Yield prediction through integration of genetic, environment, and management data through deep learning.

Accurate prediction of the phenotypic outcomes produced by different combinations of genotypes, environments, and management interventions remains a key goal in biology with direct applications to agriculture, research, and conservation. The past decades have seen an expansion of new methods applied toward this goal. Here we predict maize yield using deep neural networks, compare the efficacy of 2 model development methods, and contextualize model performance using conventional linear and machine learning models.

Engineered Agrobacterium improves transformation by mitigating plant immunity detection.

Agrobacterium tumefaciens microbe-associated molecular pattern elongation factor Tu (EF-Tu) is perceived by orthologs of the Arabidopsis immune receptor EFR activating pattern-triggered immunity (PTI) that causes reduced T-DNA-mediated transient expression. We altered EF-Tu in A. tumefaciens to reduce PTI and improved transformation efficiency.

Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass.

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.

Plant Single-Cell/Nucleus RNA-seq Workflow.

Single-cell transcriptomics technologies allow researchers to investigate how individual cells, in complex multicellular organisms, differentially use their common genomic DNA. In plant biology, these technologies were recently applied to reveal the transcriptomes of various plant cells isolated from different organs and different species and in response to environmental stresses. These first studies support the potential of single-cell transcriptomics technology to decipher the biological function of plant cells, their developmental programs, cell-type-specific gene networks, programs controlling plant cell response to environmental stresses, etc.

Exercise facilitates regeneration after severe nerve transection and further modulates neural plasticity.

Patients with severe traumatic peripheral nerve injury (PNI) always suffer from incomplete recovery and poor functional outcome. Physical exercise-based rehabilitation, as a non-invasive interventional strategy, has been widely acknowledged to improve PNI recovery by promoting nerve regeneration and relieving pain. However, effects of exercise on chronic plastic changes following severe traumatic PNIs have been limitedly discussed.

RNA-binding protein MAC5A interacts with the 26S proteasome to regulate DNA damage response in Arabidopsis.

DNA damage response (DDR) in eukaryotes is essential for the maintenance of genome integrity in challenging environments. The regulatory mechanisms of DDR have been well-established in yeast and humans. However, increasing evidence supports the idea that plants seem to employ different signaling pathways that remain largely unknown.

Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume.

Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia. This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria, as well as the initiation of nodule primordia from root cortical, endodermal, and pericycle cells, leading to the development of a new root organ, the nodule, where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant. Here, we report the isolation and use of the nuclei from mock and rhizobia-inoculated roots for the single nuclei RNA-seq (sNucRNA-seq) profiling to gain a deeper understanding of early responses to rhizobial infection in Medicago roots.

Seasonal variation of alkaloids and polyphenol in Ephedra sinica cultivated in Japan and controlling factors.

We investigated the seasonal variation of alkaloids (ephedrine and pseudoephedrine), total polyphenol, and sugar contents in Ephedra sinica cultivated in Japan and elucidated the controlling factors for the variation. In 2018, alkaloids and polyphenol contents increased dramatically from May to July, decreased to their lowest in October, and slightly increased again in November. The reduction of alkaloids and polyphenol contents in the autumn may be affected by precipitation in summer.

Review: Challenges and perspectives in applying single nuclei RNA-seq technology in plant biology.

Plant single-cell RNA-seq technology quantifies the abundance of plant transcripts at a single-cell resolution. Deciphering the transcriptomes of each plant cell, their regulation during plant cell development, and their response to environmental stresses will support the functional study of genes, the establishment of precise transcriptional programs, the prediction of more accurate gene regulatory networks, and, in the long term, the design of de novo gene pathways to enhance selected crop traits. In this review, we will discuss the opportunities, challenges, and problems, and share tentative solutions associated with the generation and analysis of plant single-cell transcriptomes.

SNP discovery in proso millet ( L.) using low-pass genome sequencing.

Domesticated ~10,000 years ago in northern China, Proso millet ( L.) is a climate-resilient and human health-promoting cereal crop. The genome size of this self-pollinated allotetraploid is 923 Mb.

Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome.

Prebiotic fibers, polyphenols and other molecular components of food crops significantly affect the composition and function of the human gut microbiome and human health. The abundance of these, frequently uncharacterized, microbiome-active components vary within individual crop species. Here, we employ high throughput in vitro fermentations of pre-digested grain using a human microbiome to identify segregating genetic loci in a food crop, sorghum, that alter the composition and function of human gut microbes.

Cell-Type-Specific Profiling of the Membrane Protein-Encoding Genes.

Membrane proteins work in large complexes to perceive and transduce external signals and to trigger a cellular response leading to the adaptation of the cells to their environment. Biochemical assays have been extensively used to reveal the interaction between membrane proteins. However, such analyses do not reveal the unique and complex composition of the membrane proteins of the different plant cell types.

The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments.

