When thinking about evolutionary change, many practicing biologists will focus on changes in allele frequencies over time. This gene-centric view of evolution has strongly impacted how evolution (and biological science in general) is thought, taught, and funded. In this viewpoint, we join recent criticisms of the gene-centric view and call for reinstalling a phenotypic view of evolution. The assumptions

The ability to induce precise genetic modifications through genome editing has greatly enhanced crop improvement efforts. However, the presence of transgenes in the edited crops necessitates regulatory approval for market introduction (Gao, 2021). Typically, transgene-free genome editing is achieved by inserting a nuclease-encoding T-DNA cassette into the plant genome, which is subsequently removed

The tapetum plays a pivotal role in the precise development of anther and pollen by supplying nutrients and signaling molecules to the microspores and controlling their release (Jung et al., 2005; Ariizumi & Toriyama, 2011). Numerous transcription factors have been reported to regulate the timely degradation of the tapetum and pollen development in rice (Jung et al., 2005; Li et al., 2006; Niu et al

Summary Flowering phenology is an indicator of the impact of climate change on natural systems. Anthropogenic climate change has progressed over more than two centuries, but ecological studies are mostly short in comparison. Here we harness the large‐scale digitization of herbaria specimens to investigate temporal trends in flowering phenology at a global scale. We trained a convolutional neural network

Summary The compact genome and lack of recent whole‐genome multiplication (WGM) events make the boreal pioneer tree silver birch (Betula pendula) a promising model for primary and secondary cell wall (PCW and SCW) regulation in forest trees. Here, we constructed regulatory networks through combined co‐expression and promoter motif analysis and carried out a tissue‐wide analysis of xylan using mass

In arbuscular mycorrhizal (AM) fungi, only c. 370 species have been formally described despite these fungal organisms having coevolved with plants for hundreds of millions of years. In contrast to this, dozens of thousands of species are known for many fungal lineages with shorter evolutionary timescales. This Viewpoint highlights some plausible reasons for these striking discrepancies in species description

Cold stress is a major environmental challenge affecting the production of crops. Calcium-dependent protein kinases (CDPKs/CPKs) are crucial regulators relaying calcium (Ca2+) signals into cellular stress responses. However, the specific mechanisms of CPKs in regulating cold stress signaling are not well understood. In this study, through genetic, physiological and molecular biology assays, we characterized

SummaryDendrobium devonianum, a species of the Orchidaceae family, is notable for its unique floral characteristics, which include two yellow spots and purple tips on its labellum, as well as fringed edges. However, the molecular mechanisms underlying flower pattern formation in D. devonianum remain poorly understood, hindering advancements in its breeding process. Here, a chromosome‐scale genome of

High-temperature stress hinders seed filling, reducing seed quality and crop yield. However, the molecular mechanisms underlying this process remain unclear. Here, we identify SAP AND MIZ1 DOMAIN-CONTAINING LIGASE1 (SIZ1) as a key regulator of seed filling under prolonged high temperatures in Arabidopsis (Arabidopsis thaliana). SIZ1 and WRINKLED1 (WRI1) are co-expressed during seed filling, and overexpressing

Despite its low abundance, rhamnogalacturonan-II (RG-II) is an essential structural component of the cell wall and is present in a highly conserved molecular configuration across all plants. RG-II is a branched pectin domain that contains 13 different sugars linked by over 20 different bond types, and uniquely among pectins it can be covalently dimerized via borate diesters. RG-II is hypothesized to

Summary Metal metabolism in plant–galler interactions is largely unknown. We hypothesise that the mites manipulate metal distribution by sequestration of excessive levels and differential regulation of metalloproteins to support the main functions of gall‐nutrition, protection and microenvironment. Using the Tilia cordata–eriophyid mites system, we aimed to reveal the role of metals in galls by investigating

In many plant species, exposure to a changing environmental temperature regime induces an acclimation response that ultimately increases thermotolerance. Under elevated temperature, membrane systems undergo remodeling to counteract destabilizing thermodynamic effects. Elevated temperature also affects photosynthesis and carbohydrate metabolism due to altered protein functions, enzyme activities, and

