Cadmium Minimization in Crops: A Trade-Off With Mineral Nutrients in Safe Breeding.

Cadmium (Cd) contamination poses a threat to global crop safety. To address this issue, researchers mainly focused on the Cd, explored mechanism of accumulation to low-Cd breeding technologies and created several low-Cd varieties over the past decades. However, new challenges have emerged, particularly the yield reduction due to disturbances in mineral nutrient balance. The goals of breeding have been transferred from a primary focus on 'low-Cd crops' to 'low-Cd/nutrient-balanced' crops, which means limiting Cd content while maintaining other nutrient elements like iron (Fe), manganese (Mn) and zinc (Zn) at a proper content, thus to meet the future agricultural demands. Here, on a multielement perspective, we reviewed the mechanisms of Cd and mineral nutrient transport system in crops and summarized the research advances in Cd minimization through artificial mutations, natural variations and genetic engineering. Furthermore, the challenge of disruption of mineral nutrients in low-Cd crops was discussed and two potential approaches designing Cd-mineral nutrient-optimized artificial transporters and pyramiding Cd-mineral nutrient-optimized variations were proposed. Aiming at addressing these challenges, these approaches represent promising advancements in the field and offer potential pathways for future research and development in the creation of safe and high-quality crops.

Integrative multi-omic analysis identifies genes associated with cuticular wax biogenesis in adult maize leaves.

Studying the genetic basis of leaf wax composition and its correlation with leaf cuticular conductance (gc) is crucial for improving crop productivity. The leaf cuticle, which comprises a cutin matrix and various waxes, functions as an extracellular hydrophobic layer, protecting against water loss upon stomatal closure. To address the limited understanding of genes associated with the natural variation of adult leaf cuticular waxes and their connection to gc, we conducted statistical genetic analyses using leaf transcriptomic, metabolomic, and physiological data sets collected from a maize (Zea mays L.) panel of ∼300 inbred lines. Through a random forest analysis with 60 cuticular wax traits, it was shown that high molecular weight wax esters play an important role in predicting gc. Integrating results from genome-wide and transcriptome-wide studies (GWAS and TWAS) via a Fisher's combined test revealed 231 candidate genes detected by all three association tests. Among these, 11 genes exhibit known or predicted roles in cuticle-related processes. Throughout the genome, multiple hotspots consisting of GWAS signals for several traits from one or more wax classes were discovered, identifying four additional plausible candidate genes and providing insights into the genetic basis of correlated wax traits. Establishing a partially shared genetic architecture, we identified 35 genes for both gc and at least one wax trait, with four considered plausible candidates. Our study enhances the understanding of how adult leaf cuticle wax composition relates to gc and implicates both known and novel candidate genes as potential targets for optimizing productivity in maize.

Life history in Caenorhabditis elegans: from molecular genetics to evolutionary ecology.

Life history is defined by traits that reflect key components of fitness, especially those relating to reproduction and survival. Research in life history seeks to unravel the relationships among these traits and understand how life history strategies evolve to maximize fitness. As such, life history research integrates the study of the genetic and developmental mechanisms underlying trait determination with the evolutionary and ecological context of Darwinian fitness. As a leading model organism for molecular and developmental genetics, Caenorhabditis elegans is unmatched in the characterization of life history-related processes, including developmental timing and plasticity, reproductive behaviors, sex determination, stress tolerance, and aging. Building on recent studies of natural populations and ecology, the combination of C. elegans' historical research strengths with new insights into trait variation now positions it as a uniquely valuable model for life history research. In this review, we summarize the contributions of C. elegans and related species to life history and its evolution. We begin by reviewing the key characteristics of C. elegans life history, with an emphasis on its distinctive reproductive strategies and notable life cycle plasticity. Next, we explore intraspecific variation in life history traits and its underlying genetic architecture. Finally, we provide an overview of how C. elegans has guided research on major life history transitions both within the genus Caenorhabditis and across the broader phylum Nematoda. While C. elegans is relatively new to life history research, significant progress has been made by leveraging its distinctive biological traits, establishing it as a highly cross-disciplinary system for life history studies.

