'Green revolution' genes encode mutant gibberellin response modulators

Comparative Review of Fusarium graminearum Infection in Maize and Wheat: Similarities in Resistance Mechanisms and Future Directions

Fusarium graminearum is one of the most important plant-pathogenic fungi that causes disease on wheat and maize, as it decreases yield in both crops and produces mycotoxins that pose a risk to human and animal health. Resistance to Fusarium head blight (FHB) in wheat is well studied and documented. However, resistance to Gibberella ear rot (GER) in maize is less understood, despite several similarities to FHB. In this review, we synthesize existing literature on the colonization strategies, toxin accumulation, genetic architecture, and potential mechanisms of resistance to GER in maize and compare it with what is known regarding FHB in wheat. There are several similarities in the infection and colonization strategies of F. graminearum in maize and wheat. We describe multiple types of GER resistance in maize and identify distinct genetic regions for each resistance type. We discuss the potential of phenylpropanoids for biochemical resistance to F. graminearum. Phenylpropanoids are well characterized, and there are many similarities in their functional roles for resistance between wheat and maize. These insights can be utilized to improve maize germplasm for GER resistance and are also useful for FHB resistance breeding and management. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

TabHLH489 suppresses nitrate signaling by inhibiting the function of TaNLP7-3A in wheat

Nitrate not only serves as the primary nitrogen source for terrestrial plants but also serves as a critical signal in regulating plant growth and development. Understanding how plant responses to nitrate availability is essential for improving nitrogen use efficiency in crops. Herein, we demonstrated that the basic helix-loop-helix (bHLH) transcription factor TabHLH489 plays a crucial negative regulatory role in wheat nitrate signaling. Overexpressing TabHLH489 significantly reduced nitrate-promoted wheat growth and grain yield. Transcriptomic analysis showed that approximately 75% of nitrate-responsive genes were no longerregulated by nitrate in the TabHLH489 overexpression lines. TabHLH489 directly interacts with TaNLP7-3A, the wheat homolog protein of NIN-like protein 7 (NLP7), a central transcription factor in nitrate signaling. This interaction impairs TaNLP7-3A's ability to bind DNA, thereby inhibiting its transcriptional activity. Moreover, TabHLH489 induces the accumulation of reactive oxygen species (ROS) to reduce the nuclear localization of TaNLP7-3A, thereby diminishing its effectiveness in regulating the plant nitrogen response. These findings highlight the intricate regulatory mechanism by which TabHLH489 modulates TaNLP7-3A activity through direct interaction and ROS-mediated inhibition of nuclear localization. Our research highlights the critical roles of TabHLH489 and TaNLP7-3A in modulating nitrate signaling, providing new gene targets for developing wheat varieties with enhanced nitrogen use efficiency.

Mapping and molecular marker development for the BnaSBT gene controlling inflorescence and plant architectures in B. napus

Exploring the molecular mechanism underlying plant architecture and breeding new varieties suitable for mechanized harvesting are primary objectives for rapeseed breeders in China. However, few genes controlling plant architecture have been cloned in Brassica napus. In this study, SX3, a scattered-bud B. napus line with a dwarf and compact plant architecture, was characterized. To identify the genes underlying bud arrangement, plant height and branch angle, segregating populations were constructed by crossing SX3 with two clustered-bud lines with a tall and loose plant architecture. Genetic analysis revealed that the scattered-bud trait (SBT) was controlled by a single dominant gene, BnaSBT. BnaSBT is likely a pleiotropic gene that simultaneously controls plant height and branch angle. Using BSA-seq analysis, BnaSBT was mapped to a 4.15 Mb region on ChrA10. Owing to the lack of recombinants within this region, it was infeasible to finely map BnaSBT. RNA-seq analysis of BC2 plants with contrasting inflorescence and plant architectures revealed that the upregulation of genes involved in amino acid and lipid metabolism and genes encoding MADS-box transcription factors is related to the the phenotype of SX3. These findings together with comparative sequencing indicated that BnaA10.SEP1, BnaA10.AGL15, BnaA10.GLN1-4 and BnaA10.AGP15 are candidate genes for BnaSBT. Markers closely linked to the scattered-bud trait were developed for selecting dwarf and compact plants. These findings provide molecular markers and germplasms for breeding new varieties with ideal plant types and lay a theoretical foundation for cloning key genes and elucidating the genetic basis of inflorescence and plant architectures in B. napus.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01556-2.

Identification of a novel dwarfing gene, Rht_m097, on chromosome 4BS in common wheat

Plant height is a crucial agronomic trait in wheat, regulated by multiple genes, and significantly influences plant architecture and wheat yield. In this study, a novel dwarf mutant, designated as m097, was developed and characterized through the treatment of seeds from the common wheat cultivar Jinmai47 with ethyl methanesulfonate (EMS). Microscopic analysis revealed that the dwarf phenotype was attributed to a reduction in the longitudinal cell size of the stem. Similar to the wild type, m097 exhibited sensitivity to exogenous gibberellic acid (GA). Genetic analysis indicated that the reduced plant height in m097 was regulated by a semi-dominant dwarfing gene, Rht_m097. Through bulk segregant analysis (BSA) utilizing the wheat 660K SNP array, Rht_m097 was mapped and confined to a region of approximately 2.58 Mb on chromosome arm 4BS, encompassing 16 high-confidence annotated genes. In addition, transcriptome sequencing (RNA-seq) was conducted on the first internode below the panicle of JM47 and m097 at the jointing stage, leading to the identification of two potential candidate genes exhibiting differential expression. Furthermore, the analysis of gene ontology and metabolic pathways from RNA-seq data indicated that the down-regulated differentially expressed genes (DEGs) in m097 were biologically classified as regulating actin cortical patch organization and assembly. Concurrently, it was observed that the up-regulated DEGs were significantly enriched in various phytohormone metabolic pathways, including those involved in indole-3-acetic acid (IAA) biosynthesis, jasmonic acid biosynthesis, and gibberellin signaling. Overall, this study provides a novel genetic resource for the breeding of dwarf wheat and establishes a foundation for subsequent gene cloning.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01558-0.

The VcGID1-VcDELLA-VcGID2 complex participates in regulating the dormancy release of blueberry flower buds

Bud dormancy is a crucial mechanism that allows perennial woody plants to withstand adverse environmental conditions, and gibberellin (GA) typically promotes the dormancy release of buds. DELLA protein is the core factor in the GA signaling pathway. This study identified 11 VcDELLA genes from the blueberry genome and performed a comprehensive bioinformatics analysis and prediction of the VcDELLA gene family. GA not only inhibits the dormancy entry of blueberry flower buds under low temperature and short-day conditions but also promotes the dormancy release of flower buds. During the dormancy release process, exogenous GA4+7 significantly increased the GA level and VcDELLA2/4/7/10/11 expression, while it significantly decreased VcDELLA3/6/8 expression. It is widely accepted that the GA-GID1-DELLA signaling module plays important roles in regulating the dormancy process of flower buds. In this study, Y2H and BiFC experiments showed that VcDELLA3/6 proteins could interact withVcGID1b/c, VcGID2, and VcSOC1 proteins. Regardless of the presence or absence of GA, VcGID1b/c and VcGID2 proteins could interact with VcDELLA3/6 proteins to form the VcGID1-VcDELLA-VcGID2 complex. In the leaves of VcDELLA3/6-silenced blueberry plants, VcDELLA3/6, VcGA3ox, VcGA20ox, and VcSOC1 expression was significantly decreased. Meanwhile, VcGID1b and VcGID1c expression was significantly increased. The leaf shedding rates of blueberry plants overexpressing VcDELLA3 and VcDELLA6 increased by 25 % and 33.33 %, respectively. In VcDELLA3/6-overexpressing plants, the GA level and VcDELLA3/6, VcGA2ox, VcGA3ox, VcGA20ox, VcGID2, and VcSOC1 expression were significantly increased, whereas VcGID1b/c expression levels were significantly decreased in VcDELLA6-overexpressing plants. Furthermore, exogenous GA effectively alleviated the deciduous phenotype of VcDELLA3/6 overexpressing blueberry plants and downregulated VcGA2ox, VcGA3ox, and VcGA20ox expression. It could be inferred that VcDELLA3/6 could regulate the transition of dormancy states in blueberry flower buds through interactions with GA biosynthesis (VcGA2ox, VcGA3ox, and VcGA20ox), GA signal transduction (VcGID1b/c and VcGID2), and the flowering related protein VcSOC1. Additionally, it is proposed that there might be a pathway with VcDELLA6 as the core to regulate the chilling-mediated dormancy release of blueberry flower buds. The formation of the GA4+7-VcGID1b/c-VcDELLA6-VcGID2 complex could activate VcSOC1 expression, thereby promoting the dormancy release of blueberry flower buds.

