GmFtsH25 overexpression increases soybean seed yield by enhancing photosynthesis and photosynthates

Plant height measurement using UAV-based aerial RGB and LiDAR images in soybean

Phenotypic traits like plant height are crucial in assessing plant growth and physiological performance. Manual plant height measurement is labor and time-intensive, low throughput, and error-prone. Hence, aerial phenotyping using aerial imagery-based sensors combined with image processing technique is quickly emerging as a more effective alternative to estimate plant height and other morphophysiological parameters. Studies have demonstrated the effectiveness of both RGB and LiDAR images in estimating plant height in several crops. However, there is limited information on their comparison, especially in soybean (Glycine max [L.] Merr.). As a result, there is not enough information to decide on the appropriate sensor for plant height estimation in soybean. Hence, the study was conducted to identify the most effective sensor for high throughput aerial phenotyping to estimate plant height in soybean. Aerial images were collected in a field experiment at multiple time points during soybean growing season using an Unmanned Aerial Vehicle (UAV or drone) equipped with RGB and LiDAR sensors. Our method established the relationship between manually measured plant height and the height obtained from aerial platforms. We found that the LiDAR sensor had a better performance (R2 = 0.83) than the RGB camera (R2 = 0.53) when compared with ground reference height during pod growth and seed filling stages. However, RGB showed more reliability in estimating plant height at physiological maturity when the LiDAR could not capture an accurate plant height measurement. The results from this study contribute to identifying ideal aerial phenotyping sensors to estimate plant height in soybean during different growth stages.

Genome-wide identification of the ATP-dependent zinc metalloprotease (FtsH) in Triticeae species reveals that TaFtsH-1 regulates cadmium tolerance in Triticum aestivum

The ATP-dependent zinc metalloprotease (FtsH) protein gene family is essential for plant growth, development, and stress responses. Although FtsH genes have been identified in various plant species, the FtsH gene family in wheat (Triticum aestivum) remains unstudied. In this study, we identified 11 TaFtsH genes with uneven chromosomal distribution, significant variations in gene sequence length, and differing intron numbers among individual members. Additionally, these proteins exhibit similar physicochemical characteristics as well as secondary and tertiary structures. The FtsH genes can be classified into eight groups, each characterized by similar structures and conserved motifs. Intraspecific and interspecific comparisons further revealed extensive gene duplications within the TaFtsH gene family, indicating a closer relationship to maize. Analysis of cis-acting elements in the promoter regions of TaFtsH genes revealed developmental and stress-responsive elements in most of the genes. Expression pattern analysis showed that TaFtsH genes are expressed in all wheat tissues, though with varying patterns. TaFtsH genes displayed differential responses to CdCl2, ZnSO4, and MnSO4 stress treatments. Gene Ontology (GO) enrichment analysis indicated that TaFtsH genes are involved in protein hydrolysis. Barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) technology confirmed the function of TaFtsH-1, indicating that silencing TaFtsH-1 enhances common wheat's resistance to cadmium (Cd) toxicity. In summary, this study offers an in-depth understanding of the FtsH gene family in wheat, establishing a solid basis for comprehending its functions, genetic mechanisms, and improving wheat's tolerance to heavy metal contamination.

Genome-Wide Identification, Expression and Interaction Analysis of GLN Gene Family in Soybean

