Background Nitrogen (N) and phosphorus (P) are macronutrients essential for crop growth and productivity. In cultivated fields, N and P levels are rarely sufficient, contributing to the gap between realized and potential production. Fertilizer application increases nutrient availability, but is not available to all farmers, nor are current rates of application sustainable or environmentally desirable. Transcriptomic studies of cereal crops have revealed dramatic responses to either low N or low P single stress treatments. In the field, however, levels of both N and P may be suboptimal. The interaction between N and P starvation responses remains to be fully characterized. Results We characterized growth and root and leaf transcriptomes of young maize plants under nutrient replete, low N, low P or combined low NP conditions. We identified 1555 genes to respond to our nutrient treatments, in one or both tissues. A large group of genes, including many classical P starvation response genes, were regulated antagonistically between low N and P conditions. An additional experiment over a range of N availability indicated that a mild reduction in N levels was sufficient to repress the low P induction of P starvation genes. Although expression of P transporter genes was repressed under low N or low NP, we confirmed earlier reports of P hyper accumulation under N limitation. Conclusions Transcriptional responses to low N or P were distinct, with few genes responding in a similar way to the two single stress treatments. In combined NP stress, the low N response dominated, and the P starvation response was largely suppressed. A mild reduction in N availability was sufficient to repress the induction of P starvation associated genes. We conclude that activation of the transcriptional response to P starvation in maize is contingent on N availability.

A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum (Paspalum vaginatum) is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here, we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologues conserved in 6 related grass species places paspalum as an outgroup of the maize-sorghum clade. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibits a significant increase in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, results in autophagy dependent increases in biomass accumulation.

Background: Nitrogen (N) and phosphorus (P) are macronutrients essential for crop growth and productivity. In cultivated fields, N and P levels are rarely sufficient, contributing to the yield gap between realized and potential production. Fertilizer application increases nutrient availability, but not all farmers have access to such additions, nor are current rates of application sustainable or environmentally desirable. Transcriptomic studies of cereal crops have revealed dramatic responses to either low N or low P single stress treatments. In the field, however, levels of both N and P may be suboptimal. The interaction between N and P starvation responses remains to be fully characterized. Results: We characterized the root and leaf transcriptomes of young maize plants grown under control, low N, low P or combined low NP conditions. We identified 1, 555 genes that responded to at least one of the treatments, in at least one of the tissues. Transcriptional responses to low N and low P were distinct, with very few genes responding in a similar way to the two single stress treatments. Furthermore, the regulation of a large group of genes was antagonistic between the two conditions. In combined NP stress, the low N response dominated, the classical P starvation response being largely suppressed. An additional experiment over a range of N availability indicated that even a mild reduction in N levels was sufficient to repress the low P induction of well-characterized P starvation genes. Although expression of P transporter genes was repressed under low N or low NP, we confirmed earlier reports of P hyper accumulation under low N. To lay the foundations for further study of the mechanistic basis of NP signaling in maize, we annotated the complete set of maize Spx genes, and found evidence of N and P regulation across the family. Conclusions: A mild reduction in N availability is sufficient to repress the P starvation response in young maize plants. The Spx gene family are candidates for integrating low N and low P responses.

Changing patterns of weather and climate are limiting breeders ability to conduct trials in the same environments in which their released varieties will be grown 7-10 years later. Flowering time plays a crucial role in determining regional adaptation, and mismatch between flowering time and environment can substantially impair yield. Different approaches based on genetic markers or gene expression can be used to predict flowering time before conducting large scale field evaluation and phenotyping. The more accurate prediction of a trait using genetic markers could be hindered due to all the intermediate steps (i.e. transcription, translation, epigenetic modification, and epistasis among others) connecting the trait and their genetic basics. The use of some intermediate steps as predictors could improve the accuracy of the model. Here, we are using two public gene expression (RNA-Seq) data-sets from 14-day-old-maize-seedling roots and whole-seedling tissue at v1 stage (~10 day after planting) for which flowering data (days to anthesis and days to silking expressed in growing degree days) and genetic markers were also available to test the predictability of flowering time. In total, 20 different combinations between phenotypic and gene expression data-sets were evaluated. To explore prediction accuracy a random forest model was trained with the expression values of 44,303 gene models hosted in the current B73 maize reference version 5 and then the feature importance was scored based on the decrease in root mean squared error. Later several random forest models with different subsets of the most important features (genes) were trained, and this process was repeated ten times. Results from these analyses show a curve in the prediction accuracy, with an increase in the prediction accuracy as the top most important genes were added. The maximum accuracy was attained when 500 genes for whole-seedling and 100 genes for root gene expression data were used in the analysis, and thereafter adding more genes lead to a decrease in the prediction accuracy. The highest prediction accuracy using the top-most important genes was higher than that of using randomly selected whole-genome 400,000 SNPs. Finally, we described the genes controlling flowering time by looking at the most important genes in the Random forest model with the expression data from all genes. We further found MADS-transcription factor 69 (Mads69) using whole-seedling gene expression, and the MADS-transcription factor 67 (Mads67) using root gene expression data, both genes previously described with effect on flowering time. Here, we aim to demonstrate the potential of selecting and using the expression of most informative genes to predict a complex trait, also to demonstrate the robustness and limitations of this analysis by using phenotypic data-sets from different environments.

