Kernel Development Research Articles

Genetic variation in ZmKW1 contributes to kernel weight and size in dent corn and popcorn.

Kernel weight is a critical factor that essentially affects maize (Zea mays) yield. In natural inbred lines, popcorn kernels exhibit overtly smaller sizes compared to dent corn kernels, and kernel weight, which is controlled by multiple genetic loci, varies widely. Here, we characterized a major quantitative trait locus on chromosome 1, responsible for controlling kernel weight (qKW1) andsize. The qKW1 locus encodes a protein containing a seven in absentia domain with E3 ubiquitin ligase activity, expressed prominently from the top to the middle region of the endosperm. The presence and function of qKW1 were confirmed through ZmKW1 gene editing, where the mutations in ZmKW1 within dent corn significantly increased kernel weight, consistent with alterations in kernel size, while overexpression of ZmKW1 had the opposite effect. ZmKW1 acts as a negative regulator of kernel weight and size by reducing both the number and size of the endosperm cells and impacting endosperm filling. Notably, the popcorn allele qKW1N and the dent corn allele qKW1D encode identical proteins; however, the differences in promoter activity arise due to the insertion of an Indel-1346 sequence in the qKW1N promoter, resulting in higher expression levels compared to qKW1D, thus contributing to the variation in kernel weight and size between popcorn and dent corn kernels. Linkage disequilibrium analysis of the 2.8 kb promoter region of ZmKW1 in a dataset comprising 111 maize association panels identified two distinct haplotypes. Our results provide insight into themechanisms underlying kernel development and yield regulation in dent corn and popcorn, with a specific focus on the role of the ubiquitinationsystem.

Starlight: A kernel optimizer for GPU processing

Over the past few years, GPUs have found widespread adoption in many scientific domains, offering notable performance and energy efficiency advantages compared to CPUs. However, optimizing GPU high-performance kernels poses challenges given the complexities of GPU architectures and programming models. Moreover, current GPU development tools provide few high-level suggestions and overlook the underlying hardware. Here we present Starlight, an open-source, highly flexible tool for enhancing GPU kernel analysis and optimization. Starlight autonomously describes Roofline Models, examines performance metrics, and correlates these insights with GPU architectural bottlenecks. Additionally, Starlight predicts potential performance enhancements before altering the source code. We demonstrate its efficacy by applying it to literature genomics and physics applications, attaining speedups from 1.1× to 2.5× over state-of-the-art baselines. Furthermore, Starlight supports the development of new GPU kernels, which we exemplify through an image processing application, showing speedups of 12.7× and 140× when compared against state-of-the-art FPGA- and GPU-based solutions.

ZmELP1, an Elongator complex subunit, is required for the maintenance of histone acetylation and RNA Pol II phosphorylation in maize kernels.

The Elongator complex was originally identified as an interactor of hyperphosphorylated RNA polymerase II (RNAPII) in yeast and has histone acetyltransferase (HAT) activity. However, the genome-wide regulatory roles of Elongator on transcriptional elongation and histone acetylation remain unclear. We characterized a maize miniature seed mutant, mn7 and map-based cloning revealed that Mn7 encodes one of the subunits of the Elongator complex, ZmELP1. ZmELP1 deficiency causes marked reductions in the kernel size and weight. Molecular analyses showed that ZmELP1 interacts with ZmELP3, which is required for H3K14 acetylation (H3K14ac), and Elongator complex subunits interact with RNA polymerase II (RNAPII) C-terminal domain (CTD). Genome-wide analyses indicated that loss of ZmELP1 leads to a significant decrease in the deposition of H3K14ac and the CTD of phosphorylated RNAPII on Ser2 (Ser2P). These chromatin changes positively correlate with global transcriptomic changes. ZmELP1 mutation alters the expression of genes involved in transcriptional regulation and kernel development. We also showed that the decrease of Ser2P depends on the deposition of Elongator complex-mediated H3K14ac. Taken together, our results reveal an important role of ZmELP1 in the H3K14ac-dependent transcriptional elongation, which is critical for kernel development.

Maize Dek407 Encodes the Nitrate Transporter 1.5 and Is Required for Kernel Development.