As a globally significant economic crop, the seed size of soybean (Glycine max [L.] Merr.) is jointly regulated by internal genetic factors and external environmental signals. This study discovered that the GLN family proteins in soybean are similar to the KIX-PPD-MYC transcriptional repressor complex in Arabidopsis, potentially influencing seed size by regulating the expression of the downstream gene GIF1. Additionally, β-1,3-glucanase (βGlu) plays a crucial role in antifungal activity, cell composition, flower development, pollen development, abiotic resistance, seed germination, and maturation in soybean. Through a detailed analysis of the structure, chromosomal localization, phylogenetic relationships, and expression situations in different tissues at different stages of the soybean GLN gene family members, this research certifies a theoretical foundation for subsequent research on the biological functions of GLN genes in soybean. This research incorporated a comprehensive genomic identification and expression analysis of the GLN gene family in soybean. The results indicate that the 109 soybean GLN genes are unevenly distributed across soybean chromosomes and exhibit diverse expression patterns in different tissues, suggesting they may have distinct functions in soybean morphogenesis. GO enrichment analysis shows that the GLN gene family may participate in a variety of biological activities, cellular components, and molecular biological processes, particularly in catalytic activity, cellular components, and metabolic processes. These findings provide important information for comprehending the role of the GLN gene family in soybean and offer potential targets for molecular breeding of soybean.

Exploiting light energy utilization strategies in Populus simonii through multitrait-GWAS: insights from stochastic differential models

The photosynthetic phenotype of trees undergoes changes and interactions that reflect their abilities to exploit light energy. Environmental disturbances and genetic factors have been recognized as influencing these changes and interactions, yet our understanding of the underlying biological mechanisms remains limited, particularly in stochastic environments. Here, we developed a high-dimensional stochastic differential framework (HDSD) for the genome-wide mapping of quantitative trait loci (QTLs) that regulate competition or cooperation in environment-dependent phenotypes. The framework incorporates random disturbances into system mapping, a dynamic model that views multiple traits as a system. Not only does this framework describe how QTLs regulate a single phenotype, but also how they regulate multiple phenotypes and how they interact with each other to influence phenotypic variations. To validate the proposed model, we conducted mapping experiments using chlorophyll fluorescence phenotype data from Populus simonii. Through this analysis, we identified several significant QTLs that may play a crucial role in photosynthesis in stochastic environments, in which 76 significant QTLs have already been reported to encode proteins or enzymes involved in photosynthesis through functional annotation. The constructed genetic regulatory network allows for a more comprehensive analysis of the internal genetic interactions of the photosynthesis process by visualizing the relationships between SNPs. This study shows a new way to understand the genetic mechanisms that govern the photosynthetic phenotype of trees, focusing on how environmental stochasticity and genetic variation interact to shape their light energy utilization strategies.

Combined transcriptome and physiological analysis reveals exogenous sucrose enhances photosynthesis and source capacity in foxtail millet

Foxtail millet (Setaria italica (L.) P. Beauv.) is an environmentally friendly crop that meets the current requirements of international food security and is widely accepted as a photosynthesis research model. However, whether exogenous sucrose treatment has a positive effect on foxtail millet growth remains unknown. Here, we employed physiological and molecular approaches to identify photosynthesis and source capacity associated with exogenous sucrose during the growth of Jingu 21 seedlings. RNA-seq analysis showed that some differentially expressed genes (DEGs) related to photosynthesis and carotenoid biosynthesis were induced by exogenous sucrose and that most of these genes were up-regulated. An increase in gas exchange parameters, chlorophyll content, and chlorophyll fluorescence of Jingu 21 was noted after exogenous sucrose addition. Furthermore, exogenous sucrose up-regulated genes encoding sucrose and hexose transporters and enhanced starch and sucrose metabolism. More DEGs were up-regulated by sucrose, the nonstructural carbohydrate (NSC) content in the leaves increased and energy metabolism and sucrose loading subsequently improved, ultimately enhancing photosynthesis under normal and dark conditions. Further analysis revealed that WRKYs, ERFs, HY5, RAP2, and ABI5 could be key transcription factors involved in growth regulation. These results indicate that exogenous sucrose affects the normal photosynthetic performance of foxtail millet by increasing NSC transport and loading. They improve our understanding of the molecular mechanisms of the effects of exogenous sucrose on photosynthesis in foxtail millet, providing an effective measure to enhance source-sink relationships and improve yield.

