The chloroplast is the primary organelle for photosynthesis in plants. A clade of proteins containing RanBP2-type zinc-finger domain, known as the Organelle Zinc (OZ) finger family, are known or predicted to be targeted to mitochondria or chloroplast. While some OZ proteins have been studied in Arabidopsis, there are few reports of their roles in rice. In this study, we characterized the Organelle Zinc finger family gene OsOZ1 and generated the oz1 mutants using the CRISPR-Cas9 genome editing system in rice. The oz1 mutants exhibited a seedling-lethal chlorosis phenotype, with a significantly reduced chlorophyll content at the third-leaf stage compared to the wild type. Transmission electron microscopy and quantitative real-time PCR analysis revealed that the oz1 mutants displayed abnormal chloroplast development relative to the wild type, along with significant alterations in gene expression levels related to chloroplast development and photosynthesis. The oz1 mutants demonstrated defects in chloroplast RNA editing, particularly in atpA-1148, ndhB-467, ndhB-586, ndhB-737 and ndhB-830, while the splicing of ndhA, trnG and ycf3-1 was significantly decreased in the oz1 mutants compared to the wild type. The yeast two-hybrid assay demonstrated that OsOZ1 interacts with the PPR protein OsSLC1, the ORRM protein OsORRM1 and the MORF/RIP protein OsMORF9. This suggests that OsOZ1 may form complexes with OsSLC1, OsORRM1 and OsMORF9, thereby participating in chloroplast RNA editing and splicing activities. Overall, these findings indicate that OsOZ1 plays a crucial role in chloroplast development by regulating the editing and splicing of chloroplast RNA in rice.

The molecular mechanisms underlying the variation in N-use efficiency (NUE) in pepper (Capsicum annuum L.) genotypes are poorly understood. In this work, two genotypes (750-1, low-N tolerant; ZCFB, low-N sensitive) with contrasting low-N tolerance were selected from 100 pepper cultivars on the basis of their relative leaf areas, shoot dry weights, root dry weights, and plant dry weights at the seedling stage. Subsequently, using RNA-Seq, the transcriptome of these two pepper genotypes under N starvation for 28 days was analyzed. We detected 2621/2470 and 3936/4218 different expressed genes (DEGs) in the leaves/roots of 750-1 and ZCFB, respectively. The changes in the expression of basic N metabolism genes were similar between 750-1 and ZCFB. However, different DEGs not directly involved in N metabolism were identified between the 750-1 and ZCFB cultivars. In 750-1, 110 unique DEGs were detected in the leaves, of which 103 were down-regulated, including genes associated with protein metabolism, photosynthesis, secondary metabolism, cell wall metabolism, stress response, and disease resistance. In ZCFB, 142 unique DEGs were detected in the roots, of which 117 were up-regulated, resulting in enhancement of processes such as protein degradation, secondary metabolites synthesis, lipid metabolism, endocytosis, the tricarboxylic acid cycle (TCA), transcriptional regulation, stress response, and disease resistance. Our results not only facilitate an understanding of the different regulatory process in low-N-tolerant and low-N-sensitive pepper cultivars, but also provide abundant candidate genes for improving the low-N tolerance of pepper cultivars.

Background: Gossypium hirsutum L. is one of the main economic crops worldwide, and increasing the size/weight of its seeds is a potential strategy to improve its seed-related yield. AINTEGUMENTA (ANT) is an organogenesis transcription factor mediating cell proliferation and expansion in Arabidopsis, but little is known about its candidate function in upland cotton seed. Results: In this study, functional characterization of GhANT in the cotton seed development stage was performed. The expression pattern analysis showed that GhANT was predominantly expressed in the ovules, and its expression was consistent with the ovules’ development stage. Heterologous expression of GhANT in Arabidopsis promoted plant organ growth and led to larger seeds. Importantly, specific expression of GhANT by the TFM7 promoter in the cotton ovules enlarged the seeds and increased the cotton seed yield, as compared with the wild-type in a three-year field trial. Furthermore, transcription level analysis showed that numerous genes involved in cell division were up-regulated in the ovules of TFM7::GhANT lines in comparison to the wild-type. These results indicate that GhANT is a potential genetic resource for improving cotton seed yield through its molecular links with cell cycle controllers.