The kernel serves as the storage organ and harvestable component of maize, and it plays a crucial role in determining crop yield and quality. Understanding the molecular and genetic mechanisms of kernel development is of considerable importance for maize production. In this study, we obtained a mutant, which we designated defective kernel 407 (dek407), through ethyl methanesulfonate mutagenesis. The dek407 mutant exhibited reduced kernel size and kernel weight, as well as delayed grain filling compared with those of the wild type. Positional cloning and an allelism test revealed that Dek407 encodes a nitrate transporter 1/peptide transporter family (NPF) protein and is the allele of miniature 2 (mn2) that was responsible for a poorly filled defective kernel phenotype. A transcriptome analysis of the developing kernels showed that the mutation of Dek407 altered the expression of phytohormone-related genes, especially those genes associated with indole-3-acetic acid synthesis and signaling. Phytohormone measurements and analysis indicated that the endogenous indole-3-acetic acid content was significantly reduced by 66% in the dek407 kernels, which may be the primary cause of the defective phenotype. We further demonstrated that natural variation in Dek407 is associated with kernel weight and kernel size. Therefore, Dek407 is a potential target gene for improvement of maize yield.

The E3 ligase TaGW2 mediates transcription factor TaARR12 degradation to promote drought resistance in wheat.

Drought stress limits crop yield, but the molecular modulators and their mechanisms underlying the trade-off between drought resistance and crop growth and development remain elusive. Here, a grain width and weight2 (GW2)-like really interesting new gene finger E3 ligase, TaGW2, was identified as a pivotal regulator of both kernel development and drought responses in wheat (Triticum aestivum). TaGW2 overexpression enhances drought resistance but leads to yield drag under full irrigation conditions. In contrast, TaGW2 knockdown or knockout attenuates drought resistance but remarkably increases kernel size and weight. Furthermore, TaGW2 directly interacts with and ubiquitinates the type-B Arabidopsis response regulator TaARR12, promoting its degradation via the 26S proteasome. Analysis of TaARR12 overexpression and knockdown lines indicated that TaARR12 represses the drought response but does not influence grain yield in wheat. Further DNA affinity purification sequencing combined with transcriptome analysis revealed that TaARR12 downregulates stress-responsive genes, especially group-A basic leucine zipper (bZIP) genes, resulting in impaired drought resistance. Notably, TaARR12 knockdown in the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated tagw2 knockout mutant leads to significantly higher drought resistance and grain yield compared to wild-type plants. Collectively, these findings show that the TaGW2-TaARR12 regulatory module is essential for drought responses, providing a strategy for improving stress resistance in high-yield wheat varieties.

Insights into ZmWAKL in maize kernel development: genome-wide investigation and GA-mediated transcription

BackgroundThe functional roles of the Wall Associated Kinase (WAK) and Wall Associated Kinase Like (WAKL) families in cellular expansion and developmental processes have been well-established. However, the molecular regulation of these kinases in maize development is limited due to the absence of comprehensive genome-wide studies.ResultsThrough an in-depth analysis, we identified 58 maize WAKL genes, and classified them into three distinct phylogenetic clusters. Moreover, structural prediction analysis showed functional conservation among WAKLs across maize. Promoter analysis uncovered the existence of cis-acting elements associated with the transcriptional regulation of ZmWAKL genes by Gibberellic acid (GA). To further elucidate the role of WAKL genes in maize kernels, we focused on three highly expressed genes, viz ZmWAKL38, ZmWAKL42 and ZmWAKL52. Co-expression analyses revealed that their expression patterns exhibited a remarkable correlation with GA-responsive transcription factors (TF) TF5, TF6, and TF8, which displayed preferential expression in kernels. RT-qPCR analysis validated the upregulation of ZmWAKL38, ZmWAKL42, ZmWAKL52, TF5, TF6, and TF8 following GA treatment. Additionally, ZmWAKL52 showed significant increase of transcription in the present of TF8, with ZmWAKL52 localizing in both the plasma membrane and cell wall. TF5 positively regulated ZmWAKL38, while TF6 positively regulated ZmWAKL42.ConclusionsCollectively, these findings provide novel insights into the characterization and regulatory mechanisms of specific ZmWAKL genes involved in maize kernel development, offering prospects for their utilization in maize breeding programs.