Developmental Dynamics of Intercalary Meristem and Pith Cavity in Rice Stems

In rice, internode elongation is a critical aspect of plant development and agricultural productivity. Previous morphological and histochemical studies using [3H]thymidine have visualized the cell division zone (intercalary meristem) in internodes. However, it has remained unclear how the intercalary meristem forms during stem development. In addition, while a pith cavity forms in the central part of the rice stem, the spatiotemporal relationship between pith cavity formation and intercalary meristem development is not well understood. Therefore, we performed histological analysis of intercalary meristem and pith cavity development using C9285, a deepwater rice variety that shows internode elongation from the vegetative growth stage. We classified the developmental stages of the stem into four stages based on the analysis of pith cavity formation using Trypan blue, Calcein-AM, and MitoRed staining, and visualized dividing cells using the Click-iT EdU imaging assay. In Stage 1, no pith cavity was formed. Vertical cell rows were observed between above the axillary bud attachment and the upper node, suggesting anticlinal divisions that lead to internode formation in the early stage of stem development. In Stage 2, the first pith cavity formed in the pith of the foot, which is the region of axillary bud attachment. Compared to cell division in the internode, that in the foot was significantly activated resulting in slight elongation from Stage 1 to Stage 2. In Stage 3, cell division in the foot ceased, while active cell division at the base of the internode led to significant vertical elongation. The second pith cavity formed due to cell death in the pith of the internode. In Stage 4, the two pith cavities connected to form a single large pith cavity. Although the intercalary meristem maintained cell division activity, the number of cell divisions decreased. Based on these results, we propose a model for stem development that involves two phases of elongation regulation: primary elongation involving slight elongation in the foot, and secondary elongation involving significant internode elongation due to the activation of cell division and cell elongation in the intercalary meristem. This is the first study to anatomically elucidate the spatiotemporal relationship between intercalary meristem development and pith cavity formation in rice stem development. It provides new insights for future research on rice stem development and studies of other grass species.

Molecular genetic regulation of the vegetative-generative transition in wheat from an environmental perspective

The key to the wide geographical distribution of wheat is its high adaptability. One of the most commonly used methods for studying adaptation is investigation of the transition between the vegetative-generative phase and the subsequent intensive stem elongation process. These processes are determined largely by changes in ambient temperature, the diurnal and annual periodicity of daylength, and the composition of the light spectrum. Many genes are involved in the perception of external environmental signals, forming a complex network of interconnections that are then integrated by a few integrator genes. This hierarchical cascade system ensures the precise occurrence of the developmental stages that enable maximum productivity. This review presents the interrelationship of molecular-genetic pathways (Earliness per se, circadian/photoperiod length, vernalization - cold requirement, phytohormonal - gibberellic acid, light perception, ambient temperature perception and ageing - miRNA) responsible for environmental adaptation in wheat. Detailed molecular genetic mapping of wheat adaptability will allow breeders to incorporate new alleles that will create varieties best adapted to local environmental conditions.

Unraveling the genetic basis of heat tolerance and yield in bread wheat: QTN discovery and Its KASP-assisted validation

BACKGROUND

Wheat (Triticum aestivum L.), a globally significant cereal crop and staple food, faces major production challenges due to abiotic stresses such as heat stress (HS), which pose a threat to global food security. To address this, a diverse panel of 126 wheat genotypes, primarily landraces, was evaluated across twelve environments in India, comprising of three locations, two years and two growing conditions. The study aimed to identify genetic markers associated with key agronomic traits in bread wheat, including germination percentage (GERM_PCT), ground cover (GC), days to booting (DTB), days to heading (DTHD), days to flowering (DTFL), days to maturity (DTMT), plant height (PH), grain yield (GYLD), thousand grain weight (TGW), and the normalized difference vegetation index (NDVI) under both timely and late-sown conditions using 35 K SNP genotyping assays. Multi-locus GWAS (ML-GWAS) was employed to detect significant marker-trait associations, and the identified markers were further validated using Kompetitive Allele Specific PCR (KASP).

RESULTS

Six ML-GWAS models were employed for this purpose, leading to the identification of 42 highly significant and consistent quantitative trait nucleotides (QTNs) under both timely and late sown conditions, controlled by 20 SNPs, explaining 3-58% of the total phenotypic variation. Among these, noteworthy QTNs were a major grain yield QTN (qtn_nbpgr_GYLD_3B) on chromosome 3B, a pleiotropic SNP AX-95018072 on chromosome 7A influencing phenology and NDVI, and robust TGW QTNs on chromosomes 2B (qtn_nbpgr_TGW_2B), 1A (qtn_nbpgr_TGW_1A), and 4B (qtn_nbpgr_TGW_4B). Furthermore, annotation revealed that candidate genes near these QTNs encoded stress-responsive proteins, such as chaperonins, glycosyl hydrolases, and signaling molecules. Additionally, three major SNPs AX-95018072 (7A), AX-94946941 (6B), and AX-95232570 (1B) were successfully validated using KASP assay.

CONCLUSION

Our study effectively uncovered novel QTNs and candidate genes linked to heat tolerance and yield-related traits in wheat through an extensive genetic approaches. These QTNs not only corresponded with previously identified QTLs and genes associated with yield traits but also highlighted several new loci, broadening the existing genetic understanding. These findings provide valuable insights into the genetic basis of heat tolerance in wheat and offer genomic resources, including validated markers that could accelerate marker-assisted breeding and the development of next-generation heat-resilient cultivars.

Uncovering the genetic basis of competitiveness and the potential for cooperation in plant groups

Crop productivity was transformed by incorporating dwarfing genes that made plants smaller and less competitive (more cooperative). Beyond such major shifts in plant size, however, it is not clear how much variation in competitiveness remains and how to find its genetic basis. We performed plant density experiments, using 484 lines of the Arabidopsis thaliana multi-parent advanced generation inter-cross population, to compare methods for mapping the genetic basis of plant competitiveness. We first found that a major dwarfing gene, the erecta allele, caused reduced competitiveness and higher group productivity. Then, measuring competitiveness more generally, we found: (i) extensive variation in generic measures of competitiveness that extended beyond the effects of the erecta allele; (ii) a novel genomic region underlying variation in competitiveness; and (iii) that some measures of competitiveness were more useful than others. Our results show how modern genomic resources, including multi-parent populations, could uncover hidden genes for more cooperative crop plants.

Allelism of Uncharacterized Dwarf Mutants in Maize

Gibberellic acid (GA) is a phytohormone that is important for plant growth and development. Mutants in GA biosynthesis, signaling and metabolism have been critical to understanding the role GA plays in plants. GA mutants have also revolutionized global production of staple crops such as rice, wheat, and barley. GA mutants have been isolated in maize and characterization of the underlying genes has helped map the GA biosynthesis and signaling pathways. However, the number of maize dwarf mutants is far less than other species. Here, we identify new dwarf mutants that could benefit our understanding of maize plant height control.