Plant PHO1 proteins play a central role in the translocation and sensing of inorganic phosphate. The maize (Zea mays ssp. mays) genome encodes two co-orthologs of the Arabidopsis PHO1 gene, designated ZmPho1;2a and ZmPho1;2b. Here, we report the characterization of the transposon footprint allele Zmpho1;2a 0 -m1.1, which we refer to hereafter as pho1;2a. The pho1;2a allele is a stable derivative formed by excision of an Activator transposable element from the ZmPho1;2a gene. The pho1;2a allele contains an 8-bp insertion at the point of transposon excision that disrupts the reading frame and is predicted to generate a premature translational stop. We show that the pho1;2a allele is linked to a dosage-dependent reduction in Pho1;2a transcript accumulation and a mild reduction in seedling growth. Characterization of shoot and root transcriptomes under full nutrient, low nitrogen, low phosphorus, and combined low nitrogen and low phosphorus conditions identified 1100 differentially expressed genes between wild-type plants and plants carrying the pho1;2a mutation. Of these 1100 genes, 966 were upregulated in plants carrying pho1;2a, indicating the wildtype PHO1;2a to predominantly impact negative gene regulation. Gene set enrichment analysis of the pho1;2a-misregulated genes revealed associations with phytohormone signaling and the phosphate starvation response. In roots, differential expression was broadly consistent across all nutrient conditions. In leaves, differential expression was largely specific to low phosphorus and combined low nitrogen and low phosphorus conditions. Of 276 genes upregulated in the leaves of pho1;2a mutants in the low phosphorus condition, 153 were themselves induced in wild-type plants with respect to the full nutrient condition. Our observations suggest that Pho1;2a functions in the fine-tuning of the transcriptional response to phosphate starvation through maintenance and/or sensing of plant phosphate status.

PHO1 proteins play a central role in plant inorganic phosphorus translocation and sensing. The maize (Zea mays ssp. mays) genome encodes two co-orthologs of the ArabidopsisPHO1 gene, designated ZmPho1;2a and ZmPho1;2b. Here, we report the characterization of the transposon-footprint allele Zmpho1;2a'-m1.1, which we refer to hereafter as pho1;2a. The pho1;2a allele is a stable derivative formed by excision of an Activator element from the ZmPho1;2a gene. The pho1;2a allele contains an 8 bp insertion at the point of excision that disrupts the reading frame and is predicted to generate a premature translational stop. We show that the pho1;2a allele is linked to a dosage-dependent reduction in transcript accumulation and a mild reduction in seedling growth that is enhanced under nutrient deficient conditions. Characterization of the shoot and root transcriptomes of seedlings segregating the pho1;2a mutation under different nutrient conditions revealed pho1;2a to have a dominant effect on patterns of transcript accumulation. Gene set enrichment analysis of the transcripts mis-regulated in pho1;2a mutants suggests that Pho1;2a functions in the fine-tuning of the transcriptional phosphate starvation response. We discuss our results with reference to possible genetic redundancy among maize Pho1 genes and in the context of reports linking functional variation in Pho1;2a to agronomically important traits.

The morphological and genetic identification of hydrozoans collected in the reef patches of Santa Marta, Colombia was carried out. This study allows to present two new records of hydroids species for the Colombian Caribbean: Halopteris alternata and Dentitheca dendritica. A total of 11 species and 1 genus were found using morphological and genetic identification with partial sequences of the mitochondrial 16S rRNA gene. The order Leptothecata was the most abundant represented by 9 families: Aglaopheniidae, Clytiidae, Haleciidae, Halopterididae, Kirchenpaueriidae, Plumulariidae, Sertularellidae, Sertulariidae and Thyroscyphidae, while the order Anthoathecata was represented by 2 families: Eudendriidae and Pennariidae. Despite the lack of studies on this group of organisms in the country, the use of the 16S rRNA gene proved to be very useful to provide complementary evidence in our understanding of the biological diversity of hydrozoans in Colombia.

The specific identity of the common octopus fished along the Colombian Caribbean was studied based on 58 specimens collected from artisanal fishing in five localities (Providencia, San Andrés, Santa Marta, Cartagena and Isla Fuerte). A molecular systematic analysis of the mitochondrial genes 16S ribosomal RNA and cytochrome c oxidase subunit III was carried out, along with a reanalysis of data for the cytochrome c oxidase subunit I gene. These analyses revealed that the common shallow-water octopus of the Colombian Caribbean is Octopus insularis. The trees generated for the three genes and the genetic distances for each of the genes (0–0.3%) confirmed the specimens collected in this study as belonging to a single clade and the species as O. insularis. Our results confirm that the octopus described recently as O. tayrona is in fact O. insularis and this extends the known distribution of the latter species to the southwestern Caribbean (i.e. Colombian coast). We discuss our findings in the context of the species misidentification of the O. vulgaris species complex.