SiSTL2 Is Required for Cell Cycle, Leaf Organ Development, Chloroplast Biogenesis, and Has Effects on C4 Photosynthesis in Setaria italica (L.) P. Beauv

Transcriptome Analysis Revealed ZmPTOX1 Is Required for Seedling Development and Stress Tolerance in Maize

Plant seedling morphogenesis is considerably related to photosynthesis, pigment synthesis, and circadian periodicity during seedling development. We identified and cloned a maize zebra or crossbanding leaves mutant wk3735, which produces pale white kernels and was identified and plays a role in the equilibrium of the Redox state the in/out of ETC by active oxygen scavenging. Interestingly, it produces the zebra leaves during the production of the first seven leaves, which is apparently different from the mutation of homologs AtPTOX in Arabidopsis. It is intriguing to investigate how and why yellow crossbands (zebra leaf phenotype) emerge on leaves. As expected, chlorophyll concentration and photosynthetic efficiency both significantly declined in the yellow sector of wk3735 leaves. Meanwhile, we observed the circadian expression pattern of ZmPTOX1, which was further validated by protein interaction assays of the circadian clock protein TIM1 and ZmPTOX1. The transcriptome data of yellow (muW) and green (muG) sectors of knock-out lines and normal leaves of overexpression lines (OE) at the 5th-leaf seedling stage were analyzed. Zebra leaf etiolated sections exhibit a marked defect in the expression of genes involved in the circadian rhythm and rhythmic stress (light and cold stress) responses than green sections. According to the analysis of co-DEGs of muW vs. OE and muG vs. OE, terms linked to cell repair function were upregulated while those linked to environmental adaptability and stress response were downregulated due to the mutation of ZmPTOX1. Further gene expression level analyses of reactive oxygen species (ROS) scavenging enzymes and detection of ROS deposition indicated that ZmPTOX1 played an essential role in plant stress resistance and ROS homeostasis. The pleiotropic roles of ZmPTOX1 in plant ROS homeostasis maintenance, stress response, and circadian rhythm character may collectively explain the phenotype of zebra leaves during wk3735 seedling development.

Melatonin enhances drought tolerance by affecting jasmonic acid and lignin biosynthesis in wheat (Triticum aestivum L.)

Drought severely affects the yield of wheat (Triticum aestivum L.), which is mainly grown in arid and semi-arid regions. Melatonin plays an important role in various types of stress resistance in plants, including drought resistance. However, the molecular mechanism through which melatonin affects drought tolerance remains largely unknown. In this study, we revealed that melatonin (100 μM) significantly improved drought resistance during the maturation stage of Chinese Spring, Shi4185, and Hanxuan10 varieties, but not Chang6878. Further physiological, transcriptomic, and proteomic data analysis at the wheat seedling stage revealed that melatonin increased jasmonic acid (JA) content, upregulating the expression of JA genes (LOX1.5 and LOX2.1) and two transcription factors (HY5 and MYB86) under drought conditions. It also upregulated genes related to lignin biosynthesis (4CL2, P5CS1, and CCR2) as well as starch and sucrose metabolism (PME53 and SUS4). Additionally, melatonin alleviated photosynthetic and cell membrane damage caused by drought stress through maintaining low levels of hydrogen peroxide. The current results elucidate melatonin-regulated pathways in wheat and provide evidence for using melatonin as a potential biostimulant to improve wheat drought resistance under field conditions in the future.

An E2-E3 pair contributes to seed size control in grain crops

Understanding the molecular mechanisms that regulate grain yield is important for improving agricultural productivity. Protein ubiquitination controls various aspects of plant growth but lacks understanding on how E2-E3 enzyme pairs impact grain yield in major crops. Here, we identified a RING-type E3 ligase SGD1 and its E2 partner SiUBC32 responsible for grain yield control in Setaria italica. The conserved role of SGD1 was observed in wheat, maize, and rice. Furthermore, SGD1 ubiquitinates the brassinosteroid receptor BRI1, stabilizing it and promoting plant growth. Overexpression of an elite SGD1 haplotype improved grain yield by about 12.8% per plant, and promote complex biological processes such as protein processing in endoplasmic reticulum, stress responses, photosystem stabilization, and nitrogen metabolism. Our research not only identifies the SiUBC32-SGD1-BRI1 genetic module that contributes to grain yield improvement but also provides a strategy for exploring key genes controlling important traits in Poaceae crops using the Setaria model system.

