TaTPP-7A positively feedback regulates grain filling and wheat grain yield through T6P-SnRK1 signalling pathway and sugar-ABA interaction

Integrative physiological and transcriptome analyses elucidate the effect of shading during the grain-filling stage of wheat (Triticum aestivum) cv. ZY96-3

Shading plays an important role in determining nutrient content and yield fo wheat (Triticum aestivum ). However, the genetic mechanism underlying the effects of shading treatment on grain filling remains unclear. Therefore, we performed phenotypic and transcriptome analyses on wheat cv. ZY96-3 during grain development under normal and shaded conditions. Shading resulted in a significant decrease in grain size and 1000-grain weight. Correlation analysis revealed the strong effect of shading on the mean and maximum grain-filling rate and secondary grain-filling parameters R 2 and R 3 . And shading reduced starch content and starch-related enzyme activity (including granule-bound starch synthase and soluble starch synthase). Transcriptomic analyses showed that shading mainly affected pathways related to photosynthetic antenna proteins, carbon fixation in photosynthetic organisms, and starch and sucrose metabolism. Sixteen genes related to photosynthetic antenna protein and carbon fixation pathways were first upregulated and then downregulated; whereas all differentially expressed genes (PetC , Fd , LFNR1 , LFNR2 , PC , PsbO , PsaG , and PSB28 ) in the photosynthetic antenna protein pathway belonged to electron transport chain proteins. We found that shading treatment affects the physiological and molecular properties of grain development during the grain-filling stage. This study reveals new candidate genes (such as TaLFNR1-7A and TaFd-7A ) for breeding wheat varieties with high photosynthetic efficiency in regions with insufficient light intensity.

TaFT-D1 positively regulates grain weight by acting as a coactivator of TaFDL2 in wheat

FLOWERING LOCUS T (FT), a multifunctional regulator in crops, modulates multiple key agronomic traits such as flowering time or heading date and plant height; however, its role in grain development regulation is unclear. Herein, through genome-wide association studies (GWAS), we identified TaFT-D1, which encodes a phosphatidylethanolamine-binding protein (PEBP), as a candidate gene for grain weight in wheat. A one-bp insertion/deletion (InDel) (G/-) in the third exon of TaFT-D1, resulting in different protein lengths, was significantly associated with grain weight. TaFT-D1 knockout via the CRISPR-Cas9 system reduced grain size and weight, and TaFT-D1 increased grain size by promoting cell proliferation and starch synthesis. Transcriptome analysis revealed a significant decrease in the expression of cell cycle- and starch synthesis-related genes, including TaNAC019-3A, TaSWEET15-like-7B, TaCYCD4;1 and TaCYCD3;2, in the taft-d1 knockout line. TaFT-D1 interacted with the bZIP transcription factor TaFDL2, and the tafdl2 mutant presented relatively small grains, suggesting that TaFDL2 is a positive regulator of grain size. Moreover, TaFDL2 bound to the promoters of downstream cell cycle- and starch synthesis-related genes, activating their expression, whereas TaFT-D1 increased this activation via TaFDL2. Interaction assays demonstrated that TaFT-D1, Ta14-3-3A and TaFDL2 formed a regulatory complex. Furthermore, the TaFT-D1(G) allele was significantly correlated with greater thousand-grain weight and earlier heading. This favourable allele has undergone strong positive selection during wheat breeding in China. Our findings provide novel insights into how TaFT-D1 regulates grain weight and highlight its potential application for yield improvement in wheat.

Multi-Omics Analyses Offer Novel Insights into the Selection of Sugar and Lipid Metabolism During Maize Domestication and Improvement

Over thousands of years of domestication, maize has undergone significant environmental changes. Understanding the genetic and metabolic trace during maize evolution can better contribute to molecular breeding and nutrition quality improvement. This study examines the metabolic profiles and transcriptomes of maize kernels from teosinte, landrace, and maize accessions at 15 days post-pollination. Differentially accumulated metabolites were enriched in sugar and lipid metabolism pathways. The metabolic selection profile exhibited four distinct patterns: continuous increases, constant decrease, initial decline or stability followed by an increase, and initial growth or stability followed by a subsequent decline. Sugars and JA were positive selection while LPCs/LPEs were negative selection during evolution. The expression level of genes related to sugar accumulation was significantly higher in maize, contrasting with enhanced glycolysis and lipid metabolism activity in teosinte. The correlation network highlighted distinct hormonal regulation of sugar and lipid metabolism. We identified 27 candidate genes associated with sugar, lipid, and JA that have undergone strong selection by population genomic regions. The positive selection of the PLD may explain the negative selection of LPCs/LPEs due to substrate competition. These findings enhance our understanding of the evolutionary trajectory of primary metabolism in maize and provide valuable resources for breeding and improvement.

