Natural alleles of the abscisic acid catabolism gene ZmAbh4 modulate water use efficiency and carbon isotope discrimination in maize

Genome editing in maize and sorghum: A comprehensive review of CRISPR/Cas9 and emerging technologies

The increasing changes in the climate patterns across the globe have deeply affected food systems where unparalleled and unmatched challenges are created. This jeopardizes food security due to an ever-increasing population. The extreme efficiency of C4 crops as compared to C3 crops makes them incredibly significant in securing food safety. C4 crops, maize (Zea mays L.) and sorghum (Sorghum bicolor L. Moench) in particular, have the ability to withstand osmotic stress induced by oxidative stress. Osmotic stress causes a series of physical changes in a plant thus facilitating reduced water uptake and photosynthesis inhibition, such as membrane tension, cell wall stiffness, and turgor changes. There has been a great advancement in plant breeding brought by introduction of clustered regularly interspaced short palindromic repeats (CRISPR) gene editing technology. This technology offers precise alterations to an organism's DNA through targeting specific genes for desired traits in a wide number of crop species. Despite its immense opportunities in plant breeding, it faces limitations such as effective delivery systems, editing efficiency, regulatory concerns, and off-target effects. Future prospects lie in optimizing next-generation techniques, such as prime editing, and developing novel genotype-independent delivery methods. Overall, the transformative role of CRISPR/Cas9 in sorghum and maize breeding underscores the need for responsible and sustainable utilization to address global food security challenges.

Identification of the maize drought-resistant gene Zinc-finger Inflorescence Meristem 23 through high-resolution temporal transcriptome analysis

Drought is a major abiotic stress that significantly limits maize productivity. However, previous transcriptomic studies with limited time-point sampling have hindered the construction of robust co-expression networks, making it challenging to identify reliable hub genes involved in drought tolerance. To overcome this limitation, we generated a high-temporal-resolution transcriptome dataset spanning 108 time points from maize seedlings subjected to two consecutive rounds of drought and re-watering treatments. A total of 8477 drought-responsive genes (DRGs) were identified by comparing drought-stressed and well-watered controls. Using weighted gene co-expression network analysis (WGCNA), we constructed 17 co-expression modules, of which 8 were strongly associated with drought stress responses and collectively contained 353 hub genes. Among them, we validated the drought resistance functions of ZmCPK35, a known drought-responsive gene, and Zinc-finger Inflorescence Meristem 23 (ZmZIM23), a newly identified drought-regulatory gene, within the M10 module. Functional analysis revealed that ZmZIM23 enhances drought tolerance by improving water-use efficiency, reducing transpiration rates, and promoting biomass accumulation. Furthermore, yeast one-hybrid (Y1H) and dual-luciferase (LUC) assays demonstrated that ZmWRKY40, another M10 module member, transcriptionally regulates both ZmZIM23 and ZmCPK35. By integrating high-resolution transcriptomic data with co-expression network analyses, this study unveils key drought-responsive regulatory networks in maize and identifies novel candidate genes for improving drought tolerance. These findings provide valuable insights into the genetic foundation of drought adaptation and offer potential targets for the development of drought-resistant maize cultivars.

The combined effect of decreased stomatal density and aperture increases water use efficiency in maize

Stomata play a crucial role in balancing carbon dioxide uptake and water vapor loss, thereby regulating plant water use efficiency (WUE). Enhancing WUE is important for sustainable agriculture and food security, particularly for crops such as maize (Zea mays L.), as climate change and growing global food demand exacerbate limitations on water availability. Genetic factors controlling stomatal density and levels of the plant hormone abscisic acid (ABA) in leaves, which affect stomatal aperture, are key determinants of stomatal conductance (gs) and intrinsic WUE (iWUE). In this study, we demonstrate that stomatal density and stomatal aperture have a combined effect on gs and iWUE in maize. Using near-isogenic lines (NILs) and CRISPR/Cas9 mutants, we show that combining reduced stomatal density and reduced stomatal aperture can improve iWUE without compromising photosynthesis. This effect is pronounced at both, optimal and high temperatures. These findings highlight the potential of targeting multiple stomatal traits through genetic stacking to enhance WUE, offering a promising strategy for crop adaptation to water-limited environments.

