Seed-development programs: a systems biology-based comparison between dicots and monocots

Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants

The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies.

Genome-Wide Identification and Evolutionary and Expression Analyses of the Cyclin B Gene Family in Brassica napus

Cyclin B (CYCB) is a regulatory subunit of cyclin-dependent kinase (CDK), the concentration of which fluctuates to regulate cell cycle progression. Extensive studies have been performed on cyclins in numerous species, yet the evolutionary relationships and biological functions of the CYCB family genes in Brassica napus remain unclear. In this study, we identified 299 CYCB genes in 11 B. napus accessions. Phylogenetic analysis suggests that CYCB genes could be divided into three subfamilies in angiosperms and that the CYCB3 subfamily members may be a newer group that evolved in eudicots. The expansion of BnaCYCB genes underwent segmental duplication and purifying selection in genomes, and a number of drought-responsive and light-responsive cis-elements were found in their promoter regions. Additionally, expression analysis revealed that BnaCYCBs were strongly expressed in the developing seed and silique pericarp, as confirmed by the obviously reduced seed size of the mutant cycb3;1 in Arabidopsis thaliana compared with Col-0. This study provides a comprehensive evolutionary analysis of CYCB genes as well as insight into the biological function of CYCB genes in B. napus.

Plant beta-turnover rather than nestedness shapes overall taxonomic and phylogenetic beta-diversity triggered by favorable spatial-environmental conditions in large-scale Chinese grasslands

Introduction

Although it is widely acknowledged that biodiversity maintains plant community assembly processes, exploring the patterns and drivers of beta-diversity (β-diversity; species variation among local plant communities) has received much less attention compared to alpha-diversity (α-diversity; species variation within a local plant community). Here, we aim to examine the patterns and spatial-environmental drivers of taxonomic and phylogenetic β-diversity, and their components such as species turnover and nestedness, in large-scale Leymus chinensis grassland communities.

Methods

We collected plant community data from 166 sites across widely distributed L. chinensis communities in northern China, and then calculated the taxonomic and phylogenetic β-diversity indices (overall, turnover and nestedness) using a pairwise dissimilarity approach. To assess the effects and to explain the variation in the patterns of β-diversity, we collected data on geospatial, climate and soil conditions. We applied descriptive statistics, Mental correlations, and multiple linear regression models to assess the patterns and spatial-environmental drivers of β-diversity.

Results

The β-turnover, as compared to β-nestedness, exhibited a predominant influence, constituting 92.6% of the taxonomic β-diversity and 80.4% of the phylogenetic β-diversity. Most of the spatial-environmental variables were significantly positively correlated with the overall taxonomic and phylogenetic β-diversity and β-turnover, but not with β-nestedness. Climatic factors such as MAP and MAT were the strongest predictors of both taxonomic and phylogenetic β-diversity and β-turnover. The variance partitioning analysis showed that the combined effects of spatial and environmental factors accounted for 19% and 16% of the variation in the taxonomic and phylogenetic β-diversity (overall), 17% and 12% of the variation in the β-turnover, and 7% and 1% of the variation in the β-nestedness, respectively, which were higher than independent effects of either spatial or environmental factors.

Discussion

At larger spatial scales, the turnover component of β-diversity may be associated with the species complementarity effect, but dominant or functionally important species can vary among communities due to the species selection effect. By incorporating β-diversity into grassland management strategies, we can enhance the provision of vital ecosystem services that bolster human welfare, serving as a resilient barrier against the adverse effects of climate change at regional and global scales.

Antibody array-based proteome approach reveals proteins involved in grape seed development

Grape (Vitis vinifera) is one of the most widely cultivated fruits globally, primarily used for processing and fresh consumption. Seedless grapes are favored by consumers for their convenience, making the study of seedlessness a subject of great interest to scientists. To identify regulators involved in this process in grape, a monoclonal antibody (mAb)-array-based proteomics approach, which contains 21,120 mAbs, was employed for screening proteins/antigens differentially accumulated in grape during development. Differences in antigen signals were detected between seeded and seedless grapes revealing the differential accumulation of 2,587 proteins. After immunoblotting validation, 71 antigens were further immunoprecipitated and identified by mass spectrometry (MS). An in planta protein-protein interaction (PPI) network of those differentially accumulated proteins was established using mAb antibody by immunoprecipitation (IP)-MS, which reveals the alteration of pathways related to carbon metabolism and glycolysis. To validate our result, a seedless-related protein, DUF642 domain-containing protein (VvDUF642), which is functionally uncharacterized in grapes, was ectopically overexpressed in tomato (Solanum lycopersicum "MicroTom") and led to a reduction in seed production. PPI network indicated that VvDUF642 interacts with pectin acetylesterase (VvPAE) in grapes, which was validated by BiFC and Co-IP. As anticipated, overexpression of VvPAE substantially reduced seed production in tomato. Moreover, S. lycopersicum colourless non-ripening expression was altered in VvDUF642- and VvPAE-overexpressing plants. Taken together, we provided a high-throughput method for the identification of proteins involved in the seed formation process. Among those, VvDUF642 and VvPAE are potential targets for breeding seedless grapes and other important fruits in the future.