Identification of Rht1 for plant height reduction in two wheat mutants and the effects on yield components

Plant height determines lodging resistance and is closely linked to yield stability in wheat. In this study, we identified two semi-dwarf wheat mutants, designated je0370 and je0344, using the winter wheat cultivar Jing411 as the wild type (WT). Field experiments revealed that the plant height of these two mutants was significantly lower than that of the WT. In contrast, the thousand-grain weight was significantly higher in je0370 but lower in je0344 compared to the WT. Bulk Segregant Analysis (BSA) based on exome capture sequencing indicated that the gene responsible for height reduction is located on chromosome 4B. Further genetic linkage analysis mapped the dwarf gene to the interval of 29.26-48.61 Mb on chromosome 4B, corresponding to a genetic distance of 10.79 cM. This region encompasses the Rht1 gene; we subsequently sequenced the Rht1 gene in je0370 and je0344 and identified a C-T mutation at position 190 bp, resulting in a truncation of the DELLA domain in both mutants. Further analysis using Cleaved Amplified Polymorphic Sequences (CAPS) markers in F2 populations demonstrated that plants with homozygous Rht1 mutations exhibited significantly reduced plant height and thousand-grain weight, while heterozygous plants displayed intermediate effects. However, the mutation did not significantly affect spikelet number, effective spike number, or spike length. These findings conclusively demonstrate that the Rht1 mutation is responsible for plant dwarfism and reduced grain weight, without substantial impacts on other yield components. This study provides invaluable insights into the utilization of Rht1 in wheat breeding.

The role of trehalose metabolism in plant stress tolerance

BACKGROUND

Trehalose is a nonreducing disaccharide containing two glucose molecules linked through an α,α-1,1-glycosidic bond. This unique chemical structure causes trehalose levels to fluctuate significantly in plants under stress, where it functions as an osmoprotectant, enhancing plant resistance to stress. Previous studies have confirmed that the trehalose synthesis pathway is widely conserved across most plants. However, the protective role of trehalose is limited only to organelles or tissues where the concentration is sufficiently high.

AIM OF REVIEW

In this review, we summarize previous reports on improving plant stress tolerance (drought, cold, heat, salt, pathogen, etc.) by applying trehalose-6-phosphate (T6P) or trehalose and manipulating the expression of trehalose metabolism-related genes. The molecular mechanisms underlying T6P, trehalose, and their related genes that regulate plant stress resistance are reviewed. More progressive studies on the spatiotemporal control of trehalose metabolism will provide a novel tool that allows for the simultaneous enhancement of crop yield and stress tolerance.

KEY SCIENTIFIC CONCEPTS OF REVIEW

We introduce the history of trehalose and discuss the possibility of trehalose and its metabolity-related genes binding to T6P to participate in stress response through unknown signaling pathways. In addition, the effects of trehalose metabolism regulation on plant growth and stress resistance were reviewed, and the molecular mechanism was fully discussed. In particular, we came up with new insights that the molecular mechanism of trehalose metabolism to enhance plant stress resistance in the future and we propose the need to use biotechnology methods to cultivate crops with stress resistance and high yield potential.

Combined Physiological and Transcriptomic Analyses of the Effects of Exogenous Trehalose on Salt Tolerance in Maize (Zea mays L.)

Soil salinization severely affects the quality and yield of maize. As a C4 plant with high efficiency in utilizing light and carbon dioxide, maize (Zea mays L.) is one of the most important crops worldwide. This study aims to investigate the pathways and mechanisms by which trehalose mediates the improvement of salt tolerance in maize through a combined analysis of physiology and transcriptomics. The results indicate that foliar application of trehalose treatment significantly increased maize biomass and antioxidant enzyme activity while reducing the H2O2 and Na+/K+ ratios in both the aerial and underground parts of the plant. Additionally, trehalose enhanced the total secretion of organic acids from maize roots, improving the soil microenvironment for maize growth under salt stress and alleviating Na+ toxicity. Transcriptomic data revealed that under salt stress, most differentially expressed genes (DEGs) were enriched in pathways related to photosynthesis, abscisic acid signaling, and sugar metabolism, and trehalose application increased the expression levels of these pathways, thereby mitigating the growth inhibition caused by salinity. This study elucidates mechanisms for enhancing salt tolerance in maize, providing theoretical support for improving its resilience and offering innovative strategies for utilizing a wide range of saline-alkali land.