Rapeseed is an important commercial crop globally, used for both animal fodder and human consumption. Varied insolation duration and intensity are among the main factors affecting the seed yield and quality of Brassica napus (B. napus) worldwide. In this study, the high-oil-content rapeseed cultivar “Qingyou 3” was subjected to a light supplementation trial during both the vegetative growth period and the seed productive stage. Different light intensity conditions were stimulated using light-emitting diodes (LEDs). The main plot factor was land condition, with LED treatment (Treatment) and without LED treatment (Control) under natural conditions. The results showed that the leaf size and thickness, photosynthesis efficiency, and seed oil content of B. napus increased significantly after light supplementation. Then, 18 cDNA libraries were constructed from leaf segments (30 days after transplanting—DAT) and seeds 30 and 40 days after pollination (DPA) for RNA transcriptome sequencing. It was found that genes encoding lipid transfer protein, phenylpropanoid biosynthesis, photosynthesis, and plant hormone signal transduction were enriched in differentially expressed genes (DEGs). The qRT-PCR analysis showed that eight key genes had significant variations, a finding also consistent with the RNA-seq results. The aim of this study was to identify the DEGs and signaling pathways in the leaves and seeds of B. napus during the vegetative and seed productive stages under different light intensities. The results provide insight into how sufficient light plays a critical role in promoting photosynthesis and serves as the foundation for material accumulation and yield formation.

The benefits of citrus fruits are strongly associated with their secondary metabolites. In this study, we conducted widely targeted metabolomics analyses to compare the variability of the ingredients in four scion–rootstock combinations. A total of 376 differential metabolites were obtained by a multivariate statistical analysis, and a KEGG pathway analysis showed that the enriched metabolic pathways were mainly related to the biosynthesis of flavonoids as well as lipid metabolism. The anthocyanin-targeted metabolomic features showed that cyanidin 3-O-glucoside, cyanidin 3-O-(6-O-malonyl-beta-D-glucoside), cyanidin 3-O-sophoroside, and cyanidin 3-O-xyloside were the pigments responsible for the red color of Tarocco. A lipid metabolomics analysis revealed that when Tarocco was hetero-grafted with rootstock H, there was an increase in the content of each lipid subclass, accompanied by an increase in the levels of unsaturated fatty acids, including polyunsaturated linoleic and linolenic acids, thus impacting the ratio of unsaturated fatty acids to saturated fatty acids. Additionally, we determined their antioxidant capacity (‘Trifoliate orange’ (Z) > ‘Citrange’ (ZC) > ‘Hongju’ (H) > ‘Ziyang Xiangcheng’ (X)) using in vitro assays. Finally, we utilized a network pharmacology analysis to explore the antioxidant mechanisms and potential pharmacological ingredients; we obtained 26 core targets proteins and 42 core metabolites associated with oxidative damage, providing a basis for future preventive and therapeutic applications of these metabolites.

Introduction: Fruit color is a crucial quality factor strongly influencing consumer preference for citrus. The coloration of citrus fruit is primarily determined by carotenoids, which produce a range of hues. Gibberellic acid (GA) and ethylene are critical in fruit coloration during the ripening process. Nevertheless, the underlying mechanisms remain poorly understood.Methods: The present study utilized transcriptomic and metabolomic analyses to investigate the molecular regulatory mechanisms affecting peel pigment metabolism in tangors (Citrus reticulata Blanco×Citrus sinensis L. Osbeck) following GA and ethephon (ETH) treatments.Results and discussion: Collectively, our findings indicated that GA inhibits chlorophyll degradation and the accumulation of numerous carotenoids, including five violaxanthin esters (violaxanthin palmitate, violaxanthin myristate–caprate, violaxanthin myristate–laurate, violaxanthin dilaurate, violaxanthin myristate) and two β-cryptoxanthin derivatives (β–cryptoxanthin laurate, β–cryptoxanthin myristate), while ETH promotes these processes. Furthermore, GA inhibited the downregulation of lutein, the predominant carotenoid in immature fruits. Notably, integrated transcriptomic and metabolomic analyses identified 33 transcription factors associated with pigment metabolism. Of these, two novel transcription factors, the ethylene-responsive transcription factor ABR1 and the HD-Zip transcription factor ATHB7, were uncovered through both transcriptomic analysis and weighted gene co-expression network analysis. These two transcription factors positively regulated the colouration process, as validated by transient overexpression assays in tobacco. Taken together, our findings elucidated the global carotenoid changes and transcriptional alterations in regulating citrus peel color under hormone induction, with significant implications for improving citrus production.