The effect of foliar application of Ascophyllum nodosum (L.) Le Jol. seaweed extract on biochemical traits related to abiotic stresses in pistachio (Pistacia vera L. cv. Kaleh-Ghoochi)

BackgroundDue to the important economic role of pistachio (Pistacia vera L.) the cultivation of this valuable crop has been extended. Various abiotic stresses harm the growth and performance of pistachio. Seaweed extract containing various substances such as pseudo-hormones that stimulate growth, nutritional elements, and anti-stress substances can cause more resistance to abiotic stresses, and increase the quantity and the quality of the fruit. The present study was conducted to evaluate the effect of foliar application of Ascophyllum nodosum (L.) Le Jol. seaweed extract on some biochemical traits related to abiotic stress in Pistacia vera L. cv. Kaleh-Ghoochi. The first factor of foliar spraying treatment included A. nodosum seaweed extract at four levels (0, 1, 2, and 3 g/L), and the second factor was the time of spraying solution which was done at three times (1- at the beginning of pistachio kernel growth period at the end of June, 2- at the stage of full kernel development at the end of August, and 3- Spraying in both late June and August).ResultsThe results showed that all investigated traits were significant under the treatment of seaweed extract compared with the control. The seaweed extract concentrations had a significant effect on all traits except soluble carbohydrates, but the time of consumption of seaweed extract on soluble carbohydrates, protein, peroxidase, ascorbate peroxidase, and superoxide dismutase enzymes was significant, while had no significant effect on the rest of the traits. According to the interaction effect of time and concentration of consumption of seaweed extract, the highest values of the biochemical characters were as follows: total phenol content: 168.30 mg CAE/g DW, flavonoid content: mg CE/g DW, catalase: 12.66 µmol APX min− 1 mg− 1 protein, superoxide dismutase: 231.4 µmol APX min− 1 mg− 1 protein, and ascorbate peroxidase: 39.53 µmol APX min− 1 mg− 1 protein.ConclusionsBased on the results of this study, it seems that it is possible to use fertilizers containing A. nodosum seaweed extract with a concentration of 3 g/L in August to increase the tolerance of the pistachio cultivar “Kaleh-Ghoochi” to abiotic stresses.

Kernel Transcriptome Profiles of Susceptible Wheat Genotypes in Response to Wheat Dwarf Bunt.

Wheat dwarf bunt is caused by Tilletia controversa J. G. Kühn (TCK), which is a serious fungal diseases affecting kernels of wheat. In order to identify candidate genes involved in the abnormal development of kernels in wheat, we used RNA sequencing technology to analyze the transcriptome of the abnormal and healthy kernels of a susceptible variety (Yili053) at the mid-filling stage, late-filling stage, and maturity stage, respectively. The differentially expressed genes (DEGs) were analyzed, and there were 3930 DEGs, 28,422 DEGs, and 20,874 DEGs found at the mid-filling stage, late-filling stage, and maturity stage in Yili053, respectively. A total of 1592 DEGs (506 DEGs up-regulated) showed continuously differential expression in the three stages. Gene ontology analysis showed that these DEGs were related to biological regulation, metabolic processes, and the response to stimulus. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that these DEGs play major roles in pathways including photosynthesis, carbon metabolism, carbon fixation in photosynthetic organisms, and glyoxylate and dicarboxylate metabolism. Moreover, we predicted that 13 MADS-MIKC transcription factors, which were continuously up-regulated, were crucial for regulating the maturation and senescence of eukaryotes. Some 21 genes related to the plant hormone signaling transduction pathway and 61 genes related to the response to stimulus were analyzed. A total of 26 of them were successful validated with a qPCR analysis. These genes were thought to be involved in the abnormal development of kernels infected by TCK. A transcriptomics analysis of wheat kernels in response to TCK will contribute to understanding the interaction of TCK and wheat, and may provide a basis for knowledge of molecular events in the abnormal development of kernels, which will be helpful for more efficient TCK management.