A wheat phytohormone atlas spanning major tissues across the entire life cycle provides novel insights into cytokinin and jasmonic acid interplay

Although numerous studies have focused on phytohormones in specific organs or tissues at different development stages or under various abiotic and biotic stress conditions, our understanding of the distribution and relative abundance of phytohormones throughout the entire life cycle of plants remains insufficient. Here, we present a phytohormone atlas resource obtained from the quantitative analysis of eight major classes of phytohormones, comprising a total of 40 hormone-related compounds, throughout the complete life cycle of wheat. In combination with transcriptome analysis, we established a wheat phytohormone metabolic regulatory network (WPMRN). Using the WPMRN dataset and Gene Ontology enrichment analysis, we swiftly characterized the function of TaLOG5-B1 in cytokinin biosynthesis. Furthermore, a detailed investigation of the WPMRN dataset uncovered transcription factor-mediated co-regulatory mechanisms among different classes of phytohormones. We focused specifically on the metabolic regulation of cytokinin and jasmonic acid, and functionally characterized the genes TaLOG3-D1 and TaAOS-D1 that are involved in the biosynthesis of these phytohormones, respectively, along with their regulatory transcription factor genes TaDOF3A and TaDOF5.6B. The functions of these genes were validated in transgenic plants, revealing their ability to co-regulate radicle length. These findings serve as a case study that highlights the utility of this resource for studying phytohormone metabolic regulatory networks in cereal crops and for gaining insights into the roles of phytohormones in enhancing agronomic traits.

Wheat2035: Integrating pan-omics and advanced biotechnology for future wheat design

Wheat (Triticum aestivum) production is vital for global food security, providing energy and protein to millions of people worldwide. Recent advancements in wheat research have led to significant increases in production, fueled by technological and scientific innovation. Here, we summarize the major advancements in wheat research, particularly the integration of biotechnologies and a deeper understanding of wheat biology. The shift from multi-omics to pan-omics approaches in wheat research has greatly enhanced our understanding of the complex genome, genomic variations, and regulatory networks to decode complex traits. We also outline key scientific questions, potential research directions, and technological strategies for improving wheat over the next decade. Since global wheat production is expected to increase by 60% in 2050, continued innovation and collaboration are crucial. Integrating biotechnologies and a deeper understanding of wheat biology will be essential for addressing future challenges in wheat production, ensuring sustainable practices and improved productivity.

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.

A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity

A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed a barley pan-transcriptome using 20 inbred genotypes representing domesticated barley diversity by generating and analyzing short- and long-read RNA-sequencing datasets from multiple tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific reference transcript datasets (RTDs) and integrated these into a linear pan-genome framework to create a pan-RTD, allowing transcript categorization as core, shell or cloud. Focusing on the core (expressed in all genotypes), we observed significant transcript abundance variation among tissues and between genotypes driven partly by RNA processing, gene copy number, structural rearrangements and conservation of promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations and frequent functional diversification. To complement the pan-transcriptome, we constructed a comprehensive cultivar (cv.) Morex gene-expression atlas and illustrate how these combined datasets can be used to guide biological inquiry.

CsIREH1 phosphorylation regulates DELLA protein affecting plant height in cucumber (Cucumis sativus)

Plant height is a critical agronomic trait that affects crop yield, plant architecture, and environmental adaptability. Gibberellins (GAs) regulate plant height, with DELLA proteins acting as key repressors in the GA signaling pathway by inhibiting GA-induced growth. While DELLA phosphorylation is essential for regulating plant height, the precise mechanisms underlying this process remain incompletely understood. In this study, we identified a cucumber mutant with delayed growth, which exhibited reduced sensitivity to GA treatment. Through bulked segregant analysis (BSA-seq) combined with molecular marker linkage analysis, we successfully identified and cloned the gene responsible for the dwarf phenotype, CsIREH1 (INCOMPLETE ROOT HAIR ELONGATION 1), which encodes an AGC protein kinase. Further research revealed that CsIREH1 interacts with and phosphorylates DELLA proteins, specifically targeting CsGAIP and CsGAI2. We propose that IREH1-dependent phosphorylation of DELLA proteins prevents their excessive accumulation, thereby maintaining normal plant growth. Therefore, investigating the role of IREH1-mediated DELLA phosphorylation provides valuable insights and theoretical foundations for understanding how plants regulate growth mechanisms.

Evolutionary analysis of DELLA proteins in sweet potato and related species reveals their roles in development and stress responses

DELLA proteins act as master negative regulators in the gibberellin signaling pathway, which controls numerous aspects of plant growth and development. Despite the pivotal role of DELLA proteins, a comprehensive genome-wide analysis of the DELLA gene family in sweet potato (Ipomoea batatas) and its related species has yet to be conducted. Here, we performed a comparative analysis of this gene family among six Ipomoea species, including Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, Ipomoea nil, Ipomoea cairica, and Ipomoea aquatica. Among the six Ipomoea species, only I. nil contains five DELLA genes, while the remaining species have three DELLA genes each. The DELLA genes were categorized into three distinct subgroups based on the phylogenetic topology in selected Ipomoea species. Comparative analysis of gene structure and protein motifs revealed that members within the same phylogenetic group exhibit comparable exon/intron and motif organization. The cis-regulatory elements of the DELLA gene in selected Ipomoea species contain unique promoter elements, indicating the presence of species-specific regulatory mechanisms. A multitude of shared cis-regulatory elements related to stress responses were identified in the DELLA gene promoters. Furthermore, a syntenic analysis indicates two groups of syntenic DELLA genes have undergone several rearrangements. The results of the duplication analysis indicated that dispersed duplications contribute to the expansion of the DELLA genes. Moreover, the DELLA genes in sweet potato display an expression pattern that tends to control the growth and development of either the aerial or below-ground parts, and they are responsive to a range of hormones and abiotic stresses. Thus, these findings provide insights into the evolutionary history of DELLA genes within the genus Ipomoea and the functions of sweet potato DELLA genes.

Genetic dissection of flag leaf morphology traits and fine mapping of a novel QTL (Qflw.sxau-6BL) in bread wheat (Triticum aestivum L.)

KEY MESSAGE

Total 60-QRC for FLM traits were detected by meta-genomics analysis, nine major and stable QTL identified by DH population and validated, and a novel QTL  Qflw.sxau-6BL was fine mapped. The flag leaf is an "ideotypic" morphological trait providing photosynthetic assimilates in wheat. Although flag leaf morphology (FLM) traits had been extensively investigated through genetic mapping, there is a desire for FLM-related loci to be validated in multi-environments and fine mapping. In order to identify the stable genomic regions for FLM traits, we conducted a meta-genomic analysis based on reports from 2008 to 2024. Experimentally, a doubled haploid (DH) population was used to assess the genetic regions associated with FLM traits in nine environments. The meta-genomic analysis extracted 60 QTL-rich clusters (QRC), 45 of which were verified in marker-trait association (MTA) study. Nine major and stable QTL were found being associated with FLM traits across three-to-seven environments including BLUP, with phenotypic variance explained (PVE) ranging from 5.05 to 34.95%. The KASP markers of the nine QTL were validated (P < 0.005) in more than three environments using a panel of diverse wheat collections from Shanxi Province in China. Two co-located major and stable QTL viz. Qflw.sxau-6B.5 and Qfla.sxau-6B.4 were found novel and contributed to increase FLW by 12.09-19.21% and FLA by 5.45-13.28%. They also demonstrated high recombination rates in LD analysis based on the resequencing of 145 wheat landmark cultivars. The fine mapping of Qflw.sxau-6BL narrowed it down to a 1.27 Mb region as a result of the combined genotypic and phenotypic analysis for secondary mapping population. Comparing to NIL-ND3338, the NIL-LF5064 showed higher FLW by 20.45-27.37%, thousand-grain weight by 1.88-2.57% and grain length by 0.47-2.30% across all environments. The expression analysis of 11 tissues revealed seven highly expressed genes within the fine map region. This study provides a genetic basis for the FLM traits for further map-based cloning of FLW genes in wheat.

A favorable natural variation in CCD7 from orchardgrass confers enhanced tiller number

Tiller number is a crucial determinant that significantly influences the productivity and reproductive capacity of forage. The regeneration potential, biomass production, and seed yield of perennial forage species are highly reliant on the development of tillering. Strigolactones (SLs) are recently discovered carotenoid-derived phytohormones that play a crucial role in the regulation of tillering in annual crops. However, the modulation of tiller growth in perennial forage by SLs remains insufficiently investigated. In this study, we identified two alleles of the SLs biosynthesis gene, DgCCD7A and DgCCD7D, which encode CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7), from two distinct subspecies of orchardgrass (Dactylis glomerata) exhibiting contrasting tillering phenotype and SLs content. The functionality of the DgCCD7A allele derived from high-tillering phenotypic orchardgrass was found to be diminished compared to that of DgCCD7D from the low-tillering type in rescuing the increased branching phenotype of CCD7-defective mutants in Arabidopsis and rice (Oryza sativa). Notably, the introduction of DgCCD7A in rice resulted in an increase in tiller number without significantly compromising grain yield. Moreover, we demonstrated that the L309P variation in DgCCD7A is a rare natural variant exclusively found in orchardgrass. Our findings revealed that DgCCD7A, a rare favorable natural variation of CCD7 in orchardgrass, holds significant potential for breeding application in improving the plant architecture of perennial forage and crops.