Identification of two postharvest ripening regulatory models in kiwifruit: based on plant hormones, physiology, and transcriptome analysis

Kiwifruit (Actinidia spp.), celebrated for its unique flavor and rich nutritional content, is a globally popular fruit. This fruit requires post-harvest ripening before consumption. However, the unpredictable ripening pace significantly impacts consumer acceptance and sales, thereby hindering the commercial growth of kiwifruit. To address this, understanding the key molecular mechanisms and metabolites governing postharvest ripening and senescence could offer valuable insights for developing storage strategies and breeding techniques in yellow-fleshed kiwifruits. We constructed two models that integrated these findings with existing theories. The first model suggests that, unlike the T6P-sucrose regulatory mechanism observed in plant leaves, the separation of harvested kiwifruit from the mother plant leads to an insufficient supply of T6P, which activates the SnRK1 kinase. This, in turn, inhibits the TOR kinase signaling pathway, regulating starch metabolism. The T6P-SnRK1-TOR-starch metabolism pathway plays a regulatory role during postharvest ripening, limiting excessive starch degradation that could accelerate aging and decay in yellow-fleshed kiwifruit. The second model highlights the role of abscisic acid (ABA), cytokinins (CKs), and ethylene in regulating the process, inducing the activation of ERFs and cell wall-degrading enzymes, promoting fruit postharvest softening. These findings indicate that at least two models, the T6P-SnRK1-TOR-starch metabolism model and the ABA-CKs-ethylene-cell wall degradation model, regulate postharvest fruit ripening, offering new insights into the artificial regulation of yellow-fleshed kiwifruit ripening speed.

Incomplete filling in the basal region of maize endosperm: timing of development of starch synthesis and cell vitality

Starch synthesis in maize endosperm adheres to the basipetal sequence from the apex downwards. However, the mechanism underlying nonuniformity among regions of the endosperm in starch accumulation and its significance is poorly understood. Here, we examined the spatiotemporal transcriptomes and starch accumulation dynamics in apical (AE), middle (ME), and basal (BE) regions of endosperm throughout the filling stage. Results demonstrated that the BE had lower levels of gene transcripts and enzymes facilitating starch synthesis, corresponding to incomplete starch storage at maturity, compared with AE and ME. Contrarily, the BE showed abundant gene expression for genetic processing and slow progress in physiological development (quantified by an index calculated from the expression values of development progress marker genes), revealing a sustained cell vitality of the BE. Further analysis demonstrated a significant parabolic correlation between starch synthesis and physiological development. An in-depth examination showed that the BE had more active signaling pathways of IAA and ABA than the AE throughout the filling stage, while ethylene showed the opposite pattern. Besides, SNF1-related protein kinase1 (SnRK1) activity, a regulator for starch synthesis modulated by trehalose-6-phosphate (T6P) signaling, was kept at a lower level in the BE than the AE and ME, corresponding to the distinct gene expression in the T6P pathway in starch synthesis regulation. Collectively, the findings support an improved understanding of the timing of starch synthesis and cell vitality in regions of the endosperm during development, and potential regulation from hormone signaling and T6P/SnRK1 signaling.

Physiological and Transcriptome Analyses Reveal the Effects of Fertilization on the Yield of Winter Wheat and on the Photosynthetic Performance of Leaves during the Flowering Period

Fertilization significantly affects the growth and development of wheat. However, the precise mechanisms underlying gene regulation during flowering in response to fertilization deficiency remain elusive. In this study, fertilization (F) and non-fertilization (CK) ) treatments were set up to reveal examine the effect of fertilization on the photosynthetic capacity of winter wheat during the flowering period through physiological, biochemical, and transcriptome analyses. Upon analyzing analysing their yield, leaf photosynthetic system exchange parameters during flowering, antioxidant enzyme activity, and endogenous hormone parameters, we found that the F treatment resulted in higher net photosynthetic rates during flowering periods than the CK treatment. The superoxide dismutase (SOD) (83.92%), peroxidase (POD) (150.75%), and catalase (CAT) (22.74%) activities of leaves in treated with F during the flowering period were notably elevated compared to those of CK-treated leaves. Abscisic acid (ABA) (1.86%) and gibberellin acid (GA3) (33.69%) levels were reduced, whereas Auxin auxin (IAA) (98.27%) content was increasedwas increased under F treatment compared to those the results under the CK treatment. The chlorophyll a (32.53%), chlorophyll b (56%), total chlorophyll (37.96%), and carotenoid contents (29.80%) under F treatment were also increased compared to CK., exceeded exceeding those obtained under the CK treatment. Furthermore, transcriptional differences between the F and CK conditions were analyzed, and key genes were screened and validated by using q-PCR. Transcriptome analysis identified 2281 differentially expressed genes (DEGs), with enriched pathways related to photosynthesis and light harvesting. DEGs were subjected to cluster simulation, which revealed that 53 DEGS, both up- and down-regulated, responded to the F treatment. qRT-PCR-based validation confirmed the differential expression of genes associated with carbohydrate transport and metabolism, lipid transport, and signal transduction. This study revealed distinctive transcriptional patterns and crucial gene regulation networks in wheat during flowering under fertilization, providing transcriptomic guidance for the precise regulation of wheat breeding.

