Leaf Senescence Regulation Mechanism Based on Comparative Transcriptome Analysis in Foxtail Millet.

Leaf senescence, a pivotal process in plants, directly influences both crop yield and nutritional quality. Foxtail millet (Setaria italica) is a C4 model crop renowned for its exceptional nutritional value and stress tolerance characteristics. However, there is a lack of research on the identification of senescence-associated genes (SAGs) and the underlying molecular regulatory mechanisms governing this process. In this study, a dark-induced senescence (DIS) experimental system was applied to investigate the extensive physiological and transcriptomic changes in two foxtail millet varieties with different degrees of leaf senescence. The physiological and biochemical indices revealed that the light senescence (LS) variety exhibited a delayed senescence phenotype, whereas the severe senescence (SS) variety exhibited an accelerated senescence phenotype. The most evident differences in gene expression profiles between these two varieties during DIS included photosynthesis, chlorophyll, and lipid metabolism. Comparative transcriptome analysis further revealed a significant up-regulation of genes related to polysaccharide and calcium ion binding, nitrogen utilization, defense response, and malate metabolism in LS. In contrast, the expression of genes associated with redox homeostasis, carbohydrate metabolism, lipid homeostasis, and hormone signaling was significantly altered in SS. Through WGCNA and RT-qPCR analyses, we identified three SAGs that exhibit potential negative regulation towards dark-induced leaf senescence in foxtail millet. This study establishes the foundation for a further comprehensive examination of the regulatory network governing leaf senescence and provides potential genetic resources for manipulating senescence in foxtail millet.

Mapping and Screening of Candidate Gene Regulating the Biomass Yield of Sorghum (Sorghum bicolor L.).

Biomass yield is one of the important traits of sorghum, which is greatly affected by leaf morphology. In this study, a lobed-leaf mutant (sblob) was screened and identified, and its F2 inbred segregating line was constructed. Subsequently, MutMap and whole-genome sequencing were employed to identify the candidate gene (sblob1), the locus of which is Sobic.003G010300. Pfam and homologous analysis indicated that sblob1 encodes a Cytochrome P450 protein and plays a crucial role in the plant serotonin/melatonin biosynthesis pathway. Structural and functional changes in the sblob1 protein were elucidated. Hormone measurements revealed that sblob1 regulates both leaf morphology and sorghum biomass through regulation of the melatonin metabolic pathway. These findings provide valuable insights for further research and the enhancement of breeding programs, emphasizing the potential to optimize biomass yield in sorghum cultivation.

Small Papillae Regulated by SPD25 are Critical for Balancing Photosynthetic CO2 Assimilation and Water Loss in Rice.

BACKGROUND: The leaf epidermis plays an important role in the transmission of light and the regulation of water and gas exchange, which influences the photosynthesis of mesophyll cells. Small papillae (SP) are one of the important structural elements of the leaf epidermis. The mechanism of the effect that small papillae have on rice leaf photosynthetic performance remains unclear. RESULTS: In this study, a small papilla deficient 25 (spd25) mutant was isolated from japonica rice Longjin1. Small papillae were absent on the adaxial and abaxial leaf surfaces of the spd25 mutant and the silicon and cuticular wax content in the spd25 mutant leaves decreased. Map-based cloning and functional analysis revealed that SPD25, encoding a guanine nucleotide exchange factor for Rop, is a novel allele of OsRopGEF10. The spd25 mutant showed an increased water loss rate and reduced relative water content. The lower stomatal conductance in the spd25 mutant prevented water loss but decreased the intercellular CO2 concentration and net assimilation rate. The fluorescence parameters showed that the inhibited CO2 assimilation reaction feedback regulated the photochemical electron-transfer reaction, but the performance of Photosystem II was stable. Further analysis indicated that the excess light energy absorbed by the spd25 mutant was dissipated in the form of non-photochemical quenching to avoid photodamage through the optical properties of small papillae. CONCLUSIONS: SPD25 regulates the development of small papillae on the surface of rice leaves, which play an important role in balancing photosynthetic gas exchange and water loss. This study deepens our understanding of the physiological mechanisms by which small papillae affect photosynthetic performance.

Integrated Metabolomic and Transcriptomic Analyses Reveal the Basis for Carotenoid Biosynthesis in Sweet Potato (Ipomoea batatas (L.) Lam.) Storage Roots.