MaGA20ox2f, an OsSD1 homolog, regulates flowering time and fruit yield in banana

Previous studies illustrated that two banana GA20 oxidase2 (MaGA20ox2) genes, Ma04g15900 and Ma08g32850, are implicated in controlling banana growth and development; however, the biological function of each gene remains unknown. Ma04g15900 protein (termed MaGA20ox2f in this article) is the closest homolog to the Rice SD1 (encoded by 'green revolution gene', OsSD1) in the banana genome. The expression of MaGA20ox2f is confined to leaves, peduncles, fruit peels, and pulp. Knockout of MaGA20ox2f by CRISPR/Cas9 led to late flowering and low-yielding phenotypes. The flowering time of ΔMaGA20ox2f #1 and ∆MaGA20ox2f #2 lines was delayed approximately by 61 and 58 days, respectively, while fruit yield decreased by 81.13% and 76.23% compared to wild type under normal conditions. The endogenous levels of downstream products of GA20 oxidase, GA15 and GA20, were significantly reduced in ∆MaGA20ox2f mutant shoots and fruits, but bioactive GA1 was only significantly reduced in the mutant fruits. Quantitative proteomics analysis identified 118 up-regulated proteins and 309 down-regulated proteins in both ΔMaGA20ox2f #1 and ∆MaGA20ox2f #2 lines, compared to wild type, with the down-regulated proteins primarily associated with photosynthesis, porphyrin and chlorophyll metabolism. The decreased chlorophyll contents in ΔMaGA20ox2f #1 and ∆MaGA20ox2f #2 lines corroborated the findings of the proteomics data. We propose that photosynthesis inhibition caused by lower chlorophyll contents in ΔMaGA20ox2f mutant leaves and GA1 deficiency in ΔMaGA20ox2f mutant fruits may be the two critical reasons contributing to the late flowering and low-yielding phenotypes of ΔMaGA20ox2f mutants.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01523-3.

The mutation of ent-kaurenoic acid oxidase, a key enzyme involved in gibberellin biosynthesis, confers a dwarf phenotype to cucumber

KEY MESSAGE

A dwarf mutant with short branches (csdf) was identified from EMS-induced mutagenesis. Bulked segregant analysis sequencing and map-based cloning revealed CsKAO encoding ent-kaurenoic acid oxidase as the causal gene. Plant architecture is the primary target of artificial selection during domestication and improvement based on the determinate function for fruit yield. Plant architecture is regulated by complicated genetic networks, more underlying mechanism remains to be elucidated. Here, we identified a dwarf mutant (csdf) in an EMS-induced cucumber population, and genetic analysis revealed the mutated phenotype is controlled by a single recessive gene. Optical microanalysis showed the decrease in cell length is mainly contribute to the dwarf phenotype. By strategy of BSA-seq combined with map-based cloning, CsaV3_6G006520 (CsKAO) on chromosome 6 was identified as the candidate gene for csdf. Gene cloning and sequence alignment revealed a G to A mutation in the sixth exon, which causes the premature stop codon in CsKAO of csdf. Expression analysis revealed CsKAO was expressed in various tissues with abundant transcripts, and has significant differences between WT and csdf. Gene annotation indicated CsKAO encodes a cytochrome P450 family ent-kaurenoic acid oxidase which functioned in GA biosynthesis. GA-relevant analysis showed that endogenous GA contents were significantly decreased and the dwarfism phenotype could be restored by exogenous GA3 treatment; while, some of the representative enzyme genes involved in the GA pathway were up-regulated in csdf. Besides, IAA content is decreased in the terminal bud and increased in the lateral bud in csdf as well as several IAA-related genes are differentially expressed. Overall, those findings suggest that CsKAO regulated plant height via the influence on GAs pathways, and IAA might interact with GAs on plant architecture morphogenesis in cucumber.

From Images to Loci: Applying 3D Deep Learning to Enable Multivariate and Multitemporal Digital Phenotyping and Mapping the Genetics Underlying Nitrogen Use Efficiency in Wheat

The selection and promotion of high-yielding and nitrogen-efficient wheat varieties can reduce nitrogen fertilizer application while ensuring wheat yield and quality and contribute to the sustainable development of agriculture; thus, the mining and localization of nitrogen use efficiency (NUE) genes is particularly important, but the localization of NUE genes requires a large amount of phenotypic data support. In view of this, we propose the use of low-altitude aerial photography to acquire field images at a large scale, generate 3-dimensional (3D) point clouds and multispectral images of wheat plots, propose a wheat 3D plot segmentation dataset, quantify the plot canopy height via combination with PointNet++, and generate 4 nitrogen utilization-related vegetation indices via index calculations. Six height-related and 24 vegetation-index-related dynamic digital phenotypes were extracted from the digital phenotypes collected at different time points and fitted to generate dynamic curves. We applied height-derived dynamic numerical phenotypes to genome-wide association studies of 160 wheat cultivars (660,000 single-nucleotide polymorphisms) and found that we were able to locate reliable loci associated with height and NUE, some of which were consistent with published studies. Finally, dynamic phenotypes derived from plant indices can also be applied to genome-wide association studies and ultimately locate NUE- and growth-related loci. In conclusion, we believe that our work demonstrates valuable advances in 3D digital dynamic phenotyping for locating genes for NUE in wheat and provides breeders with accurate phenotypic data for the selection and breeding of nitrogen-efficient wheat varieties.

Improving grain yield and salt tolerance by optimizing plant height with beneficial haplotypes in rice (Oryza sativa)

INTRODUCTION

Rice (Oryza sativa L.), a staple food for billions worldwide, is challenged by salt stress. Owing to the limited understanding of the physiological and genetic basis of rice salt tolerance, few genes have been identified as valuable in rice breeding, causing a major bottleneck in the development of high-yield, salt-tolerant rice varieties.

OBJECTIVE

This study aims to identify salt tolerance genes/quantitative trait loci (QTLs) with breeding potential in rice.

METHODS

Field trials were conducted with 166 Chinese rice cultivars from saline-affected regions and 412 global rice accessions to assess salt tolerance. Genome-wide association study (GWAS) was performed to identify key loci related to high yield and salt tolerance. Additionally, the impact of introducing beneficial haplotypes on grain yield and salt tolerance was assessed.

RESULTS

The optimal rice plant height of 100-120 cm was crucial for sustaining high yield under both normal and salt stress conditions. GWAS revealed 6 novel QTLs/genes associated with rice plant growth and grain yield across various environments, distinct from previously recognized salt stress-related genes. Notably, the gene PHS10.1, encoding a serine/threonine protein kinase, may regulate carbon metabolism, starch and sucrose metabolism, influencing plant growth and grain yield. Certain haplotypes of the genes regulating plant height and grain yield, including SD1, Ghd7.1, GH3.5, and PHS10.1, were selected in traditional breeding. Moreover, optimizing plant height through the introgression of beneficial alleles of these genes increased grain yield in recipient lines under both normal and saline conditions.

CONCLUSION

We propose that utilizing beneficial haplotypes to optimize plant height can effectively balance the growth-stress trade-offs in rice plants. This represents a promising breeding strategy for the development of crop varieties that are both high-yielding and salt-tolerant.

Diversity of Gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement

INTRODUCTION

Gibberellin (GA) is a vital phytohormone in regulating plant growth and development. During the "Green Revolution", modification of GA-related genes created semi-dwarfing phenotype in cereal crops but adversely affected grain weight. Gibberellin 2-oxidases (GA2oxs) in barley act as key catabolic enzymes in deactivating GA, but their functions are still less known.

OBJECTIVES

This study investigates the physiological function of two HvGA2ox genes in barley and identifies novel semi-dwarf alleles with minimum impacts on other agronomic traits.