Non-equilibrium plasma assisted ignition characteristics in premixed ethylene-air flow

Reliable and stable ignition under lean conditions is essential for safe operation of the engine. Nanosecond pulsed discharge non-equilibrium plasma assisted ignition characteristics of premixed ethylene-air flow in an advective combustion chamber were investigated. The effects of the equivalence ratio, discharge gap distance, flow velocity, discharge frequency or inter-pulse time, and pulse number were quantified in terms of ignition probability. Shadow images of ignition kernel development were captured and used to extracted the averaged kernel projected area. The results indicated that increasing the equivalence ratio, a higher flow velocity, a wider discharge gap distance, and a larger number of pulses are all conducive to the increasing of ignition probability via inducing a larger initial kernel. Increasing inter-pulse time has a non-monotonic effect on ignition probability for multiple nanosecond pulsed discharges ignition. As the inter-pulse time decreases, when neighboring kernel boundaries happen to overlap each other, the partially-coupled regime shows a higher ignition probability. Longer or shorter inter-pulse time both cause the decrease in ignition probability. The shortest inter-pulse time shown as the fully-coupled regime is the most favorable for ignition with the highest ignition probability. A method is proposed to estimate the critical frequency at which partially-coupled regime transitions to fully-coupled regime by 95% of the asymptotic time of flame development time.

A phenomenological model for predicting the early development of the flame kernel in spark-ignition engines

This work presents a simple and effective phenomenological model for the prediction of the early growth of the flame kernel in SI engines, including its initiation as a result of the electrical breakdown of the fuel/air mixture between the spark plug electrodes. The present model aims to provide an improved description of the ignition-affected early phases of flame kernel development compared to the majority of models currently available in literature. In particular, these models focus on electrical energy supply and turbulence, whereas the stretch-induced kernel growth slowdown is quantified with linear models that are inconsistent with the small kernel radius. For the flame kernel initiation, this model replaces the current methods that rely on 1D heat diffusion within a plasma column with a more consistent analysis of post-breakdown conditions. Concerning the kernel growth, the present model couples the mass and energy conservation equations of a spherical kernel with the species and temperature profiles outside of it. This combination leads to a non-linear description of the flame stretch, according to which the kernel development is controlled by the Lewis-number-dependent balance between the heat gained via combustion and the heat lost via thermal diffusion. As a result, the kernel temperature differs from the adiabatic flame temperature, causing the laminar flame speed to change from its adiabatic value and ultimately affecting the overall kernel development. Kernel growth predictions are conducted for laminar flames and compared to literature data, showing a satisfactory agreement and highlighting the ability to describe the stretch-induced kernel slowdown, up to its possible extinction. A good agreement with literature data is also obtained for kernel expansions under moderately turbulent conditions, typical of internal combustion engines. The simple formulation of the present model enables swift integration into phenomenological combustion models for sparkignition engines, while simultaneously offering useful insight into the early kernel development even for CFD-based approaches.

RNA m6A modification facilitates DNA methylation during maize kernel development.

N6-methyladenosine (m6A) in mRNA and 5-methylcytosine (5mC) in DNA have critical functions for regulating gene expression and modulating plant growth and development. However, the interplay between m6A and 5mC is an elusive territory and remains unclear mechanistically in plants. We reported an occurrence of crosstalk between m6A and 5mC in maize (Zea mays) via the interaction between mRNA adenosine methylase (ZmMTA), the core component of the m6A methyltransferase complex, and decrease in DNA methylation 1 (ZmDDM1), a key chromatin-remodeling factor that regulates DNA methylation. Genes with m6A modification were coordinated with a much higher level of DNA methylation than genes without m6A modification. Dysfunction of ZmMTA caused severe arrest during maize embryogenesis and endosperm development, leading to a significant decrease in CHH methylation in the 5' region of m6A-modified genes. Instead, loss of function of ZmDDM1 had no noteworthy effects on ZmMTA-related activity. This study establishes a direct link between m6A and 5mC during maize kernel development and provides insights into the interplay between RNA modification and DNA methylation.

The expression characteristics and allelic variation of AnVromindoline-1/3 in Avena nuda L.