Allelic variants confer Arabidopsis adaptation to small regional environmental differences.

Natural populations of Arabidopsis thaliana provide powerful systems to study the adaptation of wild plant species. Previous research has predominantly focused on global populations or accessions collected from regions with diverse climates. However, little is known about the genetics underlying adaptation in regions with mild environmental clines. We have examined a diversity panel consisting of 192 A. thaliana accessions collected from the Netherlands, a region with limited climatic variation. Despite the relatively uniform climate, we identified evidence of local adaptation within this population. Notably, semidwarf accessions, due to mutation of the GIBBERELLIC ACID REQUIRING 5 (GA5) gene, occur at a relatively high frequency near the coast and these displayed enhanced tolerance to high wind velocities. Additionally, we evaluated the performance of the population under iron deficiency conditions and found that allelic variation in the FE SUPEROXIDE DISMUTASE 3 (FSD3) gene affects tolerance to low iron levels. Moreover, we explored patterns of local adaptation to environmental clines in temperature and precipitation, observing that allelic variation at LA RELATED PROTEIN 1C (LARP1c) likely affects drought tolerance. Not only is the genetic variation observed in a diversity panel of A. thaliana collected in a region with mild environmental clines comparable to that in collections sampled over larger geographic ranges but it is also sufficiently rich to elucidate the genetic and environmental factors underlying natural plant adaptation.

Association Analysis Provides Insights into Molecular Evolution in Salt Tolerance during Tomato Domestication.

Salt stress impairs plant growth and development, generally resulting in crop failure. Tomato domestication gave rise to a dramatic decrease in salt tolerance caused by the genetic variability of the wild ancestors. However, the nature of artificial selection in reducing tomato salt tolerance remains unclear. Here, we generated and analyzed datasets on the survival rates and sodium (Na+) and potassium (K+) concentrations of hundreds of tomato varieties from wild ancestors to contemporary breeding accessions under high salinity. Genome-wide association studies (GWAS) revealed that natural variation in the promoter region of the putative K+ channel regulatory subunit-encoding gene KSB1 (potassium channel beta subunit in Solanum lycopersicum) is associated with survival rates and root Na+/K+ ratios in tomato under salt stress. This variation is deposited in tomato domestication sweeps and contributes to modified expression of KSB1 by salt-induced transcription factor SlHY5 in response to high salinity. We further found that KSB1 interacts with the K+ channel protein KSL1 to maintain cellular Na+ and K+ homeostasis, thus enhancing salt tolerance in tomato. Our findings reveal the crucial role of the SlHY5-KSB1-KSL1 module in regulating ion homeostasis and salt tolerance during tomato domestication, elucidating that selective pressure imposed by humans on the evolutionary process provides insights into further crop improvement.

Natural variation in the adjustment of primary metabolism determines ammonium tolerance in the model grass Brachypodium distachyon.

Nitrogen (N) fertilization is essential to maximize crop production. However, around half of the applied N is lost to the environment causing water and air pollution and contributing to climate change. Understanding the natural genetic and metabolic basis underlying plants N use efficiency is of great interest to reach an agriculture with less N demand and thus, more sustainable. The study of ammonium (NH4+) nutrition is of particular interest, because it mitigates N losses due to nitrate (NO3-) leaching or denitrification. In this work, we studied Brachypodium distachyon, the model plant for C3 grasses, grown with NH4+ or NO3- supply. We performed gene expression analysis in the root of the B. distachyon reference accession Bd21 and examined the phenotypic variation across 52 natural accessions through analysing plant growth and a panel of 22 metabolic traits in leaf and root. We found that the adjustment of primary metabolism to ammonium nutrition is essential for the natural variation of NH4+ tolerance, notably involving NH4+ assimilation and PEPC activity. Additionally, genome-wide association studies (GWAS) indicated several loci associated with B. distachyon growth and metabolic adaptation to NH4+ nutrition. For instance, we found that the GDH2 gene was associated with the induction of root GDH activity under NH4+ nutrition and that two genes encoding malic enzyme were associated with leaf PEPC activity. Altogether, our work underlines the value of natural variation and the key role of primary metabolism to improve NH4+ tolerance.