Integrated meta-QTL and in silico transcriptome assessment pinpoint major genomic regions responsible for spike length in wheat (Triticum aestivum L.)

Spike length (SL) is one of the major contributors to wheat yield. Uncovering major genetic regions affecting SL is an integral part of elucidating the genetic basis of wheat yield traits and goes further pivotal for marker-assisted selection breeding. A genome-wide meta-quantitative trait locus (MQTL) analysis of wheat SL resulted in the refinement of 48 MQTLs using 227 initial QTLs retrieved from previous studies published over the past decades. The average confidence interval (CI) of these MQTLs amounted to a 5.16-fold reduction compared to the mean CI of the initial QTLs. As many as 2240 putative candidate genes (CGs) were identified from the MQTL intervals using transcriptomics data in silico of wheat, of which 58 CGs were identified based on wheat-rice homology analysis. For the key CG affecting SL, a functional kompetitive allele-specific PCR (KASP) marker, TaPP2C-3B-KASP, was developed to distinguish TaPP2C-3B-Hap I and TaPP2C-3B-Hap II based on the single nucleotide polymorphism at the 272 bp (A/G). The frequency of the elite allelic variation TaPP2C-3B-Hap II with high SL remained relatively stable at about 49.62% from the 1960s to 1990s. Integration of MQTL analysis and in silico transcriptome data led to a significant increase in the reliability of CGs for the genetic regulation of wheat SL, and the haplotype analysis for key CGs TaPP2C-3B of SL provided insights into the biological function of the TaPP2C-3B gene.

Integrating high-throughput phenotyping and genome-wide association studies for enhanced drought resistance and yield prediction in wheat

Drought, especially terminal drought, severely limits wheat growth and yield. Understanding the complex mechanisms behind the drought response in wheat is essential for developing drought-resistant varieties. This study aimed to dissect the genetic architecture and high-yielding wheat ideotypes under terminal drought. An automated high-throughput phenotyping platform was used to examine 28 392 image-based digital traits (i-traits) under different drought conditions during the flowering stage of a natural wheat population. Of the i-traits examined, 17 073 were identified as drought-related. A genome-wide association study (GWAS) identified 5320 drought-related significant single-nucleotide polymorphisms (SNPs) and 27 SNP clusters. A notable hotspot region controlling wheat drought tolerance was discovered, in which TaPP2C6 was shown to be an important negative regulator of the drought response. The tapp2c6 knockout lines exhibited enhanced drought resistance without a yield penalty. A haplotype analysis revealed a favored allele of TaPP2C6 that was significantly correlated with drought resistance, affirming its potential value in wheat breeding programs. We developed an advanced prediction model for wheat yield and drought resistance using 24 i-traits analyzed by machine learning. In summary, this study provides comprehensive insights into the high-yielding ideotype and an approach for the rapid breeding of drought-resistant wheat.

Integrated physiological, transcriptomic and metabolomic analyses reveal the mechanism of peanut kernel weight reduction under waterlogging stress

Waterlogging stress (WS) hinders kernel development and directly reduces peanut yield; however, the mechanism of kernel filling in response to WS remains unknown. The waterlogging-sensitive variety Huayu 39 was subjected to WS for 3 days at 7 days after the gynophores touched the ground (DAG). We found that WS affected kernel filling at 14, 21, and 28 DAG. WS decreased the average filling rate and kernel dry weight, while transcriptome sequencing and widely targeted metabolomic analysis revealed that WS inhibited the gene expression in starch and sucrose metabolism, which reduced sucrose input and transformation ability. Additionally, genes related to ethylene and melatonin synthesis and the accumulation of tryptophan and methionine were upregulated in response to WS. WS upregulated the expression of the gene encoding tryptophan decarboxylase (AhTDC), and overexpression of AhTDC in Arabidopsis significantly reduced the seed length, width, and weight. Therefore, WS reduced the kernel-filling rate, leading to a reduction in the 100-kernel weight. This survey informs the development of measures that alleviate the negative impact of WS on peanut yield and quality and provides a basis for exploring high-yield and high-quality cultivation, molecular-assisted breeding, and waterlogging prevention in peanut farming.