Embracing native diversity to enhance the maximum quantum efficiency of photosystem II in maize

The sustainability of maize cultivation would benefit tremendously from early sowing, but is hampered by low temperatures during early development in temperate climates. We show that allelic variation within the gene encoding subunit M of the NADH-dehydrogenase-like (NDH) complex (ndhm1) in a European maize landrace affects several quantitative traits that are relevant during early development in cold climates through NDH-mediated cyclic electron transport around photosystem I, a process crucial for photosynthesis and photoprotection. Beginning with a genome-wide association study for maximum potential quantum yield of photosystem II in dark-adapted leaves (Fv/Fm), we capitalized on the large phenotypic effects of a hAT transposon insertion in ndhm1 on multiple quantitative traits (early plant height [EPH], Fv/Fm, chlorophyll content, and cold tolerance) caused by the reduced protein levels of NDHM and associated NDH components. Analysis of the ndhm1 native allelic series revealed a rare allele of ndhm1 that is associated with small albeit significant improvements of Fv/Fm, photosystem II efficiency in light-adapted leaves (ΦPSII), and EPH compared with common alleles. Our work showcases the extraction of favorable alleles from locally adapted landraces, offering an efficient strategy for broadening the genetic variation of elite germplasm by breeding or genome editing.

A module involving HIGH LEAF TEMPERATURE1 controls instantaneous water use efficiency

Drought stress inhibits plant growth and agricultural production. Improving plant instantaneous water use efficiency (iWUE), which is strictly regulated by stomata, is an effective way to cope with drought stress. However, the mechanisms of iWUE regulation are poorly understood. Through genetic screening for suppressors of mpk12-4, an Arabidopsis (Arabidopsis thaliana) mutant with a major iWUE quantitative trait locus gene MITOGEN-ACTIVATED PROTEIN KINASE12 deleted, we identified HIGH LEAF TEMPERATURE1 (HT1). Genetic interaction and physiological analyses showed that MPK12 controls iWUE through multiple modules in a high CO2-induced stomatal closing pathway that regulate SLOW ANION CHANNEL-ASSOCIATED1 (SLAC1) activity. HT1 acts downstream of MPK12, whereas OPEN STOMATA1 (OST1) and GUARD CELL HYDROGEN PEROXIDE-RESISTANT1 (GHR1) function downstream of HT1 by activating SLAC1 in iWUE. Photosynthetic-CO2 response curves and biomass analyses under different water-supply conditions showed that HT1 dysfunction improved iWUE and also increased plant growth capacity, and products of HT1 putative orthologs from Brassica (Brassica napus) and rice (Oryza sativa) exhibited functions similar to that of Arabidopsis HT1 in iWUE and the CO2-signaling pathway. Our study revealed the mechanism of MPK12-mediated iWUE regulation in Arabidopsis and provided insight into the internal relationship between iWUE and CO2 signaling in guard cells and a potential target for improving crop iWUE and drought tolerance.

Phosphorylation of ZmAL14 by ZmSnRK2.2 regulates drought resistance through derepressing ZmROP8 expression

Drought stress has negative effects on crop growth and production. Characterization of transcription factors that regulate the expression of drought-responsive genes is critical for understanding the transcriptional regulatory networks in response to drought, which facilitates the improvement of crop drought tolerance. Here, we identified an Alfin-like (AL) family gene ZmAL14 that negatively regulates drought resistance. Overexpression of ZmAL14 exhibits susceptibility to drought while mutation of ZmAL14 enhances drought resistance. An abscisic acid (ABA)-activated protein kinase ZmSnRK2.2 interacts and phosphorylates ZmAL14 at T38 residue. Knockout of ZmSnRK2.2 gene decreases drought resistance of maize. A dehydration-induced Rho-like small guanosine triphosphatase gene ZmROP8 is directly targeted and repressed by ZmAL14. Phosphorylation of ZmAL14 by ZmSnRK2.2 prevents its binding to the ZmROP8 promoter, thereby releasing the repression of ZmROP8 transcription. Overexpression of ZmROP8 stimulates peroxidase activity and reduces hydrogen peroxide accumulation after drought treatment. Collectively, our study indicates that ZmAL14 is a negative regulator of drought resistance, which can be phosphorylated by ZmSnRK2.2 through the ABA signaling pathway, thus preventing its suppression on ZmROP8 transcription during drought stress response.

Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat

BACKGROUND

Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated.

RESULTS

Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency.

CONCLUSIONS

This study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.

Strategies and Methods for Improving the Efficiency of CRISPR/Cas9 Gene Editing in Plant Molecular Breeding

Following recent developments and refinement, CRISPR-Cas9 gene-editing technology has become increasingly mature and is being widely used for crop improvement. The application of CRISPR/Cas9 enables the generation of transgene-free genome-edited plants in a short period and has the advantages of simplicity, high efficiency, high specificity, and low production costs, which greatly facilitate the study of gene functions. In plant molecular breeding, the gene-editing efficiency of the CRISPR-Cas9 system has proven to be a key step in influencing the effectiveness of molecular breeding, with improvements in gene-editing efficiency recently becoming a focus of reported scientific research. This review details strategies and methods for improving the efficiency of CRISPR/Cas9 gene editing in plant molecular breeding, including Cas9 variant enzyme engineering, the effect of multiple promoter driven Cas9, and gRNA efficient optimization and expression strategies. It also briefly introduces the optimization strategies of the CRISPR/Cas12a system and the application of BE and PE precision editing. These strategies are beneficial for the further development and optimization of gene editing systems in the field of plant molecular breeding.

Relationships between stable isotope natural abundances (δ13C and δ15N) and water use efficiency in rice under alternate wetting and drying irrigation in soils with high clay contents

Natural abundance of the stable isotope (δ¹³C and δ¹⁵N) in plants is widely used to indicate water use efficiency (WUE). However, soil water and texture properties may affect this relationship, which remains largely elusive. Therefore, the purpose of this study was to evaluate δ¹³C as affected by different combinations of alternate wetting and drying irrigation (AWD) with varied soil clay contents in different organs and whole plant and assess the feasibility of using δ¹³C and δ¹⁵N as a physiological indicator of whole-plant water use efficiency (WUE_whole-plant). Three AWD regimes, I₁₀₀ (30 mm flooded when soil reached 100% saturation), I₉₀ (30 mm flooded when reached 90% saturation) and I₇₀ (30 mm flooded when reached 70% saturation) and three soil clay contents, 40% (S₄₀), 50% (S₅₀), and 60% (S₆₀), were included. Observed variations in WUE_whole-plant did not conform to theoretical expectations of the organs δ¹³C (δ¹³C_organs) of plant biomass based on pooled data from all treatments. However, a positive relationship between δ¹³C_leaf and WUE_ET (dry biomass/evapotranspiration) was observed under I₉₀ regime, whereas there were no significant relationships between δ¹³C_organs and WUE_ET under I₁₀₀ or I₇₀ regimes. Under I₁₀₀, weak relationships between δ¹³C_organs and WUE_ET could be explained by (i) variation in C allocation patterns under different clay content, and (ii) relatively higher rate of panicle water loss, which was independent of stomatal regulation and photosynthesis. Under I₇₀, weak relationships between δ¹³C_organs and WUE_ET could be ascribed to (i) bigger cracks induced by water-limited irrigation regime and high clay content soil, and (ii) damage caused by severe drought. In addition, a negative relationship was observed between WUE_whole-plant and shoot δ¹⁵N (δ¹⁵N_shoot) across the three irrigation treatments, indicating that WUE_whole-plant is tightly associated with N metabolism and N isotope discrimination in rice. Therefore, δ¹³C should be used cautiously as an indicator of rice WUE_whole-plant at different AWD regimes with high clay content, whereas δ¹⁵N could be considered an effective indicator of WUE_whole-plant.