METHODS

Virus-induced gene silencing and CRISPR/Cas9 technology were used to manipulate gene expression of HvGA2ox9 and HvGA2ox8a in barley and RNA-seq was conducted to compare the transcriptome between wild type and mutants. Also, field trials in multiple environments were performed to detect the functional haplotypes.

RESULTS

There were ten GA2oxs that distinctly expressed in shoot, tiller, inflorescence, grain, embryo and root. Knockdown of HvGA2ox9 did not affect plant height, while ga2ox8a mutants generated by CRISPR/Cas9 increased plant height and significantly altered seed width and weight due to the increased bioactive GA4 level. RNA-seq analysis revealed that genes involved in starch and sucrose metabolism were significantly decreased in the inflorescence of ga2ox8a mutants. Furthermore, haplotype analysis revealed one naturally occurring HvGA2ox8a haplotype was associated with decreased plant height, early flowering and wider and heavier seed.

CONCLUSION

Our results demonstrate the potential of manipulating GA2ox genes to fine tune GA signalling and biofunctions in desired plant tissues and open a promising avenue for minimising the trade-off effects of Green Revolution semi-dwarfing genes on grain size and weight. The knowledge will promote the development of next generation barley cultivars with better adaptation to a changing climate.

Candidate selective sweeps in US wheat populations

Exploration of novel alleles from ex situ collection is still limited in modern plant breeding as these alleles exist in genetic backgrounds of landraces that are not adapted to modern production environments. The practice of backcross breeding results in preservation of the adapted background of elite parents but leaves little room for novel alleles from landraces to be incorporated. Selection of adaptation-associated linkage blocks instead of the entire adapted background may allow breeders to incorporate more of the landrace's genetic background and to observe and evaluate novel alleles. Important adaptation-associated linkage blocks would have been selected over multiple cycles of breeding and hence are likely to exhibit signatures of positive selection or selective sweeps. We conducted genome-wide scan for candidate selective sweeps (CSS) using Fst, Rsb, and xpEHH in state, regional, spring, winter, and market-class population pairs and reported 446 CSS in 19 population pairs over time and 1033 CSS in 44 population pairs across geography and class. Further validation of these CSS in specific breeding programs may lead to identification of sets of loci that can be selected to restore population-specific adaptation in pre-breeding germplasms.

Hormonal influence on maize inflorescence development and reproduction

KEY MESSAGE

Different plant hormones contribute to maize reproductive success. Maize is a major crop species and significantly contributes directly and indirectly to human calorie uptake. Its success can be mainly attributed to its unisexual inflorescences, the tassel and the ear, whose formation is regulated by complex genetic and hormonal networks, and is influenced by environmental cues such as temperature, and nutrient and water availability. Traditional genetic analysis of classic developmental mutants, together with new molecular approaches, have shed light on many crucial aspects of maize reproductive development including the influence that phytohormones exert on key developmental steps leading to successful reproduction and seed yield. Here we will review both historical and recent findings concerning the main roles that phytohormones play in maize reproductive development, from the commitment to reproductive development to sexual reproduction.

A MYB transcription factor underlying plant height in sorghum qHT7.1 and maize Brachytic 1 loci

Manipulating plant height is an essential component of crop improvement. Plant height was generally reduced through breeding in wheat, rice, and sorghum to resist lodging and increase grain yield but kept high for bioenergy crops. Here, we positionally cloned a plant height quantitative trait locus (QTL) qHT7.1 as a MYB transcription factor controlling internode elongation, cell proliferation, and cell morphology in sorghum. A 740 bp transposable element insertion in the intronic region caused a partial mis-splicing event, generating a novel transcript that included an additional exon and a premature stop codon, leading to short plant height. The dominant allele had an overall higher expression than the recessive allele across development and internode position, while both alleles' expressions peaked at 46 days after planting and progressively decreased from the top to lower internodes. The orthologue of qHT7.1 was identified to underlie the brachytic1 (br1) locus in maize. A large insertion in exon 3 and a 160 bp insertion at the promoter region were identified in the br1 mutant, while an 18 bp promoter insertion was found to be associated with reduced plant height in a natural recessive allele. CRISPR/Cas9-induced gene knockout of br1 in two maize inbred lines showed significant plant height reduction. These findings revealed functional connections across natural, mutant, and edited alleles of this MYB transcription factor in sorghum and maize. This enriched our understanding of plant height regulation and enhanced our toolbox for fine-tuning plant height for crop improvement.

RNA-Seq Transcriptomics and iTRAQ Proteomics Analysis Reveal the Dwarfing Mechanism of Blue Fescue (Festuca glauca)

Blue fescue is a widely used ornamental grass because of its strong ecological adaptability. To maintain the optimal ornamental plant shape, blue fescue requires many nutrients and labor. Using dwarf varieties with slow growth is an effective way to fulfill these requirements. In this study, we investigated the dwarfing mechanism of dw-1, a blue fescue dwarfing mutant, using physiological, transcriptomic, and proteomic methods. The peroxidase (POD) enzyme activity and chlorophyll content of dw-1 significantly increased, while the lignin, gibberellin (GA), and indoleacetic acid (IAA) content significantly decreased. A total of 7668 differentially expressed genes (DEGs) were detected using RNA-seq, of which 2543 were upregulated and 5125 were downregulated. A total of 165 differentially expressed proteins (DEPs) were detected using iTRAQ, of which 68 were upregulated and 97 were downregulated. KEGG enrichment analysis showed that the diterpene biosynthesis pathway, tryptophan metabolism pathway, and phenylpropanoid biosynthesis pathway were significantly enriched at both the transcriptional and protein levels. As a result, we can formulate the following hypothesis about the dw-1 dwarfing phenotype: the downregulation of genes and proteins related to IAA and GA biosynthesis is associated with the dwarf phenotype's formation, and metabolic pathways related to lignin synthesis, such as phenylpropanoid biosynthesis, also play an important role. Our work will contribute to a new understanding of the genes and proteins involved in the blue fescue dwarf phenotype.

Identification and validation of novel plant compactness QTL in common wheat

BACKGROUND

Plant compactness (PC) is a crucial agronomic trait that affects plant density in wheat, which in turn influences biomass and grain yield potential. The canopy of high-yielding wheat varieties should exhibit appropriate aboveground plant architecture. In this study, three recombinant inbred line (RIL) populations were generated to identify and validate quantitative trait loci (QTL) related to plant compactness. The erect and compact tillering genotype SN05525 was used as a common parent. A total of 193 F8 RILs from the cross SN05525/SN22 were genotyped using the high-density Illumina iSelect 90 K single nucleotide polymorphism (SNP) assay.

RESULTS

A linkage map with 7180 SNP loci was constructed, revealing six QTL on chromosomes 3B (Qpc.sdau-3B.1, Qpc.sdau-3B.2),5B (Qpc.sdau-5B), 5D (Qpc.sdau-5D), 2 A (Qpc.sdau-2 A), and 7 A (Qpc.sdau-7 A) that control compact tillers. Qpc.sdau-3B.1, Qpc.sdau-5D, and Qpc.sdau-5B accounted for up to 16.70%, 16.89%, and 14.56% of the phenotypic variance, respectively. Kompetitive allele-specific PCR (KASP) markers were developed for these QTL, and their effects were validated in two additional RIL populations, SN05525/Luyuan 502 and SN05525/Xinong 511. Significant effects of Qpc.sdau-3B.1 and Qpc.sdau-5D on compactness were observed in the validation populations.

CONCLUSION

Three major QTL loci closely related to plant compactness in wheat were successfully identified, and their effects were validated in two additional RIL populations across multi environments. Plant architecture plays a crucial role in enhancing yield and economic value in wheat. In the process of molecular marker-assisted selection breeding, the closely linked KASP markers could potentially be utilized in molecular marker-assisted selection for adjusting plant compactness and for further characterization of the underlying gene(s).