Understanding grain development in the Poaceae family by comparing conserved and distinctive pathways through omics studies in wheat and maize

The Poaceae family, commonly known as the grass family, encompasses a diverse group of crops that play an essential role in providing food, fodder, biofuels, environmental conservation, and cultural value for both human and environmental well-being. Crops in Poaceae family are deeply intertwined with human societies, economies, and ecosystems, making it one of the most significant plant families in the world. As the major reservoirs of essential nutrients, seed grain of these crops has garnered substantial attention from researchers. Understanding the molecular and genetic processes that controls seed formation, development and maturation can provide insights for improving crop yield, nutritional quality, and stress tolerance. The diversity in photosynthetic pathways between C3 and C4 plants introduces intriguing variations in their physiological and biochemical processes, potentially affecting seed development. In this review, we explore recent studies performed with omics technologies, such as genomics, transcriptomics, proteomics and metabolomics that shed light on the mechanisms underlying seed development in wheat and maize, as representatives of C3 and C4 plants respectively, providing insights into their unique adaptations and strategies for reproductive success.

TaTPS11 enhances wheat cold resistance by regulating source-sink factor

The presence of sugar in plant tissue can lead to an increase in the osmotic pressure within cells, a decrease in the freezing point of plants, and protection against ice crystal damage to the tissue. Trehalose is closely related to sucrose, which comprises the largest proportion of sugar and has become a hot topic of research in recent years. Our previous studies have confirmed that a key trehalose synthesis gene, TaTPS11, from the cold-resistant winter wheat DM1, could enhance the cold resistance of plants by increasing sugar content. However, the underlying mechanism behind this phenomenon remains unclear. In this study, we cloned TaTPS11-6D, edited TaTPS11-6D using CRISPR/Cas9 technology and transformed 'Fielder' to obtain T2 generation plants. We screened out OE3-3 and OE8-7 lines with significantly higher cold resistance than that of 'Fielder' and Cri 4-3 edited lines with significantly lower cold resistance than that of 'Fielder'. Low temperature storage limiting factors were measured for OE3-3, OE8-7 and Cri 4-3 treated at different temperatures.The results showed that TaTPS11-6D significantly increased the content of sugar in plants and the transfer of sugar from source to storage organs under cold conditions. The TaTPS11-6D significantly increased the levels of salicylic, jasmonic, and abscisic acids while also significantly decreasing the level of gibberellic acid. Our research improves the model of low temperature storage capacity limiting factor.

The critical roles of three sugar-related proteins (HXK, SnRK1, TOR) in regulating plant growth and stress responses

Sugar signaling is one of the most critical regulatory signals in plants, and its metabolic network contains multiple regulatory factors. Sugar signal molecules regulate cellular activities and organism development by combining with other intrinsic regulatory factors and environmental inputs. HXK, SnRK1, and TOR are three fundamental proteins that have a pivotal role in the metabolism of sugars in plants. HXK, being the initial glucose sensor discovered in plants, is renowned for its multifaceted characteristics. Recent investigations have unveiled that HXK additionally assumes a significant role in plant hormonal signaling and abiotic stress. SnRK1 serves as a vital regulator of growth under energy-depleted circumstances, whereas TOR, a large protein, acts as a central integrator of signaling pathways that govern cell metabolism, organ development, and transcriptome reprogramming in response to diverse stimuli. Together, these two proteins work to sense upstream signals and modulate downstream signals to regulate cell growth and proliferation. In recent years, there has been an increasing amount of research on these three proteins, particularly on TOR and SnRK1. Furthermore, studies have found that these three proteins not only regulate sugar signaling but also exhibit certain signal crosstalk in regulating plant growth and development. This review provides a comprehensive overview and summary of the basic functions and regulatory networks of these three proteins. It aims to serve as a reference for further exploration of the interactions between these three proteins and their involvement in co-regulatory networks.