Understanding how plants survive extreme conditions is essential to breeding resilient crops. Cistanthe longiscapa, which flourishes in the Atacama Desert, provides a rare glimpse into plant resilience. To uncover the genetic basis of its stress tolerance, we investigated the ecophysiological and transcriptomic responses of C. longiscapa from 3 sites with low but different precipitation levels. Ecophysiological

High ambient temperature (HT) impairs reproductive development and grain yield in temperate crops. To ensure reproductive success under HT, plants must maintain developmental stability. However, the mechanisms integrating plant development and temperature resistance are largely unknown. Here, we demonstrate that PHOTOPERIOD 1 (PPD-H1), homologous to PSEUDO RESPONSE REGULATOR genes of the Arabidopsis

Leaf morphology affects physiological activities and contributes to environment adaptation. The phytohormones auxin and cytokinin both regulate leaf shape, but how they act together to specify leaf complexity is not fully understood. In woodland strawberry (Fragaria vesca), the wild type develops trifoliate leaves, whereas myb117a mutants produce one to five leaflets with fewer serrations. Transcriptome

Genome editing has significantly advanced in recent years, with numerous attempts to integrate it into crop breeding (Gao, 2021). Many useful agronomic traits result from subtle changes in gene expression patterns conferred by natural variations (Olsen and Wendel, 2013). Therefore, the modification of regulatory sequences through genome editing presents a potential strategy to develop practical breeding

Summary Photorespiration is a mandatory metabolic repair shunt of carbon fixation by the Calvin–Benson cycle in oxygenic phototrophs. Its extent depends mainly on the CO2 : O2 ratio in chloroplasts, which is regulated via stomatal movements. Despite a comprehensive understanding of the role of photorespiration in mesophyll cells, its role in guard cells (GC) is unknown. Therefore, a key enzyme of photorespiration

Metabolically engineered high-leaf oil plants have been developed to meet the increasing demand for plant oils. Oil production of these plants under controlled conditions is promising; however, their performance under field-like conditions with abiotic stresses remains uncertain. In this study, wild-type (WT) and high-leaf oil (HLO) transgenic tobacco (Nicotiana tabacum) plants were exposed to moderate

Wax mixtures comprising very long-chain fatty acids and their derivatives represent the major cuticular components and protect plant tissues from environmental stresses. Uncovering the regulatory mechanisms underlying wax biosynthesis is essential for the genetic improvement of the agronomically important crop bread wheat (Triticum aestivum L.). Herein, partially redundant ECERIFERUM 3 (TaCER3) proteins

ABC transporters are ubiquitous in all organisms and constitute one of the largest protein families. The substantial expansion of this family in plants coincided with the emergence of fundamental novelties that facilitated successful adaptation to a sessile lifestyle on land. It also resulted in selectivity and multispecificity toward endogenous molecules observed for certain ABC transporters. Understanding

The researchers sequenced a panel of 226 citrus accessions including sour oranges, landraces and cultivated citrus, and integrated published genomes of sweet orange, pummelo and mandarin in their analyses. Unlike sweet oranges, sour oranges exhibited high genetic and metabolic diversity and high variation in susceptibility to citrus canker. Shared heterozygous genomic segments between sour and sweet

SummaryNatural genetic variation can be used to improve important crop agronomic traits, and understanding the genetic basis of natural variation in fruit shape can help breeders develop pepper varieties that meet market demand. In this study, we identified a QTL controlling fruit length–width ratio by conventional genetic mapping, encoding a previously uncharacterized gene CaIQD1. Reduced CaIQD1 expression

Plants have emerged as powerful biofactories for producing proteins of interest. Compared to mammalian-based expression system, plant biofactories offer unique advantages in terms of higher scalability, lower production costs, reduced risk of contamination by human pathogens and faster expression rate (Chung et al., 2022; Eidenberger et al., 2023). Over the past three decades, plant-based expression

Dinoflagellates are a taxonomically diverse and ecologically significant group of phytoplankton. They are also infamous for their involvement in harmful algal blooms, which have significant ecological and economic impacts. In recent years, substantial advances have been made in the analysis of dinoflagellate genomes, including sequencing, assembly and gene annotation, alongside the accumulation of

Introduction Most plant species worldwide depend on insects for pollination (Ollerton et al., 2011), with volatile organic compounds being pivotal for mediating pollinator attraction in many of these plants (Raguso, 2008; Dötterl & Gershenzon, 2023). Among plants, orchids are exceptional in their extraordinary range of pollinators, pollination strategies, and floral volatiles (Ackerman et al., 2023;