Genetic Basis of Tillering Angle from Other Plants to Wheat: Current Progress and Future Perspectives

Plant architecture is an important agronomic trait that impacts crop yield. The tiller angle is a critical aspect of the plant's structural organization, which is influenced by both internal and external factors. The genetic mechanisms underlying the tiller angle have been extensively investigated in other plants. However, research on wheat is relatively limited. Additionally, mechanics has emerged as a connection between biochemical signaling and the development of three-dimensional biological forms. It not only reveals how physical interactions at the cellular level influence overall morphogenesis but also elucidates the interplay between these mechanical processes and molecular signaling pathways that collectively determine plant morphology. This review examines the recent advancements in the study of tillering angle in wheat and other plants. It discusses progress in research ranging from observable characteristics to the regulation of genes, as well as the physiological and biochemical aspects, and the adaptability to environmental factors. In addition, this review also discusses the effects of mechanical on plant growth and development, and provides ideas for the study of mechanical regulation mechanism of tillering angle in wheat. Consequently, based on the research of other plants and combined with the genetic and mechanical principles, this approach offers novel insights and methodologies for studying tillering in wheat. This interdisciplinary research framework not only enhances our understanding of the mechanisms underlying wheat growth and development but may also uncover the critical factors that regulate tillering angle, thereby providing a scientific foundation for improving wheat yield and adaptability.

Sex on Steroids: How Brassinosteroids Shape Reproductive Development in Flowering Plants

Since the discovery of brassinolide in the pollen of rapeseed, brassinosteroids (BRs) have consistently been associated with reproductive traits. However, compared to what is known for how BRs shape vegetative development, the understanding of how these hormones regulate reproductive traits is comparatively still lacking. Nevertheless, there is now considerable evidence that BRs regulate almost all aspects of reproduction, from ovule and pollen formation to seed and fruit development. Here, we review the current body of knowledge on how BRs regulate reproductive processes in plants and what is known about how these pathways are transduced at the molecular level. We also discuss how the manipulation of BR biosynthesis and signaling can be a promising avenue for improving crop traits that rely on efficient reproduction. We thus propose that BRs hold an untapped potential for plant breeding, which could contribute to attaining food security in the coming years.

EARLY FLOWERING3-1 represses Grain number, plant height, and heading date7 to promote ABC1 REPRESSOR1 and regulate nitrogen uptake in rice

The extensive use of nitrogen fertilizer boosts rice (Oryza sativa) production but also harms ecosystems. Therefore, enhancing crop nitrogen use efficiency is crucial. Here, we performed map-based cloning and identified the EARLY FLOWERING3 (ELF3) like protein-encoding gene OsELF3-1, which confers enhanced nitrogen uptake in rice. OsELF3-1 forms a ternary complex (OsEC) with OsELF4s and OsLUX, the putative orthologs of ELF4 and LUX ARRHYTHMO (LUX) in Arabidopsis (Arabidopsis thaliana), respectively. OsEC directly binds to the promoter of Grain number, plant height, and heading date7 (Ghd7) and represses its expression. Ghd7 encodes a transcription factor that has major effects on multiple agronomic traits. Ghd7 is also a transcriptional repressor and directly suppresses the expression of ABC1 REPRESSOR1 (ARE1), a negative regulator of nitrogen use efficiency. Therefore, targeting the OsEC-Ghd7-ARE1 module offers an approach to enhance nitrogen uptake, presenting promising avenues for sustainable agriculture.

Genome wide association study and transcriptome analysis identify candidate genes regulating wheat coleoptile length

Coleoptile length, in wheat, is a significant agronomic trait impacting yield by facilitating the successful establishment of seedlings. In arid regions, varieties possessing longer coleoptile can evade harsh conditions by deep sowing, paving the way for improved yield. However, the study of genes involved in coleoptile development is insufficient. In this study, a high-density 660 K SNP array was used for genome-wide association study (GWAS) on coleoptile length in 150 wheat varieties. The findings revealed the detection of 353 significantly associated SNPs across all environments. The integration of linkage disequilibrium analysis and haplotype analysis mined 23 core QTLs capable responsible for the stable regulating coleoptile length in wheat. In wheat varieties characterized by extended coleoptile length, 6,600, 11,524, and 6,059 genes were found to be differentially expressed at three distinct developmental stages within the coleoptile, respectively. Through GWAS, gene expression levels, and functional annotation, we concluded the identification of two candidate genes (TraesCS2B02G423500, TraesCS2B02G449200) regulating wheat coleoptile length. By employing WGCNA and protein interactions prediction, discovered that the 19 genes were found to interact with candidate genes and participate in plant hormone metabolism and signaling, cell elongation or proliferation, which collectively contributing to coleoptile elongation. Additionally, two KASP markers were developed which can be used in breeding. These results offer a basis for understanding the genetic regulatory network responsible for wheat coleoptile length formation. The QTLs and candidate genes identified in this study can be further utilized for genetic improvement of wheat coleoptile length.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01520-6.

Unraveling the Secrets of Early-Maturity and Short-Duration Bread Wheat in Unpredictable Environments

In response to the escalating challenges posed by unpredictable environmental conditions, the pursuit of early maturation in bread wheat has emerged as a paramount research endeavor. This comprehensive review delves into the multifaceted landscape of strategies and implications surrounding the unlocking of early maturation in bread wheat varieties. Drawing upon a synthesis of cutting-edge research in genetics, physiology, and environmental science, this review elucidates the intricate mechanisms underlying early maturation and its potential ramifications for wheat cultivation in dynamic environments. By meticulously analyzing the genetic determinants, physiological processes, and environmental interactions shaping early maturation, this review offers valuable insights into the complexities of this trait and its relevance in contemporary wheat breeding programs. Furthermore, this review critically evaluates the trade-offs inherent in pursuing early maturation, navigating the delicate balance between accelerated development and optimal yield potential. Through a meticulous examination of both challenges and opportunities, this review provides a comprehensive framework for researchers, breeders, and agricultural stakeholders to advance our understanding and utilization of early maturation in bread wheat cultivars, ultimately fostering resilience and sustainability in wheat production systems worldwide.

Molecular and genetic basis of plant architecture in soybean

Plant architecture determines canopy coverage, photosynthetic efficiency, and ultimately productivity in soybean (Glycine max). Optimizing plant architecture is a major goal of breeders to develop high yield soybean varieties. Over the past few decades, the yield per unit area of soybean has not changed significantly; however, rice and wheat breeders have succeeded in achieving high yields by generating semi-dwarf varieties. Semi-dwarf crops have the potential to ensure yield stability in high-density planting environments because they can significantly improve responses to fertilizer input, lodging resistance, and enhance resistance to various abiotic and biotic stresses. Soybean has a unique plant architecture, with leaves, inflorescences, and pods growing at each node; internode number greatly affects the final yield. Therefore, producing high-yielding soybean plants with an ideal architecture requires the coordination of effective node formation, effective internode formation, and branching. Dozens of quantitative trait loci (QTLs) controlling plant architecture have been identified in soybean, but only a few genes that control this trait have been cloned and characterized. Here, we review recent progress in understanding the genetic basis of soybean plant architecture. We provide our views and perspectives on how to breed new high-yielding soybean varieties.

Strigolactone-gibberellin crosstalk mediated by a distant silencer fine-tunes plant height in upland cotton

Optimal plant height is crucial in modern agriculture, influencing lodging resistance and facilitating mechanized crop production. Upland cotton (Gossypium hirsutum) is the most important fiber crop globally; however, the genetic basis underlying plant height remains largely unexplored. In this study, we conducted a genome-wide association study to identify a major locus controlling plant height (PH1) in upland cotton. This locus encodes gibberellin 2-oxidase 1A (GhPH1) and features a 1133-bp structural variation (PAVPH1) located approximately 16 kb upstream. The presence or absence of PAVPH1 influences the expression of GhPH1, thereby affecting plant height. Further analysis revealed that a gibberellin-regulating transcription factor (GhGARF) recognizes and binds to a specific CATTTG motif in both the GhPH1 promoter and PAVPH1. This interaction downregulates GhPH1, indicating that PAVPH1 functions as a distant upstream silencer. Intriguingly, we found that DWARF53 (D53), a key repressor of the strigolactone (SL) signaling pathway, directly interacts with GhGARF to inhibit its binding to targets. Moreover, we identified a previously unrecognized gibberellin-SL crosstalk mechanism mediated by the GhD53-GhGARF-GhPH1/PAVPH1 module, which is crucial for regulating plant height in upland cotton. These findings shed light on the genetic basis and gene interaction network underlying plant height, providing valuable insights for the development of semi-dwarf cotton varieties through precise modulation of GhPH1 expression.