Sucrose-associated SnRK1a1-mediated phosphorylation of Opaque2 modulates endosperm filling in maize

During maize endosperm filling, sucrose not only serves as a source of carbon skeletons for storage-reserve synthesis but also acts as a stimulus to promote this process. However, the molecular mechanisms underlying sucrose and endosperm filling are poorly understood. In this study, we found that sucrose promotes the expression of endosperm-filling hub gene Opaque2 (O2), coordinating with storage-reserve accumulation. We showed that the protein kinase SnRK1a1 can attenuate O2-mediated transactivation, but sucrose can release this suppression. Biochemical assays revealed that SnRK1a1 phosphorylates O2 at serine 41 (S41), negatively affecting its protein stability and transactivation ability. We observed that mutation of SnRK1a1 results in larger seeds with increased kernel weight and storage reserves, while overexpression of SnRK1a1 causes the opposite effect. Overexpression of the native O2 (O2-OE), phospho-dead (O2-SA), and phospho-mimetic (O2-SD) variants all increased 100-kernel weight. Although O2-SA seeds exhibit smaller kernel size, they have higher accumulation of starch and proteins, resulting in larger vitreous endosperm and increased test weight. O2-SD seeds display larger kernel size but unchanged levels of storage reserves and test weight. O2-OE seeds show elevated kernel dimensions and nutrient storage, like a mixture of O2-SA and O2-SD seeds. Collectively, our study discovers a novel regulatory mechanism of maize endosperm filling. Identification of S41 as a SnRK1-mediated phosphorylation site in O2 offers a potential engineering target for enhancing storage-reserve accumulation and yield in maize.

Transcriptomic and metabolomic profiling provide insight into the role of sugars and hormones in leaf senescence of Pinellia ternata

KEY MESSAGE

The interaction network and pathway map uncover the potential crosstalk between sugar and hormone metabolisms as a possible reason for leaf senescence in P. ternata. Pinellia ternata, an environmentally sensitive medicinal plant, undergoes leaf senescence twice a year, affecting its development and yield. Understanding the potential mechanism that delays leaf senescence could theoretically decrease yield losses. In this study, a typical senescent population model was constructed, and an integrated analysis of transcriptomic and metabolomic profiles of P. ternata was conducted using two early leaf senescence populations and two stay-green populations. The result showed that two key gene modules were associated with leaf senescence which were mainly enriched in sugar and hormone signaling pathways, respectively. A network constructed by unigenes and metabolisms related to the obtained two pathways revealed that several compounds such as D-arabitol and 2MeScZR have a higher significance ranking. In addition, a total of 130 hub genes in this network were categorized into 3 classes based on connectivity. Among them, 34 hub genes were further analyzed through a pathway map, the potential crosstalk between sugar and hormone metabolisms might be an underlying reason of leaf senescence in P. ternata. These findings address the knowledge gap regarding leaf senescence in P. ternata, providing candidate germplasms for molecular breeding and laying theoretical basis for the realization of finely regulated cultivation in future.

Fine mapping of a major QTL, qKl-1BL controlling kernel length in common wheat

KEY MESSAGE

A major stable QTL, qKl-1BL, for kernel length of wheat was narrowed down to a 2.04-Mb interval on chromosome 1BL; the candidate genes were predicated and the genetic effects on yield-related traits were characterized. As a key factor influencing kernel weight, wheat kernel shape is closely related to yield formation, and in turn affects both wheat processing quality and market value. Fine mapping of the major quantitative trait loci (QTL) for kernel shape could provide genetic resources and a theoretical basis for the genetic improvement of wheat yield-related traits. In this study, a major QTL for kernel length (KL) on 1BL, named qKl-1BL, was identified from the recombinant inbred lines (RIL) in multiple environments based on the genetic map and physical map, with 4.76-21.15% of the phenotypic variation explained. To fine map qKl-1BL, the map-based cloning strategy was used. By using developed InDel markers, the near-isogenic line (NIL) pairs and eight key recombinants were identified from a segregating population containing 3621 individuals derived from residual heterozygous lines (RHLs) self-crossing. In combination with phenotype identification, qKl-1BL was finely positioned into a 2.04-Mb interval, KN1B:698.15-700.19 Mb, with eight differentially expressed genes enriched at the key period of kernel elongation. Based on transcriptome analysis and functional annotation information, two candidate genes for qKl-1BL controlling kernel elongation were identified. Additionally, genetic effect analysis showed that the superior allele of qKl-1BL from Jing411 could increase KL, thousand kernel weight (TKW), and yield per plant (YPP) significantly, as well as kernel bulk density and stability time. Taken together, this study identified a QTL interval for controlling kernel length with two possible candidate genes, which provides an important basis for qKl-1BL cloning, functional analysis, and application in molecular breeding programs.