Natural variations of maize ZmLecRK1 determine its interaction with ZmBAK1 and resistance patterns to multiple pathogens.

Maize (Zea mays) is one of the most important crops in the world, but its yield and quality are seriously affected by diverse diseases. Identifying broad-spectrum resistance genes is crucial for developing effective strategies to control the disease in maize. In a genome-wide study in maize, we identified a G-type lectin receptor kinase ZmLecRK1, as a new resistance protein against Pythium aphanidermatum, one of the causal pathogens of stalk rot in maize. Genetic analysis showed that the specific ZmLecRK1 allele can confer resistance to multiple pathogens in maize. The cell death and disease resistance phenotype mediated by the resistant variant of ZmLecRK1 requires the co-receptor ZmBAK1. A naturally occurring A404S variant in the extracellular domain of ZmLecRK1 determines the ZmLecRK1-ZmBAK1 interaction and the formation of ZmLecRK1-related protein complexes. Interestingly, the ZmLecRK1 susceptible variant was found to possess the amino acid S404 that is present in the ancestral variants of ZmLecRK1 and conserved among the majority of grass species, while the resistance variant of ZmLecRK1 with A404 is only present in a few maize inbred lines. Substitution of S by A at position 404 in ZmLecRK1-like proteins of sorghum and rice greatly enhances their ability to induce cell death. Further transcriptomic analysis reveals that ZmLecRK1 likely regulates gene expression related to the pathways in cell wall organization or biogenesis in response to pathogen infection. Taken together, these results suggest that the ZmLecRK1 resistance variant enhances its binding affinity to the co-receptor ZmBAK1, thereby enhancing the formation of active complexes for defense in maize. Our work highlights the biotechnological potential for generating disease-resistant crops by precisely modulating the activity of ZmLecRK1 and its homologs through targeted base editing.

Environmental genome-wide association studies across precipitation regimes reveal that the E3 ubiquitin ligase MBR1 regulates plant adaptation to rainy environments.

In an era characterized by rapidly changing and less-predictable weather conditions fueled by the climate crisis, understanding the mechanisms underlying local adaptation in plants is of paramount importance for the conservation of species. As the frequency and intensity of extreme precipitation events increase, so are the flooding events resulting from soil water saturation. The subsequent onset of hypoxic stress is one of the leading causes of crop damage and yield loss. By combining genomics and remote sensing data, it is now possible to probe natural plant populations that have evolved in different rainfall regimes and look for molecular adaptation to hypoxia. Here, using an environmental genome-wide association study (eGWAS) of 934 non-redundant georeferenced Arabidopsis ecotypes, we have identified functional variants of the gene MED25 BINDING RING-H2 PROTEIN 1 (MBR1). This gene encodes a ubiquitin-protein ligase that regulates MEDIATOR25 (MED25), part of a multiprotein complex that interacts with transcription factors that act as key drivers of the hypoxic response in Arabidopsis, namely the RELATED TO AP2 proteins RAP2.2 and RAP2.12. Through experimental validation, we show that natural variants of MBR1 have different effects on the stability of MED25 and, in turn, on hypoxia tolerance. This study also highlights the pivotal role of the MBR1/MED25 module in establishing a comprehensive hypoxic response. Our findings show that molecular candidates for plant environmental adaptation can be effectively mined from large datasets. This thus supports the need for integration of forward and reverse genetics with robust molecular physiology validation of outcomes.

Natural variation of CT2 affects the embryo/kernel weight ratio in maize.