Identification and haplotype analysis of SiCHLI: a gene for yellow-green seedling as morphological marker to accelerate foxtail millet (Setaria italica) hybrid breeding

We cloned and developed functional markers for the SiCHLI gene, which is responsible for the yellow-green color of leaves in foxtail millet, a frequently used marker trait in the hybrid breeding of foxtail millet by using bulked segregant analysis sequencing and haplotype analysis on the F₂ and core-collected nature populations. The color of leaves has been widely used as a marker for the hybrid breeding of foxtail millet; however, few related gene have been cloned to date. Here, we used two F₂ populations generated from crosses between the highly male-sterile material 125A with yellow-green leaves, and CG58 and S410, which have green leaves, to identify the genes underlying the yellow-green color of the leaves of foxtail millet. The leaves of 125A seedlings were yellow-green, but they became green at the heading stage. The content of chlorophyll a and chlorophyll b was lower, the number of thylakoid lamellae and grana was reduced, and the chloroplasts was more rounded in 125A than in S410 at the yellow-green leaf stage; however, no differences were observed between 125A and S410 in these traits and photosynthetic at the heading stage. Bulked segregant analysis and map-based cloning revealed that the SiCHLI gene is responsible for the leaf colors of 125A. A nonsynonymous mutation (C/T) in exon 3 causes yellow-green leaves in 125A at the seedling stage. Haplotype analysis of the SiCHLI gene in 596 core collected accessions revealed a new haplotype associated with high photosynthetic metabolic potential at the heading and mature stages, which could be used to enhance sterile lines with yellow-green leaves. We developed a functional marker that will facilitate the identification of foxtail millet accessions with the different types of yellow-green leaves. Generally, our study provides new genetic resources to guide the future marker-assisted or target-base editing in foxtail millet hybrid breeding.

Revitalization of small millets for nutritional and food security by advanced genetics and genomics approaches

Small millets, also known as nutri-cereals, are smart foods that are expected to dominate food industries and diets to achieve nutritional security. Nutri-cereals are climate resilient and nutritious. Small millet-based foods are becoming popular in markets and are preferred for patients with celiac and diabetes. These crops once ruled as food and fodder but were pushed out of mainstream cultivation with shifts in dietary habits to staple crops during the green revolution. Nevertheless, small millets are rich in micronutrients and essential amino acids for regulatory activities. Hence, international and national organizations have recently aimed to restore these lost crops for their desirable traits. The major goal in reviving these crops is to boost the immune system of the upcoming generations to tackle emerging pandemics and disease infestations in crops. Earlier periods of civilization consumed these crops, which had a greater significance in ethnobotanical values. Along with nutrition, these crops also possess therapeutic traits and have shown vast medicinal use in tribal communities for the treatment of diseases like cancer, cardiovascular disease, and gastrointestinal issues. This review highlights the significance of small millets, their values in cultural heritage, and their prospects. Furthermore, this review dissects the nutritional and therapeutic traits of small millets for developing sustainable diets in near future.

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C₄ photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.

Foxtail millet [Setaria italica (L.) Beauv.] over-accumulates ammonium under low nitrogen supply

Nitrogen (N) deficiency is a primary limiting factor for crop production worldwide. Previously, we reported root system architectural modifications of hydroponically cultured foxtail millet [Setaria italica (L.) Beauv.] to facilitate N translocation under N limitation. Here, we investigated foxtail millet for its shoot adaptation to low N in terms of internal N regulation under hydroponic culture. The results of this study revealed that the shoot N and nitrate (NO₃^-) concentrations significantly declined as compared to control (CK); however, the shoot over-accumulated ammonium (NH₄⁺) under low N (LN). N shortage resulted in down-regulation of expressions of SiPetA, SiccsA, SipsbA, SirpoB, SipsaA, SiatpA, Sirps16, and SiPEPC which, undermined chloroplast functioning and CO₂ assimilation for the provision of carbon skeleton. Carbon deficiency and lower activities of GS decelerated ammonia assimilation and led to over-accumulation of NH₄⁺ in the LN-shoot, as indicated by lower concentrations of total amino acids. Thus, enhanced GOGAT activity was to assimilate NH₄⁺ while, those of catalase (CAT), superoxide dismutase (SOD) and peroxidase (POD) were to scavenge reactive oxygen species (ROS) of NH₄⁺ toxicity framework. The weakened chloroplast factory eventually minimized photosynthesis and reduced dry mass of the LN shoot. Such regulation of N by the shoot, perhaps, resurrected physiological functions which maintained internal mineral status under nitrogen limitation in foxtail millet.

Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety "SSR41" and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1

Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the "Yugu1" variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, "SSR41", which is morphologically similar to, and readily cross-pollinates with, "Yugu1". High-throughput resequencing of "SSR41" identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used "SSR41" and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.