Carotenoids are important compounds of quality and coloration within sweet potato storage roots, but the mechanisms that govern the accumulation of these carotenoids remain poorly understood. In this study, metabolomic and transcriptomic analyses of carotenoids were performed using young storage roots (S2) and old storage roots (S4) from white-fleshed (variety S19) and yellow-fleshed (variety BS) sweet potato types. S19 storage roots exhibited significantly lower total carotenoid levels relative to BS storage roots, and different numbers of carotenoid types were detected in the BS-S2, BS-S4, S19-S2, and S19-S4 samples. ß-cryptoxanthin was identified as a potential key driver of differences in root coloration between the S19 and BS types. Combined transcriptomic and metabolomic analyses revealed significant co-annotation of the carotenoid and abscisic acid (ABA) metabolic pathways, PSY (phytoene synthase), CHYB (ß-carotene 3-hydroxylase), ZEP (zeaxanthin epoxidase), NCED3 (9-cis-epoxycarotenoid dioxygenase 3), ABA2 (xanthoxin dehydrogenase), and CYP707A (abscisic acid 8'-hydroxylase) genes were found to be closely associated with carotenoid and ABA content in these sweet potato storage roots. The expression patterns of the transcription factors OFP and FAR1 were associated with the ABA content in these two sweet potato types. Together, these results provide a valuable foundation for understanding the mechanisms governing carotenoid biosynthesis in storage roots, and offer a theoretical basis for sweet potato breeding and management.

Identification and function analysis of yellow-leaf mutant (YX-yl) of broomcorn millet.

BACKGROUND: Broomcorn millet is highly tolerant to drought and barren soil. Changes in chlorophyll content directly affect leaf color, which subsequently leadsleading to poor photosynthetic performance and reduced crop yield. Herein, we isolated a yellow leaf mutant (YX-yl) using a forward genetics approach and evaluated its agronomic traits, photosynthetic pigment content, chloroplast ultrastructure, and chlorophyll precursors. Furthermore, the molecular mechanism of yellowing was explored using transcriptome sequencing. RESULTS: The YX-yl mutant showed significantly decreased plant height and low yield. The leaves exhibited a yellow-green phenotype and poor photosynthetic capacity during the entire growth period. The content of chlorophyll a, chlorophyll b, and carotenoids in YX-yl leaves was lower than that in wild-type leaves. Chlorophyll precursor analysis results showed that chlorophyll biosynthesis in YX-yl was hindered by the conversion of porphobilinogen to protoporphyrin IX. Examination of chloroplast ultrastructure in the leaves revealed that the chloroplasts of YX-yl accumulated on one side of the cell. Moreover, the chloroplast structure of YX-yl was degraded. The inner and outer membranes of the chloroplasts could not be distinguished well. The numbers of grana and grana thylakoids in the chloroplasts were low. The transcriptome of the yellowing mutant YX-yl was sequenced and compared with that of the wild type. Nine chlorophyll-related genes with significantly different expression profiles were identified: PmUROD, PmCPO, PmGSAM, PmPBDG, PmLHCP, PmCAO, PmVDE, PmGluTR, and PmPNPT. The proteins encoded by these genes were located in the chloroplast, chloroplast membrane, chloroplast thylakoid membrane, and chloroplast matrix and were mainly involved in chlorophyll biosynthesis and redox-related enzyme regulation. CONCLUSIONS: YX-yl is an ideal material for studying pigment metabolism mechanisms. Changes in the expression patterns of some genes between YX-yl and the wild type led to differences in chloroplast structures and enzyme activities in the chlorophyll biosynthesis pathway, ultimately resulting in a yellowing phenotype in the YX-yl mutant. Our findings provide an insight to the molecular mechanisms of leaf color formation and chloroplast development in broomcorn millet.

Higher CO2 Assimilation in Selected Rice Recombinant Inbred Lines Is Driven by Higher CO2 Diffusion and Light Use Efficiency Related to Leaf Anatomy and Mesophyll Cell Density.