Embryo size is a critical trait determining not only grain yield but also the nutrition of the maize kernel. Up to the present, only a few genes have been characterized affecting the maize embryo/kernel ratio. Here, we identify 63 genes significantly associated with maize embryo/kernel weight ratio using a genome-wide association study (GWAS). The peak GWAS signal shows that the natural variation in Zea mays COMPACT PLANT2 (CT2), encoding the heterotrimeric G protein α subunit, is significantly associated with the Embryo/Kernel Weight Ratio (EKWR). Further analyses show that a missense mutation of CT2 increases its enzyme activity and associates with EKWR. The function of CT2 on affecting embryo/kernel weight ratio is further validated by the characterization of two ct2 mutants, for which EKWR is significantly decreased. Subsequently, the key downstream genes of CT2 are identified by combining the differential expression analysis (DEG) of the ct2 mutant and quantitative trait transcript analysis in the GWAS population. In addition, the allele frequency spectrum shows that CT2 was under selective pressure during maize domestication. This study provides important genetic insights into the natural variation of maize embryo/kernel weight ratio, which could be applied in future maize breeding programs to improve grain yield and nutritional content.

Structure, function and formation of the amniote skin pattern.

From feather and hair dotted arrays to pigmented stripes and spots, the spatial distribution of skin appendages and colouration often forms visible ornaments crucial for fitness in the coat of birds and mammals. These geometrical motifs are extremely diverse in nature. Yet, phenotypic surveys evidenced common themes in variation: the orientation, appendage-specificity or pigmentation of a given region may be conserved across groups or species. Here, we review naturalist observations of natural variation in the anatomy and ecological function of the skin pattern in amniotes. We then describe several decades of genetics, mathematical modelling and experimental embryology work aiming at understanding the molecular and morphogenetic mechanisms responsible for pattern formation. We discuss how these studies provided evidence that the morphological trends and differences representative of the phenotypic landscape of skin patterns in wild amniote species is rooted in the mechanisms controlling the production of distinct compartments in the embryonic skin.

Induced and natural variation affect traits independently in hybrid Populus.

The genetic control of many plant traits can be highly complex. Both allelic variation (sequence change) and dosage variation (copy number change) contribute to a plant's phenotype. While numerous studies have investigated the effect of allelic or dosage variation, very few have documented both within the same system, leaving their relative contribution to phenotypic effects unclear. The Populus genome is highly polymorphic, and poplars are fairly tolerant of gene dosage variation. Here, using a previously established Populus hybrid F1 population, we assessed and compared the effect of natural allelic variation and induced dosage variation on biomass, phenology and leaf morphology traits. We identified QTLs for many of these traits, but our results indicate limited overlap between the QTLs associated with natural allelic variation and induced dosage variation. Additionally, the integration of data from both allelic and dosage variation identifies a larger set of QTLs that together explain a larger percentage of the phenotypic variance. Finally, our results suggest that the effect of the large indels might mask that of allelic QTLs. Our study helps clarify the relationship between allelic and dosage variation and their effects on quantitative traits.

eIF2Bß confers resistance to Turnip mosaic virus by recruiting ALKBH9B to modify viral RNA methylation.

Eukaryotic translation initiation factors (eIFs) are the primary targets for overcoming RNA virus resistance in plants. In a previous study, we mapped a BjeIF2Bß from Brassica juncea representing a new class of plant virus resistance genes associated with resistance to Turnip mosaic virus (TuMV). However, the mechanism underlying eIF2Bß-mediated virus resistance remains unclear. In this study, we discovered that the natural variation of BjeIF2Bß in the allopolyploid B. juncea was inherited from one of its ancestors, B. rapa. By editing of eIF2Bß, we were able to confer resistance to TuMV in B. juncea and in its sister species of B. napus. Additionally, we identified an N6-methyladenosine (m6A) demethylation factor, BjALKBH9B, for interaction with BjeIF2Bß, where BjALKBH9B co-localized with both BjeIF2Bß and TuMV. Furthermore, BjeIF2Bß recruits BjALKBH9B to modify the m6A status of TuMV viral coat protein RNA, which lacks the ALKB homologue in its genomic RNA, thereby affecting viral infection. Our findings have applications for improving virus resistance in the Brassicaceae family through natural variation or genome editing of the eIF2Bß. Moreover, we uncovered a non-canonical translational control of viral mRNA in the host plant.

Dissecting the genetic basis of UV-B responsive metabolites in rice.