Oat is a worldwide cultivated crop with nutritional, ecological and economic value. The hardness of oat is closely related to the damage to the grain during harvesting, washing, threshing and hulling, and has an important impact on the processing quality and eating quality of oats. Vromindolines are a group of proteins specific to the Avena genus and are responsible for the softness of oat endosperm. Avena nuda is an allohexaploid, and is an important grain and feed crop in China. Vromindolines have been studied in the genus Oat, but have not been reported in Avena nuda. In this study, we performed paraffin sectioning and scanning electron microscopy analysis on oat kernels with different hardness, and the sequence characteristics, allelic variation, expression patterns and subcellular localization of Vromindoline-1 and Vromindoline-3 genes in Avena nuda were also analyzed. The results showed that the cell structure and ultrastructure of soft oat variety grains are significantly different from those of hard oats variety. PCR amplification and sequence analysis showed that the lengths of AnVin-1 and AnVin-3 genes were 444 and 429 bp, respectively, and AnVin-1 existed in the oat A, C and D genomes. Expression analysis in different tissues showed that AnVin-1A, AnVin-1C, AnVin-1D and AnVin-3C were expressed to varying degree in roots, stems and leaves. Expression analysis at the panicle developmental stage showed that the expression levels of these four genes first increased and then decreased, with the highest expression levels at 14 days after pollination. In addition, the expression levels of AnVin-1C and AnVin-3C in soft oat variety were higher than those in hard oats at 14 DAP. Among the single nucleotide polymorphisms among 18 AnVin-1C and 9 AnVin-3C gene sequences, AnVin-1C6 and AnVin-3C2 genes had three haplotypes in a oat natural population. Based on the allelic variation sites of AnVin-1C6, a cleavage amplified polymorphic sequence marker was established, which explained 1.44% of the variation in hardness. The above results of this study indicated that AnVin-1 and AnVin-3 genes were involved in kernel development and might affect kernel firmness.

Genome-wide analysis of sugar transporter genes in maize (Zea mays L.): identification, characterization and their expression profiles during kernel development.

Sugar transporters (STs) play a crucial role in the development of maize kernels. However, very limited information about STs in maize is known. In this study, sixty-eight ZmST genes were identified from the maize genome and classified into eight major groups based on phylogenetic relationship. Gene structure analysis revealed that members within the same group shared similar exon numbers. Synteny analysis indicated that ZmSTs underwent 15 segmental duplication events under purifying selection. Three-dimensional structure of ZmSTs demonstrated the formation of a compact helix bundle composed of 8-13 trans-membrane domains. Various development-related cis-acting elements, enriched in promoter regions, were correlated with the transcriptional response of ZmSTs during kernel development. Transcriptional expression profiles exhibited expression diversity of various ZmST genes in roots, stems, leaves, tassels, cobs, embryos, endosperms and seeds tissues. During kernel development, the expression of 24 ZmST genes was significantly upregulated in the early stage of grain filling. This upregulation coincided with the sharply increased grain-filling rate observed in the early stage. Overall, our findings shed light on the characteristics of ZmST genes in maize and provide a foundation for further functional studies.

Variation in pigments in pecan testa during kernel development and storage

The pecan (Carya illinoinensis) is an important tree nut worldwide. Browning of the testa during storage considerably reduces its quality. However, the pigments that cause browning and their accumulation patterns are poorly understood. We analyzed the color changes in the testa during the five developmental stages of the kernel after storage at room temperature to compare differences in their color and identify the pigments. Samples exhibiting different colors along with their corresponding −80 °C storage samples were selected for metabolomic analysis. A total of 591 phenolic compounds were detected, 52 phenolics showed regulatory effects on testa discoloration, and 59 metabolites were identified as possible precursors of the pigments. This study revealed the most thorough phenolic composition of pecan to date. Further, the findings provide new insights into the mechanisms of testa browning, deepens our understanding of the bioactive value of pecans, and contributes to the breeding of less browning-susceptible varieties.

DEFECTIVE KERNEL 56 functions in mitochondrial RNA editing and maize seed development.