Concluding Embryogenesis After Diaspora: Seed Germination in Illicium Parviflorum

Albuminous seeds, dispersed with a minimally developed embryo surrounded by nutrient storage tissue, are pervasive across extinct and extant early diverging angiosperm lineages. Typically, seed ontogenic studies have focused on the time between fertilization and seed release, but in albuminous seeds, embryogenesis is incomplete at the time of seed dispersal. Here, I studied the morphological and nutritional relationships between the embryo and the endosperm after seed dispersal in Illicium parviflorum (Austrobaileyales). Seeds of I. parviflorum germinate over a period of three months. Different stages during the germination process were anatomically evaluated using a combination of histochemistry and immunocytochemistry. At dispersal, the seeds of Illicium contain a tiny achlorophyllous embryo with minimal histological differentiation, surrounded by copious amounts of lipo-protein globules stored in the endosperm within cell walls rich in un-esterified pectins. Six weeks later, the embryo expanded and differentiated the vascular tissues before the emergence of the radicle through the seed coat, as the stored lipids and proteins coalesced within cells. Six weeks later, the cotyledons contained starch and complex lipids intracellularly, and accumulated low-esterified pectins in their cell walls. The proteolipid-rich albuminous seeds of Illicium exemplify how woody angiosperms of the Austrobaileyales, Amborellales, and many magnoliids release seeds with high-energy storage compounds that are reprocessed by embryos that complete development during germination. Seedlings of these lineages thrive in the understory of tropical environments, which match with the predicted habitats where angiosperms evolved.

Dynamics of imprinted genes and their epigenetic mechanisms in castor bean seed with persistent endosperm

Genomic imprinting refers to parent-of-origin-dependent gene expression and primarily occurs in the endosperm of flowering plants, but its functions and epigenetic mechanisms remain to be elucidated in eudicots. Castor bean, a eudicot with large and persistent endosperm, provides an excellent system for studying the imprinting. Here, we identified 131 imprinted genes in developing endosperms and endosperm at seed germination phase of castor bean, involving into the endosperm development, accumulation of storage compounds and specially seed germination. Our results showed that the transcriptional repression of maternal allele of DNA METHYLTRANSFERASE 1 (MET1) may be required for maternal genome demethylation in the endosperm. DNA methylation analysis showed that only a small fraction of imprinted genes was associated with allele-specific DNA methylation, and most of them were closely associated with constitutively unmethylated regions (UMRs), suggesting a limited role for DNA methylation in controlling genomic imprinting. Instead, histone modifications can be asymmetrically deposited in maternal and paternal genomes in a DNA methylation-independent manner to control expression of most imprinted genes. These results expanded our understanding of the occurrence and biological functions of imprinted genes and showed the evolutionary flexibility of the imprinting machinery and mechanisms in plants.

Molecular, genetic, and genomic basis of seed size and yield characteristics in soybean

Soybean (Glycine max L. Merr.) is a crucial oilseed cash crop grown worldwide and consumed as oil, protein, and food by humans and feed by animals. Comparatively, soybean seed yield is lower than cereal crops, such as maize, rice, and wheat, and the demand for soybean production does not keep up with the increasing consumption level. Therefore, increasing soybean yield per unit area is the most crucial breeding objective and is challenging for the scientific community. Moreover, yield and associated traits are extensively researched in cereal crops, but little is known about soybeans' genetics, genomics, and molecular regulation of yield traits. Soybean seed yield is a complex quantitative trait governed by multiple genes. Understanding the genetic and molecular processes governing closely related attributes to seed yield is crucial to increasing soybean yield. Advances in sequencing technologies have made it possible to conduct functional genomic research to understand yield traits' genetic and molecular underpinnings. Here, we provide an overview of recent progress in the genetic regulation of seed size in soybean, molecular, genetics, and genomic bases of yield, and related key seed yield traits. In addition, phytohormones, such as auxin, gibberellins, cytokinins, and abscisic acid, regulate seed size and yield. Hence, we also highlight the implications of these factors, challenges in soybean yield, and seed trait improvement. The information reviewed in this study will help expand the knowledge base and may provide the way forward for developing high-yielding soybean cultivars for future food demands.

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.

Emerging roles of long non-coding RNAs in regulating agriculturally important seed traits

Seeds have enormous economic importance as source of calories, nutrition, edible oil, and biofuels. Therefore, seed traits like seed size and shape, weight, micronutrient content, oil content, quality, post-harvest sprouting, etc., are some of the main targets in crop improvement. Designing the strategies for their improvement benefits heavily from understanding the regulatory aspects of seed development. Recent studies indicate that long non-coding RNAs (lncRNAs) are one of the important regulators of seed development. They played a significant role in crop domestication by influencing seed traits. LncRNAs are conventionally defined as non-coding RNAs greater than 200 bp in length but lacking protein coding potential. Here we highlight the emerging pieces of evidence of lncRNA-mediated regulation of seed development through diverse mechanisms, for instance, by acting as target mimics or precursors of regulatory small RNAs or through chromatin remodeling and post-transcriptional repression. We also enumerate the insights from high-throughput transcriptomic studies from developing seeds of cereal, oilseed, biofuel, and pulse crops. We highlight the lncRNA candidates and lncRNA-mediated regulatory networks regulating seed development and related agronomic traits. Further, we discuss the potential of lncRNAs for improvement of agriculturally important seed traits through marker-assisted breeding and/or transgenic approaches.