ADP-glucose pyrophosphorylase gene family in soybean and implications in drought stress tolerance

BACKGROUND

ADP-glucose pyrophosphorylase (AGPase) is the key rate-limiting enzyme in starch biosynthesis pathway, and has been identified as a potential target for manipulation strategies aimed at improving crop yield and quality.

OBJECTIVE

To identify the AGPase gene family members in soybean, and explore the potential implications of GmAGPS2 in drought stress tolerance.

METHODS

The genome-wide identification and sequence analysis of soybean AGPase gene family was carried out by bioinformatics methods. The GmAGP gene expression was analyzed using transcriptome data and quantitative real-time PCR (qRT-PCR). Furthermore, transgenic yeast strains overexpressing GmAGPS2 were generated, and their growth was observed under drought stress.

RESULTS

In this study, we searched for AGPase genes (GmAGP) in the soybean genome and identified a total of 14 GmAGP genes. The GmAGP proteins had a unique conserved NTP_transferase domain and were mainly located in the chloroplast and cytosol. Evolutionarily, the GmAGP proteins can be clustered into two distinct subgroups; within the same subgroup, they displayed a similar distribution pattern of conserved motifs. The GmAGP genes exhibited an uneven distribution on 10 chromosomes, and segmental duplication contributed to AGPase gene family expansion in soybean. The GmAGP genes presented different tissue expression pattern, in which GmAGPL6, GmAGPL9, and GmAGPL10 mainly exhibited tissue-specific expression pattern. The promoter of GmAGP genes had multiple cis-acting elements related to phytohormones and stress responses, and 8 GmAGP genes contained drought-responsive cis-acting elements. qRT‒PCR analysis demonstrated a significant upregulation expression of GmAGPL6, GmAGPL10, and GmAGPS2 in response to drought stress. Further functional analysis indicated that GmAGPS2 gene could improve yeast growth under drought stress conditions and enhance the drought tolerance of yeast.

CONCLUSION

These results will contribute to further elucidation of the function of GmAGP genes, and offer important candidate genes for the genetic improvement of starch and yield-related traits and the breeding of high drought stress tolerance varieties in soybean.

Non-CG DNA hypomethylation promotes photosynthesis and nitrogen fixation in soybean

Non-CG DNA methylation, a plant-specific epigenetic mark mainly regulated by chromomethylase (CMT), is known to play important roles in Arabidopsis thaliana. However, whether and to what extent non-CG DNA methylation modulates agronomic traits in crops remain to be explored. Here, we describe the consequences of non-CG DNA hypomethylation on development, seed composition, and yield in soybean (Glycine max). We created a Gmcmt mutant line lacking function of all four CMT genes. This line exhibited substantial hypomethylation of non-CG (CHG and CHH) sites. Non-CG hypomethylation enhanced chromatin accessibility and promoted or repressed the expression of hundreds of functionally relevant genes, including upregulation of GOLDEN-LIKE 10 (GmGLK10), which led to enhanced photosynthesis and, unexpectedly, improved nitrogen fixation efficiency. The Gmcmt line produced larger seeds with increased protein content. This study provides insights into the mechanisms of non-CG methylation-based epigenetic regulation of soybean development and suggests viable epigenetic strategies for improving soybean yield and nutritional value.

Study on the Optimal Leaf Area-to-Fruit Ratio of Pear Trees on the Basis of Bearing Branch Girdling and Machine Learning

