Rice co-expression network analysis identifies gene modules associated with agronomic traits.

Identifying trait-associated genes is critical for rice (Oryza sativa) improvement, which usually relies on map-based cloning, quantitative trait locus analysis, or genome-wide association studies. Here we show that trait-associated genes tend to form modules within rice gene co-expression networks, a feature that can be exploited to discover additional trait-associated genes using reverse genetics. We constructed a rice gene co-expression network based on the graphical Gaussian model using 8,456 RNA-seq transcriptomes, which assembled into 1,286 gene co-expression modules functioning in diverse pathways. A number of the modules were enriched with genes associated with agronomic traits, such as grain size, grain number, tiller number, grain quality, leaf angle, stem strength, and anthocyanin content, and these modules are considered to be trait-associated gene modules. These trait-associated gene modules can be used to dissect the genetic basis of rice agronomic traits and to facilitate the identification of trait genes. As an example, we identified a candidate gene, OCTOPUS-LIKE 1 (OsOPL1), a homolog of the Arabidopsis (Arabidopsis thaliana) OCTOPUS gene, from a grain size module and verified it as a regulator of grain size via functional studies. Thus, our network represents a valuable resource for studying trait-associated genes in rice.

Basidiomycete-specific PsCaMKL1 encoding a CaMK-like protein kinase is required for full virulence of Puccinia striiformis f. sp. tritici.

Calcium/calmodulin-dependent kinases (CaMKs) are Ser/Thr protein kinases (PKs) that respond to changes in cytosolic free Ca2+ and play diverse roles in eukaryotes. In fungi, CAMKs are generally classified into four families CAMK1, CAMKL, RAD53 and CAMK-Unique. Among these, CAMKL constitutes the largest family. In some fungal plant pathogens, members of the CaMKL family have been shown to be responsible for pathogenesis. However, little is known about their role(s) in rust fungi. In this study, we functionally characterized a novel PK gene, PsCaMKL1, from Puccinia striiformis f. sp. tritici (Pst). PsCaMKL1 belongs to a group of PKs that is evolutionarily specific to basidiomyceteous fungi. PsCaMKL1 shows little intra-species polymorphism between Pst isolates. PsCaMKL1 transcripts are highly elevated at early infection stages, whereas gene expression is downregulated in barely germinated urediospores under KN93 treatment. Overexpression of PsCaMKL1 in fission yeast increased resistance to environmental stresses. Knock down of PsCaMKL1 using host-induced gene silencing (HIGS) reduced the virulence of Pst accompanied by reactive oxygen species (ROS) accumulation and a hypersensitive response. These results suggest that PsCaMKL1 is a novel pathogenicity factor that exerts it virulence function by regulating ROS production in wheat.

Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism.

Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated, but related comprehensive gene co-expression network analyses are lacking. We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm. The analysis identified 149 gene co-expression modules, which we considered to be gene expression programs (GEPs). By examining their spatiotemporal expression, we identified GEPs specifically expressed in major root cell types along their developmental trajectories. These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators. As examples, a GEP specific for the quiescent center (QC) contains 20 genes regulating QC and stem cell niche homeostasis, and four GEPs are expressed in sieve elements (SEs) from early to late developmental stages, with the early-stage GEP containing 17 known SE developmental regulators. We also identified GEPs for metabolic pathways with cell-type-specific expression, suggesting the existence of cell-type-specific metabolism in roots. Using the GEPs, we discovered and verified a columella-specific gene, NRL27, as a regulator of the auxin-related root gravitropism response. Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.