Autophagy in maternal tissues contributes to Arabidopsis seed development

Seeds are an essential food source, providing nutrients for germination and early seedling growth. Degradation events in the seed and the mother plant accompany seed development, including autophagy, which facilitates cellular component breakdown in the lytic organelle. Autophagy influences various aspects of plant physiology, specifically nutrient availability and remobilization, suggesting its involvement in source-sink interactions. During seed development, autophagy affects nutrient remobilization from mother plants and functions in the embryo. However, it is impossible to distinguish between the contribution of autophagy in the source (i.e. the mother plant) and the sink tissue (i.e. the embryo) when using autophagy knockout (atg mutant) plants. To address this, we employed an approach to differentiate between autophagy in source and sink tissues. We investigated how autophagy in the maternal tissue affects seed development by performing reciprocal crosses between wild type and atg mutant Arabidopsis (Arabidopsis thaliana) plants. Although F1 seedlings possessed a functional autophagy mechanism, etiolated F1 plants from maternal atg mutants displayed reduced growth. This was attributed to altered protein but not lipid accumulation in the seeds, suggesting autophagy differentially regulates carbon and nitrogen remobilization. Surprisingly, F1 seeds of maternal atg mutants exhibited faster germination, resulting from altered seed coat development. Our study emphasizes the importance of examining autophagy in a tissue-specific manner, revealing valuable insights into the interplay between different tissues during seed development. It also sheds light on the tissue-specific functions of autophagy, offering potential for research into the underlying mechanisms governing seed development and crop yield.

Metabolomics and transcriptomics strategies to reveal the mechanism of diversity of maize kernel color and quality

BACKGROUND

Maize has many kernel colors, from white to dark black. However, research on the color and nutritional quality of the different varieties is limited. The color of the maize grain is an important characteristic. Colored maize is rich in nutrients, which have received attention for their role in diet-related chronic diseases and have different degrees of anti-stress protection for animal and human health.

METHODS

A comprehensive metabolome (LC-MS/MS) and transcriptome analysis was performed in this study to compare different colored maize varieties from the perspective of multiple recombination in order to study the nutritional value of maize with different colors and the molecular mechanism of color formation.

RESULTS

Maize kernels with diverse colors contain different types of health-promoting compounds, highlighting that different maize varieties can be used as functional foods according to human needs. Among them, red-purple and purple-black maize contain more flavonoids than white and yellow kernels. Purple-black kernels have a high content of amino acids and nucleotides, while red-purple kernels significantly accumulate sugar alcohols and lipids.

CONCLUSION

Our study can provide insights for improving people's diets and provide a theoretical basis for the study of food structure for chronic diseases.

Recent progress in molecular genetics and omics-driven research in seed biology

Elucidating the mechanisms that control seed development, metabolism, and physiology is a fundamental issue in biology. Michel Caboche had long been a catalyst for seed biology research in France up until his untimely passing away last year. To honour his memory, we have updated a review written under his coordination in 2010 entitled "Arabidopsis seed secrets unravelled after a decade of genetic and omics-driven research". This review encompassed different molecular aspects of seed development, reserve accumulation, dormancy and germination, that are studied in the lab created by M. Caboche. We have extended the scope of this review to highlight original experimental approaches implemented in the field over the past decade such as omics approaches aimed at investigating the control of gene expression, protein modifications, primary and specialized metabolites at the tissue or even cellular level, as well as seed biodiversity and the impact of the environment on seed quality.

Bacterial volatile organic compounds (VOCs) promote growth and induce metabolic changes in rice

Plant growth-promoting bacteria (PGPB) represent an eco-friendly alternative to reduce the use of chemical products while increasing the productivity of economically important crops. The emission of small gaseous signaling molecules from PGPB named volatile organic compounds (VOCs) has emerged as a promising biotechnological tool to promote biomass accumulation in model plants (especially Arabidopsis thaliana) and a few crops, such as tomato, lettuce, and cucumber. Rice (Oryza sativa) is the most essential food crop for more than half of the world's population. However, the use of VOCs to improve this crop performance has not yet been investigated. Here, we evaluated the composition and effects of bacterial VOCs on the growth and metabolism of rice. First, we selected bacterial isolates (IAT P4F9 and E.1b) that increased rice dry shoot biomass by up to 83% in co-cultivation assays performed with different durations of time (7 and 12 days). Metabolic profiles of the plants co-cultivated with these isolates and controls (without bacteria and non-promoter bacteria-1003-S-C1) were investigated via ¹H nuclear magnetic resonance. The analysis identified metabolites (e.g., amino acids, sugars, and others) with differential abundance between treatments that might play a role in metabolic pathways, such as protein synthesis, signaling, photosynthesis, energy metabolism, and nitrogen assimilation, involved in rice growth promotion. Interestingly, VOCs from IAT P4F9 displayed a more consistent promotion activity and were also able to increase rice dry shoot biomass in vivo. Molecular identification by sequencing the 16S rRNA gene of the isolates IAT P4F9 and E.1b showed a higher identity with Serratia and Achromobacter species, respectively. Lastly, volatilomes of these and two other non-promoter bacteria (1003-S-C1 and Escherichia coli DH5α) were evaluated through headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. Compounds belonging to different chemical classes, such as benzenoids, ketones, alcohols, sulfide, alkanes, and pyrazines, were identified. One of these VOCs, nonan-2-one, was validated in vitro as a bioactive compound capable of promoting rice growth. Although further analyses are necessary to properly elucidate the molecular mechanisms, our results suggest that these two bacterial isolates are potential candidates as sources for bioproducts, contributing to a more sustainable agriculture.