The leaf area-to-fruit ratio (LAFR) is an important factor affecting fruit quality. Previous studies on LAFR have provided some recommendations for optimal values. However, these recommendations have been quite broad and lack effectiveness during the fruit thinning period. In this study, data on the LAFR and fruit quality of pears at 5 stages were collected by continuously girdling bearing branches throughout the entire fruit development process. Five different clustering algorithms, including KMeans, Agglomerative clustering, Spectral clustering, Birch, and Spectral biclustering, were employed to classify the fruit quality data. Agglomerative clustering yielded the best results when the dataset was divided into 4 clusters. The least squares method was utilized to fit the LAFR corresponding to the best quality cluster, and the optimal LAFR values for 28, 42, 63, 91, and 112 days after flowering were 12.54, 18.95, 23.79, 27.06, and 28.76 dm2 (the corresponding leaf-to-fruit ratio values were 19, 29, 36, 41, and 44, respectively). Furthermore, field verification experiments demonstrated that the optimal LAFR contributed to improving pear fruit quality, and a relatively high LAFR beyond the optimum value did not further increase quality. In summary, we optimized the LAFR of pear trees at different stages and confirmed the effectiveness of the optimal LAFR in improving fruit quality. Our research provides a theoretical basis for managing pear tree fruit load and achieving high-quality, clean fruit production.

Genetic dissection of ten photosynthesis-related traits based on InDel- and SNP-GWAS in soybean

KEY MESSAGE

A total of 416 InDels and 112 SNPs were significantly associated with soybean photosynthesis-related traits. GmIWS1 and GmCDC48 might be related to chlorophyll fluorescence and gas-exchange parameters, respectively. Photosynthesis is one of the main factors determining crop yield. A better understanding of the genetic architecture for photosynthesis is of great significance for soybean yield improvement. Our previous studies identified 5,410,112 single nucleotide polymorphisms (SNPs) from the resequencing data of 219 natural soybean accessions. Here, we identified 634,106 insertions and deletions (InDels) from these 219 accessions and used these InDel variations to perform principal component and linkage disequilibrium analysis of this population. The genome-wide association study (GWAS) were conducted on six chlorophyll fluorescence parameters (chlorophyll content, light energy absorbed per reaction center, quantum yield for electron transport, probability that a trapped exciton moves an electron into the electron transport chain beyond primary quinone acceptor, maximum quantum yield of photosystem II primary photochemistry in the dark-adapted state, performance index on absorption basis) and four gas-exchange parameters (intercellular carbon dioxide concentration, stomatal conductance, net photosynthesis rate, transpiration rate) and revealed 416 significant InDels and 112 significant SNPs. Based on GWAS results, GmIWS1 (encoding a transcription elongation factor) and GmCDC48 (encoding a cell division cycle protein) with the highest expression in the mapping region were determined as the candidate genes responsible for chlorophyll fluorescence and gas-exchange parameters, respectively. Further identification of favorable haplotypes with higher photosynthesis, seed weight and seed yield were carried out for GmIWS1 and GmCDC48. Overall, this study revealed the natural variations and candidate genes underlying the photosynthesis-related traits based on abundant phenotypic and genetic data, providing valuable insights into the genetic mechanisms controlling photosynthesis and yield in soybean.

MtTCP18 Regulates Plant Structure in Medicago truncatula

Plant structure has a large influence on crop yield formation, with branching and plant height being the important factors that make it up. We identified a gene, MtTCP18, encoding a TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factor highly conserved with Arabidopsis gene BRC1 (BRANCHED1) in Medicago truncatula. Sequence analysis revealed that MtTCP18 included a conserved basic helix-loop-helix (BHLH) motif and R domain. Expression analysis showed that MtTCP18 was expressed in all organs examined, with relatively higher expression in pods and axillary buds. Subcellular localization analysis showed that MtTCP18 was localized in the nucleus and exhibited transcriptional activation activity. These results supported its role as a transcription factor. Meanwhile, we identified a homozygous mutant line (NF14875) with a mutation caused by Tnt1 insertion into MtTCP18. Mutant analysis showed that the mutation of MtTCP18 altered plant structure, with increased plant height and branch number. Moreover, we found that the expression of auxin early response genes was modulated in the mutant. Therefore, MtTCP18 may be a promising candidate gene for breeders to optimize plant structure for crop improvement.

