board. Additional funding was provided by the Agricultural Experiment Station Hatch Program and Open Access Subvention Fund – both at Virginia Tech. LD was funded in part by the John Lee Pratt Fellowship Program at Virginia Tech.

Two low-phytate soybean (Glycine max (L.) Merr.) mutant lines- V99-5089 (mips mutation on chromosome 11) and CX-1834 (mrp-l and mrp-n mutations on chromosomes 19 and 3, respectively) have proven to be valuable resources for breeding of low-phytate, high-sucrose, and low-raffinosaccharide soybeans, traits that are highly desirable from a nutritional and environmental standpoint. A recombinant inbred population derived from the cross CX1834 x V99-5089 provides an opportunity to study the effect of different combinations of these three mutations on soybean phytate and oligosaccharides levels. Of the 173 recombinant inbred lines tested, 163 lines were homozygous for various combinations of MIPS and two MRP loci alleles. These individuals were grouped into eight genotypic classes based on the combination of SNP alleles at the three mutant loci. The two genotypic classes that were homozygous mrp-l/mrp-n and either homozygous wild-type or mutant at the mips locus (MIPS/mrp-l/mrp-n or mips/mrp-l/mrp-n) displayed relatively similar ~55% reductions in seed phytate, 6.94 mg g -1 and 6.70 mg g-1 respectively, as compared with 15.2 mg g-1 in the wild-type MIPS/MRP-L/MRP-N seed. Therefore, in the presence of the double mutant mrp-l/mrp-n, the mips mutation did not cause a substantially greater decrease in seed phytate level. However, the nutritionally-desirable high-sucrose/low-stachyose/low-raffinose seed phenotype originally observed in soybeans homozygous for the mips allele was reversed in the presence of mrp-l/mrp-n mutations: homozygous mips/mrp-l/mrp-n seed displayed low-sucrose (7.70%), high-stachyose (4.18%), and the highest observed raffinose (0.94%) contents per gram of dry seed. Perhaps the block in phytic acid transport from its cytoplasmic synthesis site to its storage site, conditioned by mrp-l/mrp-n, alters myo-inositol flux in mips seeds in a way that restores to wild-type levels the mips conditioned reductions in raffinosaccharides. Overall this study determined the combinatorial effects of three low phytic acid causing mutations on regulation of seed phytate and oligosaccharides in soybean.

Recapture and recycling of irrigation water is often required to meet enormous water demands at horticultural nurseries. We tested four water types associated with a recycled irrigation system at a commercial container nursery in southern California for presence of oomycete plant pathogens from July 2015 to December 2017. These water types included: the main source of water originating from a reservoir, retention water from an on-site collection pond, irrigation water received by different growing areas within the nursery, and irrigation runoff captured in polyethylene sheet-lined runoff channels. The genera Phytophthora, Pythium, and Phytopythium together contributed more than 85% of the total oomycete population detected in the recycled irrigation system. The Phytophthora and Pythium genera were represented by member species from nine (1–4, 6–10) and eight (A, B, D-F, H-J) different sub-generic clades, respectively. Incoming water sourced from the reservoir was found to harbor known plant pathogens such as Phytophthora citricola-complex, P. capsici-cluster, P. tropicalis, P citrophthora-cluster, P. nemorosa-cluster, P. riparia, P. cryptogea-complex, P. parsiana-cluster, P. sp. nov. aff. kernoviae, Pythium dissotocum-complex, Py. oligandrum-cluster, Py. irregulare, and Phytopythium litorale. Runoff water showed the highest oomycete species richness and frequency of detection with both filtration and leaf baiting methods. In addition to plant pathogens, oomycete fish pathogens such as Aphanomyces laevis, Pythium chondricola-complex, Pythium flevoense-complex, and Saprolegnia diclina-complex were also detected in greater abundance in the recycled irrigation water. The oomycete species richness in the runoff water was correlated with several environmental parameters such as soil temperature. Greater oomycete richness in incoming water was associated with higher soil temperatures, whereas richness in runoff declines with increasing soil temperature, likely suggesting connections to weather-dependent nursery operations.

Discovery of new germplasm sources and identification of haplotypes for the durable Soybean mosaic virus resistance gene, Rsv 4, provide novel resources for map-based cloning and genetic improvement efforts in soybean. The Soybean mosaic virus (SMV) resistance locus Rsv4 is of interest because it provides a durable type of resistance in soybean [Glycine max (L.) Merr.]. To better understand its molecular basis, we used a population of 309 BC3F2 individuals to fine-map Rsv4 to a ~120 kb interval and leveraged this genetic information in a second study to identify accessions 'Haman' and 'Ilpumgeomjeong' as new sources of Rsv4. These two accessions along with three other Rsv4 and 14 rsv4 accessions were used to examine the patterns of nucleotide diversity at the Rsv4 region based on high-depth resequencing data. Through a targeted association analysis of these 19 accessions within the ~120 kb interval, a cluster of four intergenic single-nucleotide polymorphisms (SNPs) was found to perfectly associate with SMV resistance. Interestingly, this ~120 kb interval did not contain any genes similar to previously characterized dominant disease resistance genes. Therefore, a haplotype analysis was used to further resolve the association signal to a ~94 kb region, which also resulted in the identification of at least two Rsv4 haplotypes. A haplotype phylogenetic analysis of this region suggests that the Rsv4 locus in G. max is recently introgressed from G. soja. This integrated study provides a strong foundation for efforts focused on the cloning of this durable virus resistance gene and marker-assisted selection of Rsv4-mediated SMV resistance in soybean breeding programs.

Background Low phytic acid (lpa) crops are potentially eco-friendly alternative to conventional normal phytic acid (PA) crops, improving mineral bioavailability in monogastric animals as well as decreasing phosphate pollution. The lpa crops developed to date carry mutations that are directly or indirectly associated with PA biosynthesis and accumulation during seed development. These lpa crops typically exhibit altered carbohydrate profiles, increased free phosphate, and lower seedling emergence, the latter of which reduces overall crop yield, hence limiting their large-scale cultivation. Improving lpa crop yield requires an understanding of the downstream effects of the lpa genotype on seed development. Towards that end, we present a comprehensive comparison of gene-expression profiles between lpa and normal PA soybean lines (Glycine max) at five stages of seed development using RNA-Seq approaches. The lpa line used in this study carries single point mutations in a myo-inositol phosphate synthase gene along with two multidrug-resistance protein ABC transporter genes. Results RNA sequencing data of lpa and normal PA soybean lines from five seed-developmental stages (total of 30 libraries) were used for differential expression and functional enrichment analyses. A total of 4235 differentially expressed genes, including 512-transcription factor genes were identified. Eighteen biological processes such as apoptosis, glucan metabolism, cellular transport, photosynthesis and 9 transcription factor families including WRKY, CAMTA3 and SNF2 were enriched during seed development. Genes associated with apoptosis, glucan metabolism, and cellular transport showed enhanced expression in early stages of lpa seed development, while those associated with photosynthesis showed decreased expression in late developmental stages. The results suggest that lpa-causing mutations play a role in inducing and suppressing plant defense responses during early and late stages of seed development, respectively. Conclusions This study provides a global perspective of transcriptomal changes during soybean seed development in an lpa mutant. The mutants are characterized by earlier expression of genes associated with cell wall biosynthesis and a decrease in photosynthetic genes in late stages. The biological processes and transcription factors identified in this study are signatures of lpa-causing mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2283-9) contains supplementary material, which is available to authorized users.