Comparing performances of different statistical models and multiple threshold methods in a nested association mapping population of wheat

Nested association mapping (NAM) populations emerged as a multi-parental strategy that combines the high statistical power of biparental linkage mapping with greater allelic richness of association mapping. Several statistical models have been developed for marker-trait associations (MTAs) in genome-wide association studies (GWAS), which ranges from simple to increasingly complex models. These statistical models vary in their performance for detecting real association with the avoidance of false positives and false negatives. Furthermore, significant threshold methods play an equally important role for controlling spurious associations. In this study, we compared the performance of seven different statistical models ranging from single to multi-locus models on eight different simulated traits with varied genetic architecture for a NAM population of spring wheat (Triticum aestivum L.). The best identified model was further used to identify MTAs for 11 different agronomic and spectral reflectance traits, which were collected on the NAM population between 2014 and 2016. The "Bayesian information and linkage disequilibrium iteratively nested keyway (BLINK)" model performed better than all other models observed based on QQ plots and detection of real association in a simulated data set. The results from model comparison suggest that BLINK controls both false positives and false negatives under the different genetic architecture of simulated traits. Comparison of multiple significant threshold methods suggests that Bonferroni correction performed superior for controlling false positives and false negatives and complements the performance of GWAS models. BLINK identified 45 MTAs using Bonferroni correction of 0.05 for 11 different phenotypic traits in the NAM population. This study helps identify the best statistical model and significant threshold method for performing association analysis in subsequent NAM population studies.

Recent advances in response to environmental signals during Arabidopsis root development

Plants grow by anchoring their roots in the soil, acquiring essential water and nutrients for growth, and interacting with other signaling factors in the soil. Root systems are crucial for both the basic growth and development of plants and their response to external environmental stimuli. Under different environmental conditions, the configuration of root systems in plants can undergo significant changes, with their strength determining the plant's ability to adapt to the environment. Therefore, understanding the mechanisms by which environmental factors regulate root development is essential for crop root architecture improvement and breeding for stress resistance. This paper summarizes the research progress in genetic regulation of root development of the model plant Arabidopsis thaliana (L.) Heynh. amidst diverse environmental stimuli over the past five years. Specifically, it focuses on the regulatory networks of environmental signals, encompassing light, energy, temperature, water, nutrients, and reactive oxygen species, on root development. Furthermore, it provides prospects for the application of root architecture improvement in crop breeding for stress resistance and nutrient efficiency.

Identification of Quantitative Trait Loci Associated with Plant Adaptation Traits Using Nested Association Mapping Population

This study evaluated 290 recombinant inbred lines (RILs) of the nested association mapping (NAM) population from the UK. The population derived from 24 families, where a common parent was "Paragon," one of the UK's spring wheat cultivar standards. All genotypes were tested in two regions of Kazakhstan at the Kazakh Research Institute of Agriculture and Plant Industry (KRIAPI, Almaty region, Southeast Kazakhstan, 2019-2022 years) and Alexandr Barayev Scientific-Production Center for Grain Farming (SPCGF, Shortandy, Akmola region, Northern Kazakhstan, 2019-2022 years). The studied traits consisted of plant adaptation-related traits, including heading date (HD, days), seed maturation date (SMD, days), plant height (PH, cm), and peduncle length (PL, cm). In addition, the yield per m2 was analyzed in both regions. Based on a field evaluation of the population in northern and southeastern Kazakhstan and using 10,448 polymorphic SNP (single-nucleotide polymorphism) markers, the genome-wide association study (GWAS) allowed for detecting 74 QTLs in four studied agronomic traits (HD, SMD, PH, and PL). The literature survey suggested that 16 of the 74 QTLs identified in our study had also been detected in previous QTL mapping studies and GWASs for all studied traits. The results will be used for further studies related to the adaptation and productivity of wheat in breeding projects for higher grain productivity.

Molecular Regulation of Shoot Architecture in Soybean

Soybean (Glycine max [L.] Merr.) serves as a major source of protein and oil for humans and animals. Shoot architecture, the spatial arrangement of a plant's above-ground organs, strongly affects crop yield and is therefore a critical agronomic trait. Unlike wheat and rice crops that have greatly benefitted from the Green Revolution, soybean yield has not changed significantly in the past six decades owing to its unique shoot architecture. Soybean is a pod-bearing crop with pods adhered to the nodes, and variation in shoot architecture traits, such as plant height, node number, branch number and number of seeds per pod, directly affects the number of pods and seeds per plant, thereby determining yield. In this review, we summarize the relationship between soybean yield and these major components of shoot architecture. We also describe the latest advances in identifying the genes and molecular mechanisms underlying soybean shoot architecture and discuss possible directions and approaches for breeding new soybean varieties with ideal shoot architecture and improved yield.

BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice

Tiller angle is a key agricultural trait that establishes plant architecture, which in turn strongly affects grain yield by influencing planting density in rice. The shoot gravity response plays a crucial role in the regulation of tiller angle in rice, but the underlying molecular mechanism is largely unknown. Here, we report the identification of the BIG TILLER ANGLE2 (BTA2), which regulates tiller angle by controlling the shoot gravity response in rice. Loss-of-function mutation of BTA2 dramatically reduced auxin content and affected auxin distribution in rice shoot base, leading to impaired gravitropism and therefore a big tiller angle. BTA2 interacted with AUXIN RESPONSE FACTOR7 (ARF7) to modulate rice tiller angle through the gravity signaling pathway. The BTA2 protein was highly conserved during evolution. Sequence variation in the BTA2 promoter of indica cultivars harboring a less expressed BTA2 allele caused lower BTA2 expression in shoot base and thus wide tiller angle during rice domestication. Overexpression of BTA2 significantly increased grain yield in the elite rice cultivar Huanghuazhan under appropriate dense planting conditions. Our findings thus uncovered the BTA2-ARF7 module that regulates tiller angle by mediating the shoot gravity response. Our work offers a target for genetic manipulation of plant architecture and valuable information for crop improvement by producing the ideal plant type.

Two dwarfing genes Rht-B1b and Rht-D1b show pleiotropic effects on grain protein content in bread wheat (Triticum aestivum L.)

KEY MESSAGE

Five QTL for wheat grain protein content were identified, and the effects of two dwarfing genes Rht-B1b and Rht-D1b on grain protein content were validated in multiple populations. Grain protein content (GPC) plays an important role in wheat quality. Here, a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) was used to identify quantitative trait loci (QTL) for GPC. Two hundred and five RILs and their parents were grown in three years in randomized complete blocks each with two replications, and genotyped using the wheat 55 K SNP array. Five QTL were identified for GPC on chromosomes 1A, 1B, 2D, 4B, and 4D. Notably, QGpc.yaas-4B (co-located with Rht-B1) and QGpc.yaas-4D (co-located with Rht-D1) were consistently detected across all experiments and best linear unbiased estimating, accounting for 6.61-8.39% and 6.05-10.21% of the phenotypic variances, respectively. The effects of these two dwarfing alleles Rht-B1b and Rht-D1b on reducing GPC and plant height were validated in two additional RIL populations and one natural population. This study lays a foundation for further investigating the effects of dwarfing genes Rht-B1b and Rht-D1b on wheat GPC.

From leaf to multiscale models of photosynthesis: applications and challenges for crop improvement

To keep up with the growth of human population and to circumvent deleterious effects of global climate change, it is essential to enhance crop yield to achieve higher production. Here we review mathematical models of oxygenic photosynthesis that are extensively used, and discuss in depth a subset that accounts for diverse approaches providing solutions to our objective. These include models (1) to study different ways to enhance photosynthesis, such as fine-tuning antenna size, photoprotection and electron transport; (2) to bioengineer carbon metabolism; and (3) to evaluate the interactions between the process of photosynthesis and the seasonal crop dynamics, or those that have included statistical whole-genome prediction methods to quantify the impact of photosynthesis traits on the improvement of crop yield. We conclude by emphasizing that the results obtained in these studies clearly demonstrate that mathematical modelling is a key tool to examine different approaches to improve photosynthesis for better productivity, while effective multiscale crop models, especially those that also include remote sensing data, are indispensable to verify different strategies to obtain maximized crop yields.

