The transcriptomic responses of C4 grasses to subambient CO2 and low light are largely species specific and only refined by photosynthetic subtype

Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets

Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.

Leaf pigments and photosystems stoichiometry underpin photosynthetic efficiency of related C3 , C-C4 and C4 grasses under shade

The quantum yield of photosynthesis (QY, CO₂ fixed per light absorbed) depends on the efficiency of light absorption, the coupling between light absorption and electron transport, and the coupling between electron transport and carbon metabolism. QY is generally lower in C₃ relative to C₄ plants at warm temperatures and differs among the C₄ subtypes. We investigated the acclimation to shade of light absorption and electron transport in six representative grasses with C₃ , C₃ -C₄ and C₄ photosynthesis. Plants were grown under full (control) or 25% (shade) sunlight. We measured the in vivo activity and stoichiometry of PSI and PSII, leaf spectral properties and pigment contents, and photosynthetic enzyme activities. Under control growth-light conditions, C₄ species had higher CO₂ assimilation rates, which declined to a greater extent relative to the C₃ species. Whole leaf PSII/PSI ratios were highest in the C₃ species, while QY and cyclic electron flow (CEF) were highest in the C₄ , NADP-ME species. Shade significantly reduced leaf PSII/PSI, linear electron flow (LEF) and CEF of most species. Overall, shade reduced leaf absorptance, especially in the green region, as well as carotenoid and chlorophyll contents in C₄ more than non-C₄ species. The NAD-ME species underwent the greatest reduction in leaf absorptance and pigments under shade. In conclusion, shade compromised QY the least in the C₃ and the most in the C₄ -NAD-ME species. Different sensitivity to shade was associated with the ability to maintain leaf absorptance and pigments. This is important for maximising light absorption and minimising photoprotection under low light.

High intrinsic water use efficiency is underpinned by high stomatal aperture and guard cell potassium flux in C3 and C4 grasses grown at glacial CO2 and low light

We compared how stomatal morphology and physiology control intrinsic leaf water use efficiency (iWUE) in two C3 and six C4 grasses grown at ambient (400 µmol mol-1) or glacial CO2 (180 µmol mol-1) and high (1000 µmol m-2 s-1) or low light intensity (200 µmol m-2 s-1). C4 grasses tended to have higher iWUE and CO2 assimilation rates, and lower stomatal conductance (gs), operational stomatal aperture (aop), and guard cell K+ influx rate relative to C3 grasses, while stomatal size (SS) and stomatal density (SD) did not vary according to the photosynthetic type. Overall, iWUE and gs depended most on aop and density of open stomata. In turn, aop correlated with K+ influx, stomatal opening speed on transition to high light, and SS. Species with higher SD had smaller and faster-opening stomata. Although C4 grasses operated with lower gs and aop at ambient CO2, they showed a greater potential to open stomata relative to maximal stomatal conductance (gmax), indicating heightened stomatal sensitivity and control. We uncovered promising links between aop, gs, iWUE, and K+ influx among C4 grasses, and differential K+ influx responses of C4 guard cells to low light, revealing molecular targets for improving iWUE in C4 crops.