Sucrose homeostasis: Mechanisms and opportunity in crop yield improvement

Sugar homeostasis is a critical feature of biological systems. In humans, raised and dysregulated blood sugar is a serious health issue. In plants, directed changes in sucrose homeostasis and allocation represent opportunities in crop improvement. Plant tissue sucrose varies more than blood glucose and is found at higher concentrations (cytosol and phloem ca. 100 mM v 3.9-6.9 mM for blood glucose). Tissue sucrose varies with developmental stage and environment, but cytosol and phloem exhibit tight sucrose control. Sucrose homeostasis is a consequence of the integration of photosynthesis, synthesis of storage end-products such as starch, transport of sucrose to sinks and sink metabolism. Trehalose 6-phosphate (T6P)-SnRK1 and TOR play central, still emerging roles in regulating and coordinating these processes. Overall, tissue sucrose levels are more strongly related to growth than to photosynthesis. As a key sucrose signal, T6P regulates sucrose levels, transport and metabolic pathways to coordinate source and sink at a whole plant level. Emerging evidence shows that T6P interacts with meristems. With careful targeting, T6P manipulation through exploiting natural variation, chemical intervention and genetic modification is delivering benefits for crop yields. Regulation of cereal grain set, filling and retention may be the most strategically important aspect of sucrose allocation and homeostasis for food security.

Innovative computational tools provide new insights into the polyploid wheat genome

Bread wheat (Triticum aestivum) is an important crop and serves as a significant source of protein and calories for humans, worldwide. Nevertheless, its large and allopolyploid genome poses constraints on genetic improvement. The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging. Recently, we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome. Here, we summarize the methodological innovations and applications of these tools and databases. A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits. Furthermore, we outline future perspectives on new advanced tools and databases, taking into consideration the unique features of bread wheat, to accelerate genomic-assisted wheat breeding.

Genome-Wide Identification and Expression Analysis of the Trehalose-6-phosphate Synthase and Trehalose-6-phosphate Phosphatase Gene Families in Rose (Rosa hybrida cv 'Carola') under Different Light Conditions

Trehalose, trehalose-6-phosphate synthase (TPS),and trehalose-6-phosphatase (TPP) have been reported to play important roles in plant abiotic stress and growth development. However, their functions in the flowering process of Rosa hybrida have not been characterized. In this study we found that, under a short photoperiod or weak light intensity, the content of trehalose in the shoot apical meristem of Rosa hybrida cv 'Carola' significantly decreased, leading to delayed flowering time. A total of nine RhTPSs and seven RhTPPs genes were identified in the genome. Cis-element analysis suggested that RhTPS and RhTPP genes were involved in plant hormones and environmental stress responses. Transcriptome data analysis reveals significant differences in the expression levels of RhTPSs and RhTPPs family genes in different tissues and indicates that RhTPPF and RhTPPJ are potential key genes involved in rose flower bud development under different light environments. The results of quantitative real-time reverse transcription (qRT-PCR) further indicate that under short photoperiod and weak light intensity all RhTPP members were significantly down-regulated. Additionally, RhTPS1a, RhTPS10, and RhTPS11 were up-regulated under a short photoperiod and showed a negative correlation with flowering time and trehalose content decrease. Under weak light intensity, RhTPS11 was up-regulated and negatively regulated flowering, while RhTPS5, RhTPS6, RhTPS7b, RhTPS9, and RhTPS10 were down-regulated and positively regulated flowering. This work lays the foundation for revealing the functions of RhTPS and RhTPP gene families in the regulation of rose trehalose.

Coordination of carbon assimilation, allocation, and utilization for systemic improvement of cereal yield

The growth of yield outputs is dwindling after the first green revolution, which cannot meet the demand for the projected population increase by the mid-century, especially with the constant threat from extreme climates. Cereal yield requires carbon (C) assimilation in the source for subsequent allocation and utilization in the sink. However, whether the source or sink limits yield improvement, a crucial question for strategic orientation in future breeding and cultivation, is still under debate. To narrow the knowledge gap and capture the progress, we focus on maize, rice, and wheat by briefly reviewing recent advances in yield improvement by modulation of i) leaf photosynthesis; ii) primary C allocation, phloem loading, and unloading; iii) C utilization and grain storage; and iv) systemic sugar signals (e.g., trehalose 6-phosphate). We highlight strategies for optimizing C allocation and utilization to coordinate the source-sink relationships and promote yields. Finally, based on the understanding of these physiological mechanisms, we envisage a future scenery of "smart crop" consisting of flexible coordination of plant C economy, with the goal of yield improvement and resilience in the field population of cereals crops.