Linking photosynthesis and yield reveals a strategy to improve light use efficiency in a climbing bean breeding population

Photosynthesis drives plant physiology, biomass accumulation, and yield. Photosynthetic efficiency, specifically the operating efficiency of PSII (Fq'/Fm'), is highly responsive to actual growth conditions, especially to fluctuating photosynthetic photon fluence rate (PPFR). Under field conditions, plants constantly balance energy uptake to optimize growth. The dynamic regulation complicates the quantification of cumulative photochemical energy uptake based on the intercepted solar energy, its transduction into biomass, and the identification of efficient breeding lines. Here, we show significant effects on biomass related to genetic variation in photosynthetic efficiency of 178 climbing bean (Phaseolus vulgaris L.) lines. Under fluctuating conditions, the Fq'/Fm' was monitored throughout the growing period using hand-held and automated chlorophyll fluorescence phenotyping. The seasonal response of Fq'/Fm' to PPFR (ResponseG:PPFR) achieved significant correlations with biomass and yield, ranging from 0.33 to 0.35 and from 0.22 to 0.31 in two glasshouse and three field trials, respectively. Phenomic yield prediction outperformed genomic predictions for new environments in four trials under different growing conditions. Investigating genetic control over photosynthesis, one single nucleotide polymorphism (Chr09_37766289_13052) on chromosome 9 was significantly associated with ResponseG:PPFR in proximity to a candidate gene controlling chloroplast thylakoid formation. In conclusion, photosynthetic screening facilitates and accelerates selection for high yield potential.

GmPLP1 negatively regulates soybean resistance to high light stress by modulating photosynthetic capacity and reactive oxygen species accumulation in a blue light-dependent manner

High light stress is an important factor limiting crop yield. Light receptors play an important role in the response to high light stress, but their mechanisms are still poorly understood. Here, we found that the abundance of GmPLP1, a positive blue light receptor protein, was significantly inhibited by high light stress and mainly responded to high blue light. GmPLP1 RNA-interference soybean lines exhibited higher light energy utilization ability and less light damage and reactive oxygen species (ROS) accumulation in leaves under high light stress, while the phenotype of GmPLP1:GmPLP1-Flag overexpression soybean showed the opposite characteristics. Then, we identified a protein-protein interaction between GmPLP1 and GmVTC2, and the intensity of this interaction was primarily affected by sensing the intensity of blue light. More importantly, overexpression of GmVTC2b improved soybean tolerance to high light stress by enhancing the ROS scavenging capability through increasing the biosynthesis of ascorbic acid. This regulation was significantly enhanced after interfering with a GmPLP1-interference fragment in GmVTC2b-ox soybean leaves, but was weakened when GmPLP1 was transiently overexpressed. These findings demonstrate that GmPLP1 regulates the photosynthetic capacity and ROS accumulation of soybean to adapt to changes in light intensity by sensing blue light. In summary, this study discovered a new mechanism through which GmPLP1 participates in high light stress in soybean, which has great significance for improving soybean yield and the adaptability of soybean to high light.

Regulation of seed traits in soybean

Soybean (Glycine max) is an essential economic crop that provides vegetative oil and protein for humans, worldwide. Increasing soybean yield as well as improving seed quality is of great importance. Seed weight/size, oil and protein content are the three major traits determining seed quality, and seed weight also influences soybean yield. In recent years, the availability of soybean omics data and the development of related techniques have paved the way for better research on soybean functional genomics, providing a comprehensive understanding of gene functions. This review summarizes the regulatory genes that influence seed size/weight, oil content and protein content in soybean. We also provided a general overview of the pleiotropic effect for the genes in controlling seed traits and environmental stresses. Ultimately, it is expected that this review will be beneficial in breeding improved traits in soybean.