Dynamic patterns of gene expression and regulatory variation in the maize seed coat

BACKGROUND

Seed size is an important factor contributing to maize yield, but its molecular mechanism remains unclear. The seed coat, which serves as one of the three components of the maize grain, determines seed size to a certain extent. The seed coat also shares the maternal genotype and is an ideal material for studying heterosis.

RESULTS

In this study, the self-pollinated seeds of the maize hybrid Yudan888 and its parental lines were continuously collected from 0 day after pollination (DAP) to 15 DAP for phenotyping, cytological observation and RNA-seq. The phenotypic data showed that 3 DAP and 8 DAP are the best time points to study maize seed coat heterosis. Cytological observations indicated that maize seed coat heterosis might be the result of the coordination between cell number and cell size. Furthermore, the RNA-seq results showed that the nonadditive genes changed significantly between 3 and 8 DAP. However, the number of genes expressed additively was not significantly different. Our findings suggest that seed coat heterosis in hybrid is the result of nonadditive expression caused by dynamic changes in genes at different time points during seed expansion and seed coat development. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that genes related to DNA replication, cell cycle regulation, circadian rhythms and metabolite accumulation contributed significantly to hybrid seed coat heterosis.

CONCLUSION

Maize seed coat phenotyping allowed us to infer that 3 DAP and 8 DAP are important time points in the study of seed coat heterosis. Our findings provide evidence for genes involved in DNA replication, cell cycle regulation, circadian rhythms and metabolite accumulation in hybrid with high or low parental expression as major contributors to hybrid seed coat heterosis.

Transcriptomic analysis of seed development in Paysonia auriculata (Brassicaceae) identifies genes involved in hydroxy fatty acid biosynthesis

Paysonia auriculata (Brassicaceae) produces multiple hydroxy fatty acids as major components of the seed oil. We tracked the changes in seed oil composition and gene expression during development, starting 14 days after flowers had been pollinated. Seed oil changes showed initially higher levels of saturated and unsaturated fatty acids (FAs) but little accumulation of hydroxy fatty acids (HFAs). Starting 21 days after pollination (DAP) HFA content sharply increased, and reached almost 30% at 28 DAP. Total seed oil also increased from a low of approximately 2% at 14 DAP to a high of approximately 20% by 42 DAP. We identified almost all of the fatty acid synthesis and modification genes that are known from Arabidopsis, and, in addition, a strong candidate for the hydroxylase gene that mediates the hydroxylation of fatty acids to produce valuable hydroxy fatty acids (HFAs) in this species. The gene expression network revealed is very similar to that of the emerging oil crop, Physaria fendleri, in the sister genus to Paysonia. Phylogenetic analyses indicate the hydroxylase enzyme, FAH12, evolved only once in Paysonia and Physaria, and that the enzyme is closely related to FAD2 enzymes. Phylogenetic analyses of FAD2 and FAH12 in the Brassicaceae and outgroup genera suggest that the branch leading to the hydroxylase clade of Paysonia and Physaria is under relaxed selection, compared with the strong purifying selection found across the FAD2 lineages.

Regulation of seed storage protein synthesis in monocot and dicot plants: A comparative review

Seeds are a major source of nutrients for humans and animal livestock worldwide. With improved living standards, high nutritional quality has become one of the main targets for breeding. Storage protein content in seeds, which is highly variable depending on plant species, serves as a pivotal criterion of seed nutritional quality. In the last few decades, our understanding of the molecular genetics and regulatory mechanisms of storage protein synthesis has greatly advanced. Here, we systematically and comprehensively summarize breakthroughs on the conservation and divergence of storage protein synthesis in dicot and monocot plants. With regard to storage protein accumulation, we discuss evolutionary origins, developmental processes, characteristics of main storage protein fractions, regulatory networks, and genetic modifications. In addition, we discuss potential breeding strategies to improve storage protein accumulation and provide perspectives on some key unanswered problems that need to be addressed.

Comparative Transcriptome and Co-Expression Network Analyses Reveal the Molecular Mechanism of Calcium-Deficiency-Triggered Tipburn in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis)

Chinese cabbage tipburn is characterized by the formation of necrotic lesions on the margin of leaves, including on the insides of the leafy head. This physiological disorder is associated with a localized calcium deficiency during leaf development. However, little information is available regarding the molecular mechanisms governing Ca-deficiency-triggered tipburn. This study comprehensively analysed the transcriptomic comparison between control and calcium treatments (CK and 0 mM Ca) in Chinese cabbage to determine its molecular mechanism in tipburn. Our analysis identified that the most enriched gene ontology (GO) categories are photosynthesis, thylakoid and cofactor binding. Moreover, the KEGG pathway was most enriched in photosynthesis, carbon metabolism and carbon fixation. We also analyzed the co-expression network by functional categories and identified ten critical hub differentially expressed genes (DEGs) in each gene regulatory network (GRN). These DEGs might involve abiotic stresses, developmental processes, cell wall metabolism, calcium distribution, transcription factors, plant hormone biosynthesis and signal transduction pathways. Under calcium deficiency, CNX1, calmodulin-binding proteins and CMLs family proteins were downregulated compared to CK. In addition, plant hormones such as GA, JA, BR, Auxin and ABA biosynthesis pathways genes were downregulated under calcium treatment. Likewise, HATs, ARLs and TCP transcription factors were reported as inactive under calcium deficiency, and potentially involved in the developmental process. This work explores the specific DEGs' significantly different expression levels in 0 mM Ca and the control involved in plant hormones, cell wall developments, a light response such as chlorophylls and photosynthesis, transport metabolism and defence mechanism and redox. Our results provide critical evidence of the potential roles of the calcium signal transduction pathway and candidate genes governing Ca-deficiency-triggered tipburn in Chinese cabbage.

Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean

Phaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition around the world. However, the genetic basis of most important traits in common bean remains unknown. This study aimed at identifying QTL and candidate gene models underlying twenty-six agronomically important traits in common bean. For this, we assembled and phenotyped a diversity panel of 200 P. vulgaris genotypes in the greenhouse, comprising determinate bushy, determinate climbing and indeterminate climbing beans. The panel included dry beans and snap beans from different breeding programmes, elite lines and landraces from around the world with a major focus on accessions of African, European and South American origin. The panel was genotyped using a cost-conscious targeted genotyping-by-sequencing (GBS) platform to take advantage of highly polymorphic SNPs detected in previous studies and in diverse germplasm. The detected single nucleotide polymorphisms (SNPs) were applied in marker-trait analysis and revealed sixty-two quantitative trait loci (QTL) significantly associated with sixteen traits. Gene model identification via a similarity-based approach implicated major candidate gene models underlying the QTL associated with ten traits including, flowering, yield, seed quality, pod and seed characteristics. Our study revealed six QTL for pod shattering including three new QTL potentially useful for breeding. However, the panel was evaluated in a single greenhouse environment and the findings should be corroborated by evaluations across different field environments. Some of the detected QTL and a number of candidate gene models only elucidate the understanding of the genetic nature of these traits and provide the basis for further studies. Finally, the study showed the possibility of using a limited number of SNPs in performing marker-trait association in common bean by applying a highly scalable targeted GBS approach. This targeted GBS approach is a cost-efficient strategy for assessment of the genetic basis of complex traits and can enable geneticists and breeders to identify novel loci and targets for marker-assisted breeding more efficiently.

Genome-wide identification and characterization of lncRNAs in sunflower endosperm

BACKGROUND

Long non-coding RNAs (lncRNAs), as important regulators, play important roles in plant growth and development. The expression and epigenetic regulation of lncRNAs remain uncharacterized generally in plant seeds, especially in the transient endosperm of the dicotyledons.

RESULTS

In this study, we identified 11,840 candidate lncRNAs in 12 day-after-pollination sunflower endosperm by analyzing RNA-seq data. These lncRNAs were evenly distributed in all chromosomes and had specific features that were distinct from mRNAs including tissue-specificity expression, shorter and fewer exons. By GO analysis of protein coding genes showing strong correlation with the lncRNAs, we revealed that these lncRNAs potential function in many biological processes of seed development. Additionally, genome-wide DNA methylation analyses revealed that the level of DNA methylation at the transcription start sites was negatively correlated with gene expression levels in lncRNAs. Finally, 36 imprinted lncRNAs were identified including 32 maternally expressed lncRNAs and four paternally expressed lncRNAs. In CG and CHG context, DNA methylation levels of imprinted lncRNAs in the upstream and gene body regions were slightly lower in the endosperm than that in embryo tissues, which indicated that the maternal demethylation potentially induce the paternally bias expression of imprinted lncRNAs in sunflower endosperm.

CONCLUSION

Our findings not only identified and characterized lncRNAs on a genome-wide scale in the development of sunflower endosperm, but also provide novel insights into the parental effects and epigenetic regulation of lncRNAs in dicotyledonous seeds.

A NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination

Maize early endosperm development is initiated in coordination with elimination of maternal nucellar tissues. However, the underlying mechanisms are largely unknown. Here, we characterize a major quantitative trait locus for maize kernel size and weight that encodes an EXPANSIN gene, ZmEXPB15. The encoded β-expansin protein is expressed specifically in nucellus, and positively controls kernel size and weight by promoting nucellus elimination. We further show that two nucellus-enriched transcription factors (TFs), ZmNAC11 and ZmNAC29, activate ZmEXPB15 expression. Accordingly, these two TFs also promote kernel size and weight through nucellus elimination regulation, and genetic analyses support their interaction with ZmEXPB15. Importantly, hybrids derived from a ZmEXPB15 overexpression line have increased kernel weight, demonstrates its potential value in breeding. Together, we reveal a pathway modulating the cellular processes of maternal nucellus elimination and early endosperm development, and an approach to improve kernel weight.

Current studies of maize kernel development mostly focus on endosperm and embryo development, and little is known about the control of the nucellus tissue. Here, the authors report a NAC-EXPB15 pathway that regulate maize kernel size by modulating nucellus elimination and early endosperm development.

Transcriptome analysis and identification of abscisic acid and gibberellin-related genes during seed development of alfalfa (Medicago sativa L.)

BACKGROUND

Alfalfa (Medicago sativa) is a widely cultivated plant. Unlike many crops, the main goal of breeding alfalfa is to increase its aboveground biomass rather than the biomass of its seeds. However, the low yield of alfalfa seeds limits alfalfa production. Many studies have explored the factors affecting seed development, in which phytohormones, especially ABA and GAs, play an important role in seed development.