The MdNAC72-MdABI5 module acts as an interface integrating jasmonic acid and gibberellin signals and undergoes ubiquitination-dependent degradation regulated by MdSINA2 in apple

Jasmonic acid (JA) and gibberellin (GA) coordinately regulate plant developmental programs and environmental cue responses. However, the fine regulatory network of the cross-interaction between JA and GA remains largely elusive. In this study, we demonstrate that MdNAC72 together with MdABI5 positively regulates anthocyanin biosynthesis through an exquisite MdNAC72-MdABI5-MdbHLH3 transcriptional cascade in apple. MdNAC72 interacts with MdABI5 to promote the transcriptional activation of MdABI5 on its target gene MdbHLH3 and directly activates the transcription of MdABI5. The MdNAC72-MdABI5 module regulates the integration of JA and GA signals in anthocyanin biosynthesis by combining with JA repressor MdJAZ2 and GA repressor MdRGL2a. MdJAZ2 disrupts the MdNAC72-MdABI5 interaction and attenuates the transcriptional activation of MdABI5 by MdNAC72. MdRGL2a sequesters MdJAZ2 from the MdJAZ2-MdNAC72 protein complex, leading to the release of MdNAC72. The E3 ubiquitin ligase MdSINA2 is responsive to JA and GA signals and promotes ubiquitination-dependent degradation of MdNAC72. The MdNAC72-MdABI5 interface fine-regulates the integration of JA and GA signals at the transcriptional and posttranslational levels by combining MdJAZ2, MdRGL2a, and MdSINA2. In summary, our findings elucidate the fine regulatory network connecting JA and GA signals with MdNAC72-MdABI5 as the core in apple.

A transcriptional cascade involving BBX22 and HY5 finely regulates both plant height and fruit pigmentation in citrus

Dwarfing is a pivotal agronomic trait affecting both yield and quality. Citrus species exhibit substantial variation in plant height, among which internode length is a core element. However, the molecular mechanism governing internode elongation remains unclear. Here, we unveiled that the transcriptional cascade consisting of B-BOX DOMAIN PROTEIN 22 (BBX22) and ELONGATED HYPOCOTYL 5 (HY5) finely tunes plant height and internode elongation in citrus. Loss-of-function mutations of BBX22 in an early-flowering citrus (Citrus hindsii "SJG") promoted internode elongation and reduced pigment accumulation, whereas ectopic expression of BBX22 in SJG, sweet orange (C. sinensis), pomelo (C. maxima) or heterologous expression of BBX22 in tomato (Solanum lycopersicum) significantly decreased internode length. Furthermore, exogenous application of gibberellin A3 (GA3) rescued the shortened internode and dwarf phenotype caused by BBX22 overexpression. Additional experiments revealed that BBX22 played a dual role in regulation internode elongation and pigmentation in citrus. On the one hand, it directly bound to and activated the expression of HY5, GA metabolism gene (GA2 OXIDASE 8, GA2ox8), carotenoid biosynthesis gene (PHYTOENE SYNTHASE 1, PSY1) and anthocyanin regulatory gene (Ruby1, a MYB DOMAIN PROTEIN). On the other hand, it acted as a cofactor of HY5, enhancing the ability of HY5 to regulate target genes expression. Together, our results reveal the critical role of the transcriptional cascade consisting of BBX22 and HY5 in controlling internode elongation and pigment accumulation in citrus. Unraveling the crosstalk regulatory mechanism between internode elongation and fruit pigmentation provides key genes for breeding of novel types with both dwarf and health-beneficial fortification in citrus.

Molecular Lesions in BRI1 and Its Orthologs in the Plant Kingdom

Brassinosteroids (BRs) are an essential group of plant hormones regulating numerous aspects of plant growth, development, and stress responses. BRI1, along with its co-receptor BAK1, are involved in brassinosteroid sensing and early events in the BR signal transduction cascade. Mutational analysis of a particular gene is a powerful strategy for investigating its biochemical role. Molecular genetic studies, predominantly in Arabidopsis thaliana, but progressively in numerous other plants, have identified many mutants of the BRI1 gene and its orthologs to gain insight into its structure and function. So far, the plant kingdom has identified up to 40 bri1 alleles in Arabidopsis and up to 30 bri1 orthologs in different plants. These alleles exhibit phenotypes that are identical in terms of development and growth. Here, we have summarized bri1 alleles in Arabidopsis and its orthologs present in various plants including monocots and dicots. We have discussed the possible mechanism responsible for the specific allele. Finally, we have briefly debated the importance of these alleles in the research field and the agronomically valuable traits they offer to improve plant varieties.

Morphological, anatomical, and transcriptomics analysis reveals the regulatory mechanisms of cassava plant height development

BACKGROUND

Cassava is one of three major potato crops and the sixth most important food crop globally. Improving yield remains a primary aim in cassava breeding. Notably, plant height significantly impacts the yield and quality of crops; however, the mechanisms underlying cassava plant height development are yet to be elucidated.

RESULTS

In this study, we investigated the mechanisms responsible for cassava plant height development using phenotypic, anatomical, and transcriptomic analyses. Phenotypic and anatomical analysis revealed that compared to the high-stem cassava cultivar, the dwarf-stem cassava cultivar exhibited a significant reduction in plant height and a notable increase in internode tissue xylem area. Meanwhile, physiological analysis demonstrated that the lignin content of dwarf cassava was significantly higher than that of high cassava. Notably, transcriptome analysis of internode tissues identified several differentially expressed genes involved in cell wall synthesis and expansion, plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis between the two cassava cultivars.

CONCLUSIONS

Our findings suggest that internode tissue cell division, secondary wall lignification, and hormone-related gene expression play important roles in cassava plant height development. Ultimately, this study provides new insights into the mechanisms of plant height morphogenesis in cassava and identifies candidate regulatory genes associated with plant height that can serve as valuable genetic resources for future crop dwarfing breeding.

GeCKO: user-friendly workflows for genotyping complex genomes using target enrichment capture. A use case on the large tetraploid durum wheat genome

BACKGROUND

Genotyping of individuals plays a pivotal role in various biological analyses, with technology choice influenced by multiple factors including genomic constraints, number of targeted loci and individuals, cost considerations, and the ease of sample preparation and data processing. Target enrichment capture of specific polymorphic regions has emerged as a flexible and cost-effective genomic reduction method for genotyping, especially adapted to the case of very large genomes. However, this approach necessitates complex bioinformatics treatment to extract genotyping data from raw reads. Existing workflows predominantly cater to phylogenetic inference, leaving a gap in user-friendly tools for genotyping analysis based on capture methods. In response to these challenges, we have developed GeCKO (Genotyping Complexity Knocked-Out). To assess the effectiveness of combining target enrichment capture with GeCKO, we conducted a case study on durum wheat domestication history, involving sequencing, processing, and analyzing variants in four relevant durum wheat groups.

RESULTS

GeCKO encompasses four distinct workflows, each designed for specific steps of genomic data processing: (i) read demultiplexing and trimming for data cleaning, (ii) read mapping to align sequences to a reference genome, (iii) variant calling to identify genetic variants, and (iv) variant filtering. Each workflow in GeCKO can be easily configured and is executable across diverse computational environments. The workflows generate comprehensive HTML reports including key summary statistics and illustrative graphs, ensuring traceable, reproducible results and facilitating straightforward quality assessment. A specific innovation within GeCKO is its 'targeted remapping' feature, specifically designed for efficient treatment of targeted enrichment capture data. This process consists of extracting reads mapped to the targeted regions, constructing a smaller sub-reference genome, and remapping the reads to this sub-reference, thereby enhancing the efficiency of subsequent steps.

CONCLUSIONS

The case study results showed the expected intra-group diversity and inter-group differentiation levels, confirming the method's effectiveness for genotyping and analyzing genetic diversity in species with complex genomes. GeCKO streamlined the data processing, significantly improving computational performance and efficiency. The targeted remapping enabled straightforward SNP calling in durum wheat, a task otherwise complicated by the species' large genome size. This illustrates its potential applications in various biological research contexts.