BACKGROUND: UV-B, an important environmental factor, has been shown to affect the yield and quality of rice (Oryza sativa) worldwide. However, the molecular mechanisms underlying the response to UV-B stress remain elusive in rice. RESULTS: We perform comprehensive metabolic profiling of leaves from 160 diverse rice accessions under UV-B and normal light conditions using a widely targeted metabolomics approach. Our results reveal substantial differences in metabolite accumulation between the two major rice subspecies indica and japonica, especially after UV-B treatment, implying the possible role and mechanism of metabolome changes in subspecies differentiation and the stress response. We next conduct a transcriptome analysis from four representative rice varieties under UV-B stress, revealing genes from amino acid and flavonoid pathways involved in the UV-B response. We further perform a metabolite-based genome-wide association study (mGWAS), which reveals 3307 distinct loci under UV-B stress. Identification and functional validation of candidate genes show that OsMYB44 regulates tryptamine accumulation to mediate UV-B tolerance, while OsUVR8 interacts with OsMYB110 to promote flavonoid accumulation and UV-B tolerance in a coordinated manner. Additionally, haplotype analysis suggests that natural variation of OsUVR8groupA contributes to UV-B resistance in rice. CONCLUSIONS: Our study reveals the complex biochemical and genetic foundations that govern the metabolite dynamics underlying the response, tolerance, and adaptive strategies of rice to UV-B stress. These findings provide new insights into the biochemical and genetic basis of the metabolome underlying the crop response, tolerance, and adaptation to UV-B stress.

Natural variation in photosynthetic electron transport of wheat flag leaves in response to dark-induced senescence.

Early leaf senescence affects photosynthetic efficiency and limits growth during the late production stage of winter wheat (Triticum aestivum). Natural variation in photosystem response to senescence represents a valuable resource for improving the aging traits of flag leaves. To explore the natural variation of different phases of photosynthetic electron transport in modern wheat cultivars during senescence, we exposed the flag leaves of 32 wheat cultivars to dark conditions to induce senescence process, and simultaneously measured prompt fluorescence and modulated 820 nm reflection. The results showed that the chlorophyll content, activity of PSII donor side, PSI and electron transfer between PSII and PSI were all decreased during dark-induced senescence, but they showed different sensitivity to dark-induced senescence. Furthermore, natural variation in photosynthetic parameters among the 32 wheat cultivars were also observed and showed by variation coefficient of the different parameters. We observed that PSII and PSI activity showed less sensitivity to dark-induced senescence than electron transfer between them, while PSII and PSI activity exhibit greater natural variation than electron transport between PSII and PSI. It suggests that Cytb6f might degrade faster and have less variation than PSII and PSI during dark-induced senescence.

Natural allelic diversity of the calcium signaling regulators in plants.

Calcium ions act as secondary messengers in diverse signaling pathways in plants throughout their life cycle. Studies have revealed that calcium is involved in developmental events and in responses to external stimuli, such as biotic and abiotic stresses. Cellular calcium ion levels are tightly controlled by intricate molecular machinery such as calcium channels and pumps. Transient and spatial fluctuations in calcium levels are subsequently recognized by diverse calcium-decoding molecules, resulting in signal transduction. In this review, we highlight recent findings on natural variations in genes controlling calcium signaling in diverse plant biological processes. We then show how the calcium ion context is utilized by fine-tuning the natural variation in centrally important genes.

Protein arginine methyltransferase 6 mediates antiviral immunity in plants.

Viral suppressor RNA silencing (VSR) is essential for successful infection. Nucleotide-binding and leucine-rich repeat (NLR)-based and autophagy-mediated immune responses have been reported to target VSR as counter-defense strategies. Here, we report a protein arginine methyltransferase 6 (PRMT6)-mediated defense mechanism targeting VSR. The knockout and overexpression of PRMT6 in tomato plants lead to enhanced and reduced disease symptoms, respectively, during tomato bush stunt virus (TBSV) infection. PRMT6 interacts with and inhibits the VSR function of TBSV P19 by methylating its key arginine residues R43 and R115, thereby reducing its dimerization and small RNA-binding activities. Analysis of the natural tomato population reveals that two major alleles associated with high and low levels of PRMT6 expression are significantly associated with high and low levels of viral resistance, respectively. Our study establishes PRMT6-mediated arginine methylation of VSR as a mechanism of plant immunity against viruses.