RESULTS

Here, we performed a transcriptome analysis of alfalfa seeds at five development stages. A total of 16,899 differentially expressed genes (DEGs) were identified and classified into 10 clusters, and the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined. The contents of ABA, GA₁, GA₃, GA₄ and GA₇ in alfalfa seeds at five development stages were determined. In addition, 14 ABA-related DEGs and 20 GA-related DEGs were identified and analysed. These DEGs are involved in plant hormone pathways and play an important role in seed development. Moreover, morphological and physiological analyses revealed the dynamic changes during the development of alfalfa seeds.

CONCLUSION

Overall, our study is the first to analyse the transcriptome across various stages of seed development in alfalfa. The results of our study could be used to improve alfalfa seed yield. The key ABA and GA related-genes are potential targets for improving alfalfa seed yield via genetic engineering in the future.

The ubiquitin-26S proteasome system and autophagy relay proteome homeostasis regulation during silique development

Functional studies of the ubiquitin-26S proteasome system (UPS) have demonstrated that virtually all aspects of the plant's life involve UPS-mediated turnover of abnormal or short-lived proteins. However, the role of the UPS during development, including in seeds and fruits, remains to be determined in detail, although mutants of several of its core elements are known to be embryonically lethal. Unfortunately, early termination of embryogenesis limits the possibility to characterize the activities of the UPS in reproductive organs. Given both the economic and the societal impact of reproductive production, such studies are indispensable. Here, we systematically compared expression of multiple 26S proteasome subunits along with the dynamics of proteasome activity and total protein ubiquitylation in seedlings, developing siliques, and embryos of Arabidopsis thaliana. Since autophagy plays the second largest role in maintaining proteome stability, we parallelly studied three rate-limiting enzymes that are involved in autophagy flux. Our experiments unexpectedly discovered that, in contrast to the activities in seedlings, both protein and transcript levels of six selected 26S proteasome subunits gradually decline in immature siliques or embryos toward maturation while the autophagy flux rises despite the nutrient-rich condition. We also discovered a reciprocal turnover pathway between the proteasome and autophagy. While the autophagy flux is suppressed in seedlings by UPS-mediated degradation of its three key enzymes, transcriptional reprogramming dampens this process in siliques, which in turn stimulates a bulk autophagic degradation of proteasomes. Collectively, our study of the developmental changes of the UPS and autophagy activities suggests that they relay the proteome homeostasis regulation in early silique and/or seed development, highlighting their interactions during development.

The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences

Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. Here we report a chromosome-level genome assembly of Adiantum capillus-veneris L., a model homosporous fern. This fern genome comprises 30 pseudochromosomes with a size of 4.8-gigabase and a contig N50 length of 16.22 Mb. Gene co-expression network analysis uncovered that homospore development in ferns has relatively high genetic similarities with that of the pollen in seed plants. Analysing fern defence response expands understanding of evolution and diversity in endogenous bioactive jasmonates in plants. Moreover, comparing fern genomes with those of other land plants reveals changes in gene families important for the evolutionary novelties within the euphyllophyte clade. These results lay a foundation for studies on fern genome evolution and function, as well as the origin and evolution of euphyllophytes.

Transcription Factor DOF4.1 Regulates Seed Longevity in Arabidopsis via Seed Permeability and Modulation of Seed Storage Protein Accumulation

Seed longevity is modulated by multiple genetic factors in Arabidopsis thaliana. A previous genome-wide association study using the Elevated Partial Pressure of Oxygen (EPPO) aging assay pinpointed a genetic locus associated with this trait. Reverse genetics identified the transcription factor DOF4.1 as a novel seed longevity factor. dof4.1 loss-of-function plants generate seeds exhibiting higher germination after accelerated aging assays. DOF4.1 is expressed during seed development and RNAseq data show several putative factors that could contribute to the dof4.1 seed longevity phenotype. dof4.1 has reduced seed permeability and a higher levels of seed storage proteins mRNAs (cruciferins and napins) in developing seeds, as compared to wild-type seeds. It has been reported that mutant lines defective in cruciferins or napins present reduced seed longevity. The improved longevity of dof4.1 is totally lost in the quadruple mutant dof4.1 cra crb crc, but not in a dof4.1 line depleted of napins, suggesting a prominent role for cruciferins in this process. Moreover, a negative regulation of DOF4.1 expression by the transcription factor DOF1.8 is suggested by co-inoculation assays in Nicotiana benthamiana. Indeed, DOF1.8 expression anticorrelates with that of DOF4.1 during seed development. In summary, modulation of DOF4.1 levels during seed development contributes to regulate seed longevity.

Systems seed biology to understand and manipulate rice grain quality and nutrition

Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.

Rice LEAFY COTYLEDON1 Hinders Embryo Greening During the Seed Development

LEAFY COTYLEDON1 (LEC1) is the central regulator of seed development in Arabidopsis, while its function in monocots is largely elusive. We generated Oslec1 mutants using CRISPR/Cas9 technology. Oslec1 mutant seeds lost desiccation tolerance and triggered embryo greening at the early development stage. Transcriptome analysis demonstrated that Oslec1 mutation altered diverse hormonal pathways and stress response in seed maturation, and promoted a series of photosynthesis-related genes. Further, genome-wide identification of OsLEC1-binding sites demonstrated that OsLEC1 bound to genes involved in photosynthesis, photomorphogenesis, as well as abscisic acid (ABA) and gibberellin (GA) pathways, involved in seed maturation. We illustrated an OsLEC1-regulating gene network during seed development, including the interconnection between photosynthesis and ABA/GA biosynthesis/signaling. Our findings suggested that OsLEC1 acts as not only a central regulator of seed maturation but also an inhibitor of embryo greening during rice seed development. This study would provide new understanding for the OsLEC1 regulatory mechanisms on photosynthesis in the monocot seed development.