Proper seed development is essential for achieving grain production, successful seed germination, and seedling establishment in maize (Zea mays). In the past few decades, pentatricopeptide repeat (PPR) proteins have been proven to play an essential role in regulating the development of maize kernels through posttranscriptional RNA modification of mitochondrial genes. However, the underlying mechanisms remain largely unknown. Here, we characterized a mutant of DEFECTIVE KERNEL 56 (DEK56) with defective kernels that exhibited arrested development of both the embryo and endosperm. Accordingly, we isolated DEK56 through a map-based cloning strategy and found that it encoded an E subgroup PPR protein located in the mitochondria. Dysfunction of DEK56 resulted in altered cytidine (C)-to-uridine (U) editing efficiency at 48 editing sites across 21 mitochondrial transcripts. Notably, the editing efficiency of the maturase-related (matR)-1124 site was substantially reduced or abolished in the dek56 mutant. Furthermore, we found that the splicing efficiency of NADH dehydrogenase subunit 4 (nad4) Introns 1 and 3 was substantially reduced in dek56 kernels, which might be a consequence of the defective MatR function. Through a protein-protein interaction test, we hypothesized that DEK56 carries out its function by recruiting the PPR-DYW protein PPR motif, coiled-coil, and DYW domain-containing protein 1 (PCW1). This interaction is facilitated by Multiple Organellar RNA Editing Factors (ZmMORFs) and Glutamine-Rich Protein 23 (ZmGRP23). Based on these findings, we developed a working model of PPR-mediated mitochondrial processing that plays an essential role in the development of maize kernels. The present study will further broaden our understanding of PPR-mediated seed development and provide a theoretical basis for maize improvement.

A peptide chain release factor 2a gene regulates maize kernel development by modulating mitochondrial function

Mitochondrial protein translation that is essential for aerobic energy production includes four essential steps of the mitochondrial ribosome cycle, namely, initiation, elongation, termination of the polypeptide, and ribosome recycling. Translation termination initiates when a stop codon enters the A site of the mitochondrial ribosome where it is recognized by a dedicated peptide release factor (RF). However, RFs and mechanisms involved in translation in plant mitochondria, especially in monocotyledons, remain largely unknown. Here, we identified a crumpled kernel (crk5 allele) mutant, with significantly decreased kernel size, 100-kernel weight, and an embryo-lethal phenotype. The Crk5 allele was isolated using map-based cloning and found to encode a mitochondrial localization RF2a. As it is an ortholog of Arabidopsis mitochondrial RF2a, we named the gene ZmmtRF2a. ZmmtRF2a is missing the 5th–7th exons in the crk5 resulting in deletion of domains containing motifs GGQ and SPF that are essential for release activity of RF, mitochondrial ribosome binding, and stop codon recognition. Western blot and qRT-PCR analyses indicate that the crk5 mutation results in abnormal mitochondrion structure and function. Intriguingly, we observed a feedback loop in the crk5 with up-regulated transcript levels detected for several mitochondrial ribosome and mitochondrial-related components, in particular mitochondrial complexes CI, CIV, and a ribosome assembly related PPR. Together, our data support a crucial role for ZmmtRF2a in regulation of mitochondrial structure and function in maize.

Embedded direct numerical simulation of ignition kernel evolution and flame initiation in dual-fuel spray assisted combustion

The flame initiation process in dual-fuel spray assisted combustion is presently not fully understood. Here, diesel spray assisted combustion of premixed methane/oxidizer/EGR is explored in the post-ignition phase by scale-resolved simulations. The modified dual-fuel ECN Spray A forms the baseline configuration. An extensive local grid refinement (approaching DNS limit) around one of the first high-temperature ignition kernels is carried out in order to examine the validity of hypothesized flame initiation and deflagration. A high quality LES is used to solve the spray dynamics, while the embedded quasi-DNS (eq-DNS) region offers detailed information on the ignition kernel evolution. The finite-rate chemistry is directly integrated, utilizing 54 species and 269 reactions. Local combustion modes are investigated for the ignition kernel development toward spontaneous ignition and premixed flame propagation using various approaches, including the reaction front displacement speed, energy transport budget, and chemical explosive mode analysis. Furthermore, a new criterion based on reaction flux analysis is introduced, which is compatible with dual-fuel combustion. The spatial and temporal scales associated with the ambient methane consumption and consequent flame initiation are characterized. For the first time in dual-fuel spray assisted simulations, numerical evidence is provided on the initiation of premixed flames, and the corresponding timescale is reported. Particularly, there is a transient mixed-mode combustion phase of approximately 0.2 ms after the spray second stage ignition wherein extinction, ignition fronts, and quasi-deflagrative structures co-exist. After such a transient period, the combustion mode becomes essentially deflagrative. Finally, interactions between turbulence and premixed flame front are characterized mostly in the corrugated regime.