Leaf anatomy determining the light distribution within the leaf and exerting influence on CO2 diffusion is considered to have dramatic potential for photosynthesis performance increase. In this study, we observed that two rice recombinant inbred lines, H138 and H217 (RILF11 plants from Sasanishiki × IRAT10), have higher net CO2 assimilation (An) than their parent Sasanishiki due mainly to the improvement of leaf anatomy. Our results showed that An positively correlated with anatomy traits' mesophyll cell number per cross-sectional area (NO.mescell/Acros) and mesophyll area (Ames). NO.mescell/Acros exert direct and indirect effects on An. Compared to Sasanishiki flag leaves, IRAT10, H138, and H217 have higher mesophyll cell numbers. Simultaneously, higher chlorophyll content and expression of genes encoding the light-harvesting protein of PSII and PSI (Lhcb1, 2, 3 and Lhca1, 2, 3) were recorded in IRAT10, H138, and H217, which facilitates light use efficiency. Higher electron transport rate and RuBP concentration were recorded in IRAT10, H138, and H217 flag leaves. Retinoblastoma-related gene (OsRBR1), exerting effects on mesophyll cell density, can be used to modify leaf anatomy for improving leaf photosynthesis. Additionally, higher stomatal conductance and mesophyll conductance were also recorded in H138 and H217 than in Sasanishiki. Furthermore, we modeled mesophyll conductance through anatomical traits, and the results revealed that chloroplast thickness was the dominant factor restricting CO2 diffusion within mesophyll cells rather than cell wall thickness. Higher RuBP content accompanied by higher CO2 concentration within the carboxylation set in H138 and H217 flag leaves contributed to higher CO2 assimilation.

Photorespiration Regulates Carbon-Nitrogen Metabolism by Magnesium Chelatase D Subunit in Rice.

The growth and development of plants are dependent on the interaction between carbon and nitrogen metabolism. Essential information about the metabolic regulation of carbon-nitrogen metabolism is still lacking, such as possible interactions among nitrogen metabolism, photosynthesis, and photorespiration. This study shows that higher photorespiration consumes more CO2 fixed by photosynthesis, making the high photosynthetic efficiency mutant fail to increase production. In order to clarify the effects of photosynthesis and photorespiration on carbon and nitrogen metabolism in high photosynthetic efficiency mutant, a yellow-green leaf mutant (ygl53) was isolated from rice (Oryza sativa L.). Its chlorophyll (Chl) content decreased, but chloroplast development was not affected. Genetic analysis demonstrated that YGL53 encodes the magnesium chelatase D subunit (ChlD). The ygl53 mutant showed an increased net assimilation rate (An) and electron transport flux efficiency and catalase (CAT) activity, and it also had a higher photorespiration rate (Pr), lower H2O2, and reduced nitrogen uptake efficiency (NUpE); however, there was no loss in yield. The higher activities of glutamate synthase (GOGAT) and glutamine synthetase (GS) ensure the α-ketoglutaric acid (2-OG) and ammonia (NH3) availabilities, which are produced from photorespiration in the ygl53 mutant. These have an important function for carbon and nitrogen metabolism homeostasis in ygl53. Further analysis indicated that the energy and substances derived from carbon metabolism supplemented nitrogen metabolism in the form of photorespiration to ensure its normal development when the An of photosynthesis was increased in the ygl53 mutant with reduced NUpE.

Disentangling the photosynthesis performance in japonica rice during natural leaf senescence using OJIP fluorescence transient analysis.

Rice undergoes leaf senescence accompanied with grain filling when the plants reach the end of their temporal niche, and a delay in leaf senescence ultimately improves the yield and quality of grain. To estimate the decline in photosynthesis during leaf senescence and to find an efficient and useful tool to identify rice genotypes with a longer duration of active photosynthesis, we examined PSII photosynthetic activity in the flag leaves of japonica rice Shennong265 (SN265) and Beigeng3 (BG3) during leaf senescence using chlorophyll a fluorescence kinetics. The results show that inhibition occurred in the electron transport chains, but the energetic connectivity of PSII units was not affected as dramatically during leaf senescence. PSII reaction centres (RCs) were transformed into 'silent RCs,' and the chlorophyll content decreased during leaf senescence. However the size of the 'economic' antennae increased. Further, the percentage of variation of the specific energy flux parameters can rationally be used to indicate leaf senescence from the perspective of energy balance. Although the performance indices were more sensitive than other functional and structural JIP-test parameters, they still did not serve as an indicator of crop yield.