Cloning and Functional Analysis of TaWRI1Ls, the Key Genes for Grain Fatty Acid Synthesis in Bread Wheat

WRINKLED1 (WRI1), an APETALA2 (AP2) transcription factor (TF), critically regulates the processes related to fatty acid synthesis, storage oil accumulation, and seed development in plants. However, the WRI1 genes remain unknown in allohexaploid bread wheat (Triticum aestivum L.). In this study, based on the sequence of Arabidopsis AtWRI1, two TaWRI1Ls genes of bread wheat, TaWRI1L1 and TaWRI1L2, were cloned. TaWRI1L2 was closely related to monocotyledons and clustered in one subgroup with AtWRI1, while TaWRI1L1 was clustered in another subgroup with AtWRI3 and AtWRI4. Both were expressed highly in the developmental grain, subcellular localized in the nucleus, and showed transcriptional activation activity. TaWRI1L2, rather than TaWRI1L1, promoted oil body accumulation and significantly increased triglyceride (TAG) content in tobacco leaves. Overexpression of TaWRI1L2 compensated for the functional loss of AtWRI1 in an Arabidopsis mutant and restored the wild-type phenotypes of seed shape, generation, and fatty acid synthesis and accumulation. Knockout of TaWRI1L2 reduced grain size, 1000 grain weight, and grain fatty acid synthesis in bread wheat. Conclusively, TaWRI1L2, rather than TaWRI1L1, was the key transcriptional factor in the regulation of grain fatty acid synthesis in bread wheat. This study lays a foundation for gene regulation and genetic manipulation of fatty acid synthesis in wheat genetic breeding programs.

ABA-INSENSITIVE 3 with or without FUSCA3 highly up-regulates lipid droplet proteins and activates oil accumulation

ABA-INSENSITIVE 3 (ABI3) has long been known for activation of storage protein accumulation. A role of ABI3 on oil accumulation was previously suggested based on a decrease of oil content in seeds of abi3 mutant. However, this conclusion could not exclude possibilities of indirect or pleiotropic effects, such as through mutual regulatory interactions with FUSCA3 (FUS3), an activator of oil accumulation. To identify that ABI3 functions independent of the effects of related seed transcription factors, we expressed ABI3 under the control of an inducible promoter in tobacco BY2 cells and Arabidopsis rosette leaves. Inducible expression of ABI3 activated oil accumulation in these non-seed cells, demonstrating a general role of ABI3 in regulation of oil biosynthesis. Further expressing ABI3 in rosette leaves of fus3 knockout mutant still caused up to 3-fold greater triacylglycerol accumulation, indicating ABI3 can activate lipid accumulation independently of FUS3. Transcriptome analysis revealed that LIPID DROPLET PROTEIN (LDP) genes, including OLEOSINs and CALEOSINs, were up-regulated up to 1000-fold by ABI3 in the absence of FUS3, while the expression of WRINKLED1 was doubled. Taken together, our results provide genetic evidence that ABI3 activates oil accumulation with or without FUS3, most likely through up-regulating LDPs and WRINKLED1.

Plant iron nutrition: the long road from soil to seeds

Iron (Fe) is an essential plant micronutrient since many cellular processes including photosynthesis, respiration, and the scavenging of reactive oxygen species depend on adequate Fe levels; however, non-complexed Fe ions can be dangerous for cells, as they can act as pro-oxidants. Hence, plants possess a complex homeostatic control system for safely taking up Fe from the soil and transporting it to its various cellular destinations, and for its subcellular compartmentalization. At the end of the plant's life cycle, maturing seeds are loaded with the required amount of Fe needed for germination and early seedling establishment. In this review, we discuss recent findings on how the microbiota in the rhizosphere influence and interact with the strategies adopted by plants to take up iron from the soil. We also focus on the process of seed-loading with Fe, and for crop species we also consider its associated metabolism in wild relatives. These two aspects of plant Fe nutrition may provide promising avenues for a better comprehension of the long pathway of Fe from soil to seeds.

ENB1 encodes a cellulose synthase 5 that directs synthesis of cell wall ingrowths in maize basal endosperm transfer cells

Development of the endosperm is strikingly different in monocots and dicots: it often manifests as a persistent tissue in the former and transient tissue in the latter. Little is known about the controlling mechanisms responsible for these different outcomes. Here we characterized a maize (Zea mays) mutant, endosperm breakdown1 (enb1), in which the typically persistent endosperm (PE) was drastically degraded during kernel development. ENB1 encodes a cellulose synthase 5 that is predominantly expressed in the basal endosperm transfer layer (BETL) of endosperm cells. Loss of ENB1 function caused a drastic reduction in formation of flange cell wall ingrowths (ingrowths) in BETL cells. Defective ingrowths impair nutrient uptake, leading to premature utilization of endosperm starch to nourish the embryo. Similarly, developing wild-type kernels cultured in vitro with a low level of sucrose manifested early endosperm breakdown. ENB1 expression is induced by sucrose via the BETL-specific Myb-Related Protein1 transcription factor. Overexpression of ENB1 enhanced development of flange ingrowths, facilitating sucrose transport into BETL cells and increasing kernel weight. The results demonstrated that ENB1 enhances sucrose supply to the endosperm and contributes to a PE in the kernel.