Occurrence and distribution of phytic acid and its degradation products in soybeans in China: Analytical challenges.

Phytic acid (IP6) and its degradation products lower myo-inositol phosphates exert different impacts on nutrient bioavailability and product quality characteristics. However, information regarding the occurrence of IP6 and its degradation products is scarce. In this work, simultaneous determination of IP6 and its degradation products in soybeans was developed, with emphasis on analysis by UPLC-MS/MS and a BEH Amide column both with hybrid surface technology. The retention and analyte/metal surface interactions issues were effectively addressed without ion-pairing reagents addition or derivatization. This method was applied to analyze soybeans from China. Total contents were 0.44-13.2 mg/g, and IP6 and its degradation product myo-inositol pentakisphosphate (IP5) were the predominant analytes, accounting for over 99%. Accession type significantly affected IP5 content, and landraces had significantly higher IP5 than cultivars. Geographically, the lowest IP6 was concentrated in the Huanghuaihai region. Significant correlations existed between IP6 and longitude, altitude, and annual cumulative sunshine hours. This study provides comprehensive insights into the IP6 and its degradation product profile in soybeans, which will benefit breeding soybeans based on specific requirements.

The OsSRO1c-OsDREB2B complex undergoes protein phase transition to enhance cold tolerance in rice.

Cold stress is one of the major abiotic stress factors affecting rice growth and development, leading to significant yield loss in the context of global climate change. Exploring natural variants that confer cold resistance and the underlying molecular mechanism responsible for this is the major strategy to breed cold-tolerant rice varieties. Here, we show that natural variations of a SIMILAR to RCD ONE (SRO) gene, OsSRO1c, confer cold tolerance in rice at both seedling and booting stages. Our in vivo and in vitro experiments demonstrated that OsSRO1c possesses intrinsic liquid-liquid phase-separation ability and recruits OsDREB2B, an AP2/ERF transcription factor that functions as a positive regulator of cold stress, into its biomolecular condensates in the nucleus, resulting in elevated transcriptional activity of OsDREB2B. We found that the OsSRO1c-OsDREB2B complex directly responds to low temperature through dynamic phase transitions and regulates key cold-response genes, including COLD1. Furthermore, we showed that introgression of an elite haplotype of OsSRO1c into a cold-susceptible indica rice could significantly increase its cold resistance. Collectively, our work reveals a novel cold-tolerance regulatory module in rice and provides promising genetic targets for molecular breeding of cold-tolerant rice varieties.

Natural variation in sexual traits and gene expression between selfing and outcrossing Arabidopsis lyrata suggests sexual selection at work.

Flowering plants show significant diversity in sexual strategies, profoundly impacting the evolution of sexual traits and associated genes. Sexual selection is one of the primary evolutionary forces driving sexual trait variation, particularly evident during pollen-pistil interactions, where pollen grains compete for fertilization and females select mating partners. Multiple mating may intensify competition among pollen donors for siring, while in contrast, self-fertilization reduces sire-sire competition, relaxing the sexual selection pressure. Traits involved in male-male competition and female choice are well described, and molecular mechanisms underlying pollen development and pollen-pistil interactions have been extensively studied in the model species Arabidopsis thaliana. However, whether these molecular mechanisms are involved in sexual selection in nature remains unclear. To address this gap, we measured intrinsic pollen performance and its interaction with female choice, and investigated the associated gene expression patterns in a selfing and an outcrossing population of Arabidopsis lyrata. We found that pollen germination and pollen tube growth were significantly higher in outcrossers than selfers, and this difference was accompanied by changes in expression of genes involved in vesicle transport and cytoskeleton. Outcrosser mother plants showed a negative impact on pollen tube growth compared to selfer mother plants, together with a difference of expression for genes involved in auxin and stress response, suggesting a potential mechanism for female choice through molecular crosstalk at the post-pollination stage. Our study provides insight on the impact of sexual selection on the evolution of sexual gene expression in plants.