Summary Silicon (Si) has been hypothesized to be a metabolically cheaper substitute for carbon‐based cell wall components to support leaves. However, how the biomechanical function of Si, deposited as amorphous silica, differs from cell wall components remains untested. Here, we tested the hypothesis that species with higher leaf Si concentrations have stiffer but more brittle leaf lamina. We measured

Pollen development involves cell wall alteration of the male gametophyte, which is critical for plant fertility and requires MYB80 and TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK) transcription factors in Arabidopsis (Arabidopsis thaliana). In this study, we found that the myb80 tek double mutant exhibits a compromised degradation of the tetrad callose wall and downregulation of 5 ANTHER-SPECIFIC

SummaryThe mechanism regulating fruit textural changes has not been fully elucidated. Transcription factor FcERF100 showed rapid transcription repression during drastic texture loss in fig (Ficus carica L.) fruit ripening. Transient overexpression of FcERF100 delayed fig fruit softening and significantly decreased the transcript abundance of a key cell wall‐modifying pectate lyase gene, FcPL7. Yeast

Sialylated N-glycans are widely distributed in vertebrates and represent the dominant glycoform of many human plasma proteins (Miura et al., 2015). Although knowledge of the diverse effects of this glycan formation is rapidly increasing, full understanding of its biological significance remains elusive (Lewis et al., 2022). A major reason for this is the difficulty in controlling sialylation in production

Targeted insertion of large DNA fragments holds great promise in crop breeding but is extremely challenging in plants. Prime editing (PE) can efficiently install small genomic insertion through replacement but faces challenges in mediating insertion of >100 bp. To enable larger insertion, a paired PE strategy termed GRAND editing was developed in human cells. In plants, genomic insertions of up to

SummaryCarotenoid‐rich orange‐fleshed sweet potato (OFSP) is an important staple diet and source of nutrition in developing countries, including Africa and Asia. However, the regulation of carotenoid biosynthesis remains to be better understood. A natural allelic variation closely linked to carotenoid biosynthesis was identified in the promoter region of the IbbHLH25 gene that encodes a basic helix–loop–helix

Expansion microscopy (ExM) has revolutionized biological imaging by physically enlarging samples, surpassing the light diffraction limit, and enabling nanoscale visualization using standard microscopes. While extensively employed across a wide range of biological samples, its application to plant tissues is sparse. In this work, we present ROOT-ExM, an expansion method suited for stiff and intricate

Summary Mutualistic interactions between fruiting plants and frugivorous animals are shaped by interaction‐relevant functional traits. However, it is unclear whether ‘trait matching’ underlies broad‐scale relationships in plant and frugivore species and their functional diversity. We integrated novel trait data and global occurrences for c. 1900 species in a major tropical plant family (Annonaceae)

Introduction Reducing harvest loss in soybean (Glycine max (L.) Merr.) is critical for tackling the growing issue of food insufficiency and for conserving natural resources used in fertilizer production. Although global soybean production has doubled in the last two decades, reaching 396.95 million metric tons by 2023/2024 (United States Department of Agriculture, 2024), an annual increase of 2.4%

Salt stress poses a significant challenge to the growth and productivity of rice (Oryza sativa L.). Histone deacetylases (HDACs) play a vital role in modulating responses to various abiotic stresses. However, how OsHDAC1 responds to salt stress remains largely unknown. Here, we report that OsHDAC1 decreases salt tolerance in rice through post-translational modification of metabolic enzymes. Specifically

PHYTOCHROME-INTERACTING FACTORS (PIFs), members of the basic helix-loop-helix (bHLH) transcription factor (TF) family, regulate various developmental processes in Arabidopsis (Arabidopsis thaliana). However, their involvement in fatty acid biosynthesis and seed maturation is largely unknown. WRINKLED1 (WRI1) is a pivotal TF regulating plant fatty acid biosynthesis. In this study, we identified WRI1

Agricultural environmental impact assessment provides potential measures to mitigate negative impacts, would help plant scientists broaden their view of the agricultural system.