Abscisic Acid Enhances Trehalose Content via OsTPP3 to Improve Salt Tolerance in Rice Seedlings

Salt stress is one of the major environmental stresses that imposes constraints to plant growth and production. Abscisic acid (ABA) has been well-proven to function as a central integrator in plant under salt stress, and trehalose (Tre) has emerged as an excellent osmolyte to induce salt tolerance. However, the interacting mechanism between ABA and Tre in rice seedlings under salt stress is still obscure. Here, we found that the application of exogenous Tre significantly promoted the salt tolerance of rice seedlings by enhancing the activities of antioxidant enzymes. In addition, the expression of OsNCED3 was significantly induced by salt stress. The overexpression of the OsNCED3 gene enhanced the salt tolerance, while the knockout of OsNCED3 reduced the salt tolerance of the rice seedlings. Metabolite analysis revealed that the Tre content was increased in the OsNCED3-overexpressing seedlings and reduced in the nced3 mutant. The application of both ABA and Tre improved the salt tolerance of the nced3 mutant when compared with the WT seedling. OsTPP3 was found to be induced by both the ABA and salt treatments. Consistent with the OsNCED3 gene, the overexpression of OsTPP3 enhanced salt tolerance while the knockout of OsTPP3 reduced the salt tolerance of the rice seedlings. In addition, the Tre content was also higher in the OsTPP3-overexpressing seedling and lower in the tpp3 mutant seedling than the WT plant. The application of exogenous Tre also enhanced the salt tolerance of the tpp3 mutant plant. Overall, our results demonstrate that salt-increased ABA activated the expression of OsTPP3, which resulted in elevated Tre content and thus an improvement in the salt tolerance of rice seedlings.

Genetic dissection of grain morphology and yield components in a wheat line with defective grain filling

KEY MESSAGE

We identified stable QTL for grain morphology and yield component traits in a wheat defective grain filling line and validated genetic effects in a panel of cultivars using breeding-relevant markers. Grain filling capacity is essential for grain yield and appearance quality in cereal crops. Identification of genetic loci for grain filling is important for wheat improvement. However, there are few genetic studies on grain filling in wheat. Here, a defective grain filling (DGF) line wdgf1 characterized by shrunken grains was identified in a population derived from multi-round crosses involving nine parents and a recombinant inbreed line (RIL) population was generated from the cross between wdgf1 and a sister line with normal grains. We constructed a genetic map of the RIL population using the wheat 15K single nucleotide polymorphism chip and detected 25 stable quantitative trait loci (QTL) for grain morphology and yield components, including three for DGF, eleven for grain size, six for thousand grain weight, three for grain number per spike and two for spike number per m². Among them, QDGF.caas-7A is co-located with QTGW.caas-7A and can explain 39.4-64.6% of the phenotypic variances, indicating that this QTL is a major locus controlling DGF. Sequencing and linkage mapping showed that TaSus2-2B and Rht-B1 were candidate genes for QTGW.caas-2B and the QTL cluster (QTGW.caas-4B, QGNS.caas-4B, and QSN.caas-4B), respectively. We developed kompetitive allele-specific PCR markers tightly linked to the stable QTL without corresponding to known yield-related genes, and validated their genetic effects in a diverse panel of wheat cultivars. These findings not only lay a solid foundation for genetic dissection underlying grain filling and yield formation, but also provide useful tools for marker-assisted breeding.

Identification of candidate gene for the defective kernel phenotype using bulked segregant RNA and exome capture sequencing methods in wheat

Wheat is a significant source of protein and starch worldwide. The defective kernel (Dek) mutant AK-3537, displaying a large hollow area in the endosperm and shrunken grain, was obtained through ethyl methane sulfonate (EMS) treatment of the wheat cultivar Aikang 58 (AK58). The mode of inheritance of the AK-3537 grain Dek phenotype was determined to be recessive with a specific statistical significance level. We used bulked segregant RNA-seq (BSR-seq), BSA-based exome capture sequencing (BSE-seq), and the ΔSNP-index algorithm to identify candidate regions for the grain Dek phenotype. Two major candidate regions, DCR1 (Dek candidate region 1) and DCR2, were identified on chromosome 7A between 279.98 and 287.93 Mb and 565.34 and 568.59 Mb, respectively. Based on transcriptome analysis and previous reports, we designed KASP genotyping assays based on SNP variations in the candidate regions and speculated that the candidate gene is TraesCS7A03G0625900 (HMGS-7A), which encodes a 3-hydroxy-3-methylglutaryl-CoA synthase. One SNP variation located at position 1,049 in the coding sequence (G>A) causes an amino acid change from Gly to Asp. The research suggests that functional changes in HMGS-7A may affect the expression of key enzyme genes involved in wheat starch syntheses, such as GBSSII and SSIIIa.