Genome-wide identification and molecular expression profile analysis of FHY3/FAR1 gene family in walnut (Juglans sigillata L.) development

BackgroundJuglans sigillata L. (walnut) has a high economic value for nuts and wood and has been widely grown and eaten around the world. Light plays an important role in regulating the development of the walnut embryo and promoting nucleolus enlargement, which is one of the factors affecting the yield and quality of walnut. However, little is known about the effect of light on the growth and quality of walnuts. Studies have shown that far red prolonged hypocotyl 3 (FHY3) and far red damaged response (FAR1) play important roles in plant growth, light response, and resistance. Therefore, FHY3/FAR1 genes were identified in walnuts on a genome-wide basis during their growth and development to reveal the potential regulation mechanisms involved in walnut kernel growth and development.ResultsIn the present study, a total of 61 FHY3/FAR1 gene family members in walnuts have been identified, ranging in length from 117 aa to 895 aa. These gene family members have FHY3 or FAR1 conserved domains, which are unevenly distributed on the 15 chromosomes (Chr) of the walnut (except for the Chr16). All 61 FHY3/FAR1 genes were divided into five subclasses (I, II, III, IV, and V) by phylogenetic tree analysis. The results indicated that FHY3/FAR1 genes in the same subclasses with similar structures might be involved in regulating the growth and development of walnut. The gene expression profiles were analyzed in different walnut kernel varieties (Q, T, and F). The result showed that some FHY3/FAR1 genes might be involved in the regulation of walnut kernel ripening and seed coat color formation. Seven genes (OF07056-RA, OF09665-RA, OF24282-RA, OF26012-RA, OF28029-RA, OF28030-RA, and OF08124-RA) were predicted to be associated with flavonoid biosynthetic gene regulation cis-acting elements in promoter sequences. RT-PCR was used to verify the expression levels of candidate genes during the development and color change of walnut kernels. In addition, light responsiveness and MeJA responsiveness are important promoter regulatory elements in the FHY3/FAR1 gene family, which are potentially involved in the light response, growth, and development of walnut plants.ConclusionThe results of this study provide a valuable reference for supplementing the genomic sequencing results of walnut, and pave the way for further research on the FHY3/FAR1 gene function of walnut.

Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development

Maize kernels are complex biological systems composed of three genetic sources, namely maternal tissues, progeny embryos, and progeny endosperms. The lack of gene expression profiles with spatial information has limited the understanding of the specific functions of each cell population, and hindered the exploration of superior genes in kernels. In our study, we conduct microscopic sectioning and spatial transcriptomics analysis during the grain filling stage of maize kernels. This enables us to visualize the expression patterns of all genes through electronical RNA in situ hybridization, and identify 11 cell populations and 332 molecular marker genes. Furthermore, we systematically elucidate the spatial storage mechanisms of the three major substances in maize kernels: starch, protein, and oil. These findings provide valuable insights into the functional genes that control agronomic traits in maize kernels.

The conservation of allelic DNA methylation and its relationship with imprinting in maize.

Genomic imprinting refers to allele-specific expression of genes depending on parental origin, and it is regulated by epigenetic modifications. Intraspecific allelic variation for imprinting has been detected; however, the intraspecific genome-wide allelic epigenetic variation in maize and its correlation with imprinting variants remain unclear. Here, three reciprocal hybrids were generated by crossing Zea mays inbred lines CAU5, B73, and Mo17 in order to examine the intraspecific conservation of the imprinted genes in the kernel. The majority of imprinted genes exhibited intraspecific conservation, and these genes also exhibited interspecific conservation (rice, sorghum, and Arabidopsis) and were enriched in some specific pathways. By comparing intraspecific allelic DNA methylation in the endosperm, we found that nearly 15% of DNA methylation existed as allelic variants. The intraspecific whole-genome correlation between DNA methylation and imprinted genes indicated that DNA methylation variants play an important role in imprinting variants. Disruption of two conserved imprinted genes using CRISPR/Cas9 editing resulted in a smaller kernel phenotype. Our results shed light on the intraspecific correlation of DNA methylation variants and variation for imprinting in maize, and show that imprinted genes play an important role in kernel development.