Genome-Wide Identification and Comprehensive Analysis of the FtsH Gene Family in Soybean (Glycine max)

The filamentation temperature-sensitive H (FtsH) gene family is critical in regulating plant chloroplast development and photosynthesis. It plays a vital role in plant growth, development, and stress response. Although FtsH genes have been identified in a wide range of plants, there is no detailed study of the FtsH gene family in soybean (Glycine max). Here, we identified 34 GmFtsH genes, which could be categorized into eight groups, and GmFtsH genes in the same group had similar structures and conserved protein motifs. We also performed intraspecific and interspecific collinearity analysis and found that the GmFtsH family has large-scale gene duplication and is more closely related to Arabidopsis thaliana. Cis-acting elements analysis in the promoter region of the GmFtsH genes revealed that most genes contain developmental and stress response elements. Expression patterns based on transcriptome data and real-time reverse transcription quantitative PCR (qRT-PCR) showed that most of the GmFtsH genes were expressed at the highest levels in leaves. Then, GO enrichment analysis indicated that GmFtsH genes might function as a protein hydrolase. In addition, the GmFtsH13 protein was confirmed to be localized in chloroplasts by a transient expression experiment in tobacco. Taken together, the results of this study lay the foundation for the functional determination of GmFtsH genes and help researchers further understand the regulatory network in soybean leaf development.

Cloning and functional study of GmRPI2, which is the critical gene of photosynthesis in soybean

Light provides energy for photosynthesis and is also an important environmental signal that regulates plant growth and development. Ribose-5-phosphate isomerase plays a crucial role in photosynthesis. However, ribose-5-phosphate isomerase has yet to be studied in soybean photosynthesis. To understand the biological function of GmRPI2, in this study, GmRPI2 was cloned, plant overexpression vectors and gene editing vectors were successfully constructed, and transformed into recipient soybean JN74 using the Agrobacterium-mediated method. Using qRT-PCR, we analyzed that GmRPI2 gene expression was highest in leaves, second highest in roots, and lowest in stems. Promoter analysis revealed the presence of multiple cis-acting elements related to light response in the promoter region of GmRPI2. Compared with the control soybean plants, the net photosynthetic rate and transpiration rate of the overexpression lines were higher than those of the control and gene editing lines, while the intercellular CO2 concentration was significantly lower than that of the control and gene editing lines; the total chlorophyll, chlorophyll a, chlorophyll b contents and soluble sugar contents of the overexpression plants were significantly higher than those of the recipient and editing plants, indicating that the GmRPI2 gene can increase The GmRPI2 gene can increase the photosynthetic capacity of soybean plants, providing a theoretical basis and genetic resources for improving soybean yield by regulating photosynthetic efficiency.

CsCIPK11-Regulated Metalloprotease CsFtsH5 Mediates the Cold Response of Tea Plants

Photosystem II repair in chloroplasts is a critical process involved in maintaining a plant’s photosynthetic activity under cold stress. FtsH (filamentation temperature-sensitive H) is an essential metalloprotease that is required for chloroplast photosystem II repair. However, the role of FtsH in tea plants and its regulatory mechanism under cold stress remains elusive. In this study, we cloned a FtsH homolog gene in tea plants, named CsFtsH5, and found that CsFtsH5 was located in the chloroplast and cytomembrane. RT-qPCR showed that the expression of CsFtsH5 was increased with leaf maturity and was significantly induced by light and cold stress. Transient knockdown CsFtsH5 expression in tea leaves using antisense oligonucleotides resulted in hypersensitivity to cold stress, along with higher relative electrolyte leakage and lower Fv/Fm values. To investigate the molecular mechanism underlying CsFtsH5 involvement in the cold stress, we focused on the calcineurin B-like-interacting protein kinase 11 (CsCIPK11), which had a tissue expression pattern similar to that of CsFtsH5 and was also upregulated by light and cold stress. Yeast two-hybrid and dual luciferase (Luc) complementation assays revealed that CsFtsH5 interacted with CsCIPK11. Furthermore, the Dual-Luc assay showed that CsCIPK11-CsFtsH5 interaction might enhance CsFtsH5 stability. Altogether, our study demonstrates that CsFtsH5 is associated with CsCIPK11 and plays a positive role in maintaining the photosynthetic activity of tea plants in response to low temperatures.