High light (HL)-induced chloroplast retrograde signaling originates from the photosynthetic apparatus and regulates nuclear gene expression to enhance photoprotection and coordination of cell metabolism. Here, we analyzed the transcript profiles and accumulation of ROS, stress hormones, and small molecule antioxidants to investigate the signaling mechanisms operating under HL stress, particularly during

Age-dependent reproductive development is pivotal for plant adaptability and for species perpetuation. While substantial progress has been made in elucidating age-related regulatory mechanisms in angiosperms, the molecular basis of how aging pathway interacts with reproductive development in gymnosperms, particularly conifers, remains elusive. Here, we demonstrate that DEFICIENS-AGAMOUS-LIKE 1 (DAL1)

The canonical auxin pathway in the Arabidopsis nucleus was characterized two decades ago: auxin acts as a molecular glue to bind the TIR1 F-box auxin receptor (and five AFB homologues) to small auxin and indole-3-acetic acid (Aux/IAA) proteins. These Aux/IAA proteins are then marked for degradation by ubiquitination. As they are degraded, they stop repressing ARF transcription factors, which are then

SummaryAgroinfiltration, a method utilizing agrobacteria to transfer DNA into plant cells, is widely used for transient gene expression in plants. Besides the commonly used Agrobacterium strains, Rhizobium rhizogenes can also introduce foreign DNA into host plants for gene expression. While many R. rhizogenes strains have been known for inducing hairy root symptoms, their use for transient expression

SummaryThe establishment of Nicotiana benthamiana as a robust biofactory is complicated by issues such as product toxicity and proteolytic degradation of target proteins/introduced enzymes. Here we investigate whether biomolecular condensates can be used to address these problems. We engineered biomolecular condensates in N. benthamiana leaves using transient expression of synthetic modular scaffolds

SummaryDoubled haploid (DH) technology, based on haploid induction (HI), is a crucial tool in enhancing crop‐breeding efficiency and has been successfully applied in various plant species. While many HI‐related genes have been identified using diverse strategies, the genetic basis and molecular mechanisms underlying HI remain incompletely understood. In this study, we present a novel system for inducing

Sugarcane (Saccharum spp.) is a globally significant crop, valued for its contribution to the production of sugar and bioenergy. Despite its economic and industrial importance, sugarcane is highly vulnerable to smut disease caused by Sporisorium scitamineum, a major fungal pathogen that substantially reduces yield and quality (Wu et al., 2024). The complexity of the sugarcane genome, characterized

Circular RNAs (circRNAs) are prevalent in eukaryotic cells and have been linked to disease progressions. Their unique circular structure and stability make them potential biomarkers and therapeutic targets. Compared to animal models, plant circRNA research is still in its infancy. The lack of effective tools to specifically knock down circRNAs without affecting host gene expression has slowed the progress

Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated nuclease (Cas) technologies facilitate routine genome engineering of one or a few genes at a time. However, large-scale CRISPR screens with guide RNA libraries remain challenging in plants. Here, we have developed a comprehensive all-in-one CRISPR toolbox for Cas9-based genome editing, cytosine base editing (CBE),

Chlorophyll biosynthesis must be tightly coupled to light-harvesting chlorophyll a/b-binding protein (LHCP) biogenesis, as free chlorophyll and its precursors are phototoxic. However, precisely how these 2 processes are coordinated in Arabidopsis (Arabidopsis thaliana) remains elusive. Our previous studies demonstrated the role of LHCP TRANSLOCATION DEFECT (LTD) in delivering LHCPs to the chloroplast

The molecular basis underlying crop traits is complex, with gene-by-environment interactions (GEIs) affecting phenotypes. However, quantitative trait nucleotide (QTN)-by-environment interactions (QEIs) and GEIs for seed oil content (SOC) in oil crops are rare. Here, we detected 11 environmentally specific and 10 stable additive QTNs and 11 QEIs for SOC in rapeseed (Brassica napus) using genome-wide

Arabidopsis thaliana (Arabidopsis) Ataxia Telangiectasia Mutated (ATM) kinase plays a vital role in orchestrating leaf senescence; however, the precise mechanisms remain elusive. Here, our study demonstrates that ATM kinase activity is essential for mitigating age- and reactive oxygen species-induced senescence, as restoration of wild-type ATM reverses premature senescence in the atm mutant, while