Subgenome dominance after whole-genome duplication (WGD) has been observed in many plant species. However, the degree to which the chromatin environment affects this bias has not been explored. Here, we compared the dominant subgenome (maize1) and the recessive subgenome (maize2) with respect to patterns of sequence substitutions, genes expression, transposable element accumulation, small interfering RNAs, DNA methylation, histone modifications, and accessible chromatin regions (ACRs).

Dynamic Energy Budget models: fertile ground for understanding resource allocation in plants in a changing world.

Climate change is having dramatic effects on the diversity and distribution of species. Many of these effects are mediated by how an organism's physiological patterns of resource allocation translate into fitness through effects on growth, survival and reproduction. Empirically, resource allocation is challenging to measure directly and so has often been approached using mathematical models, such as Dynamic Energy Budget (DEB) models.

Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel.

Background: Access to biologically available nitrogen is a key constraint on plant growth in both natural and agricultural settings. Variation in tolerance to nitrogen deficit stress and productivity in nitrogen limited conditions exists both within and between plant species. However, our understanding of changes in different phenotypes under long term low nitrogen stress and their impact on important agronomic traits, such as yield, is still limited.

Sugars and Jasmonic Acid Concentration in Root Exudates Affect Maize Rhizosphere Bacterial Communities.

Root exudates contribute to shaping the root-associated microbiomes, but it is unclear which of the many exudate compounds are important in this process. Here, we focused on understanding the influence of sugars and jasmonic acid (JA) concentrations in maize root exudates on the rhizobacterial communities. Twelve maize genotypes were identified with variable concentrations of sugars and JA based on a screening of 240 maize genotypes grown in a semihydroponic system.

Genome assembly of the Brassicaceae diploid Orychophragmus violaceus reveals complex whole-genome duplication and evolution of dihydroxy fatty acid metabolism.

Orychophragmus violaceus is a Brassicaceae species widely cultivated in China, particularly as a winter cover crop in northern China because of its low-temperature tolerance and low water demand. Recently, O. violaceus has also been cultivated as a potential industrial oilseed crop because of its abundant 24-carbon dihydroxy fatty acids (diOH-FAs), which contribute to superior high-temperature lubricant properties.

Association mapping across a multitude of traits collected in diverse environments in maize.

Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits.

The Unique Seed Protein Composition of Quality Protein Popcorn Promotes Growth of Beneficial Bacteria From the Human Gut Microbiome.

The effects of fiber, complex carbohydrates, lipids, and small molecules from food matrices on the human gut microbiome have been increasingly studied. Much less is known about how dietary protein can influence the composition and function of the gut microbial community. Here, we used near-isogenic maize lines of conventional popcorn and quality-protein popcorn (QPP) to study the effects of the mutation and associated quality-protein modifiers on the human gut microbiome.

Genetic and Biochemical Investigation of Seed Fatty Acid Accumulation in Arabidopsis.

As a vegetable oil, consisting principally of triacylglycerols, is the major storage form of photosynthetically-fixed carbon in oilseeds which are of significant agricultural and industrial value. Photosynthesis in chlorophyll-containing green seeds, along with photosynthesis in leaves and other green organs, generates ATP and reductant (NADPH and NADH) needed for seed fatty acid production. However, contribution of seed photosynthesis to fatty acid accumulation in seeds have not been well-defined.

High-Throughput Profiling of Metabolic Phenotypes Using High-Resolution GC-MS.

Metabolite profiling provides insights into the metabolic signatures, which themselves are considered as phonotypes closely related to the agronomic and phenotypic traits such as yield, nutritional values, stress resistance, and nutrient use efficiency. GC-MS is a sensitive and high-throughput analytical platform and has been proved to be a vital tool for the analysis of primary metabolism to provide an overview of cellular and organismal metabolic status. The potential of GC-MS metabolite profiling as a tool for detecting metabolic changes in plants grown in a high-throughput plant phenotyping platform was explored.

Experimental Design for Controlled Environment High-Throughput Plant Phenotyping.

It is essential that the scientific community develop and deploy accurate and high-throughput techniques to capture factors that influence plant phenotypes if we are to meet the projected demands for food and energy. In recognition of this fact, multiple research institutions have invested in automated high-throughput plant phenotyping (HTPP) systems designed for use in controlled environments. These systems can generate large amounts of data in relatively short periods of time, potentially allowing researchers to gain insights about phenotypic responses to environmental, biological, and management factors.

Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize.

The root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here, we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (.

Divergent evolution of extreme production of variant plant monounsaturated fatty acids.

Metabolic extremes provide opportunities to understand enzymatic and metabolic plasticity and biotechnological tools for novel biomaterial production. We discovered that seed oils of many species contain up to 92% of the unusual monounsaturated petroselinic acid (18:1Δ6), one of the highest reported levels for a single fatty acid in plants. Supporting the biosynthetic origin of petroselinic acid, we identified a Δ6-stearoyl-acyl carrier protein (18:0-ACP) desaturase from , closely related to a previously identified Δ6-palmitoyl-ACP desaturase that produces sapienic acid (16:1Δ6)-rich oils in seeds.