The MADS-domain factor AGAMOUS-Like18 promotes somatic embryogenesis

AGAMOUS-Like 18 (AGL18) is a MADS domain transcription factor (TF) that is structurally related to AGL15. Here we show that, like AGL15, AGL18 can promote somatic embryogenesis (SE) when ectopically expressed in Arabidopsis (Arabidopsis thaliana). Based on loss-of-function mutants, AGL15 and AGL18 have redundant functions in developmental processes such as SE. To understand the nature of this redundancy, we undertook a number of studies to look at the interaction between these factors. We studied the genome-wide direct targets of AGL18 to characterize its roles at the molecular level using chromatin immunoprecipitation (ChIP)-SEQ combined with RNA-SEQ. The results demonstrated that AGL18 binds to thousands of sites in the genome. Comparison of ChIP-SEQ data for AGL15 and AGL18 revealed substantial numbers of genes bound by both AGL15 and AGL18, but there were also differences. Gene ontology analysis revealed that target genes were enriched for seed, embryo, and reproductive development as well as hormone and stress responses. The results also demonstrated that AGL15 and AGL18 interact in a complex regulatory loop, where AGL15 inhibited transcript accumulation of AGL18, while AGL18 increased AGL15 transcript accumulation. Co-immunoprecipitation revealed an interaction between AGL18 and AGL15 in somatic embryo tissue. The binding and expression analyses revealed a complex crosstalk and interactions among embryo TFs and their target genes. In addition, our study also revealed that phosphorylation of AGL18 and AGL15 was crucial for the promotion of SE.

TRM61 is essential for Arabidopsis embryo and endosperm development

Post-transcriptional modifications of tRNA molecules play crucial roles in gene expression and protein biosynthesis. Across the genera, methylation of tRNAs at N¹ of adenosine 58 (A58) by AtTRM61/AtTRM6 complex plays a critical role in maintaining the stability of initiator methionyl-tRNA (tRNA_i^Met). Recently, it was shown that mutation in AtTRM61 or AtTRM6 leads to seed abortion. However, a detailed study about the AtTRM61/AtTRM6 function in plants remains vague. Here, we found that AtTRM61 has a conserved functional structure and possesses conserved binding motifs for cofactor S-adenosyl-L-methionine (AdoMet). Mutations of the complex subunits AtTRM61/AtTRM6 result in embryo and endosperm developmental defects. The endosperm and embryo developmental defects were conditionally complemented by Attrm61-1/ + FIS2pro::AtTRM61 and Attrm61-1/ + ABI3pro::AtTRM61 indicating that AtTRM61 is required for early embryo and endosperm development. Besides, the rescue of the fertility defects in trm61/ + by overexpression of initiator tRNA suggests that AtTRM61 mutation could diminish tRNA_i^Met stability. Moreover, using yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays, we showed that AtMPK4 physically interacts with AtTRM61. The data presented here suggest that AtTRM61 has a conserved structure and function in Arabidopsis. Also, AtTRM61 may be required for tRNA_i^Met stability, embryo and endosperm development.

Epigenetic regulation of seed-specific gene expression by DNA methylation valleys in castor bean

BACKGROUND

Understanding the processes governing angiosperm seed growth and development is essential both for fundamental plant biology and for agronomic purposes. Master regulators of angiosperm seed development are expressed in a seed-specific manner. However, it is unclear how this seed specificity of transcription is established. In some vertebrates, DNA methylation valleys (DMVs) are highly conserved and strongly associated with key developmental genes, but comparable studies in plants are limited to Arabidopsis and soybean. Castor bean (Ricinus communis) is a valuable model system for the study of seed biology in dicots and source of economically important castor oil. Unlike other dicots such as Arabidopsis and soybean, castor bean seeds have a relatively large and persistent endosperm throughout seed development, representing substantial structural differences in mature seeds. Here, we performed an integrated analysis of RNA-seq, whole-genome bisulfite sequencing, and ChIP-seq for various histone marks in the castor bean.

RESULTS

We present a gene expression atlas covering 16 representative tissues and identified 1162 seed-specific genes in castor bean (Ricinus communis), a valuable model for the study of seed biology in dicots. Upon whole-genome DNA methylation analyses, we detected 32,567 DMVs across five tissues, covering ~33% of the castor bean genome. These DMVs are highly hypomethylated during development and conserved across plant species. We found that DMVs have the potential to activate transcription, especially that of tissue-specific genes. Focusing on seed development, we found that many key developmental regulators of seed/endosperm development, including AGL61, AGL62, LEC1, LEC2, ABI3, and WRI1, were located within DMVs. ChIP-seq for five histone modifications in leaves and seeds clearly showed that the vast majority of histone modification peaks were enriched within DMVs, and their remodeling within DMVs has a critical role in the regulation of seed-specific gene expression. Importantly, further experiment analysis revealed that distal DMVs may act as cis-regulatory elements, like enhancers, to activate downstream gene expression.

CONCLUSIONS

Our results point to the importance of DMVs and special distal DMVs behaving like enhancers, in the regulation of seed-specific genes, via the reprogramming of histone modifications within DMVs. Furthermore, these results provide a comprehensive understanding of the epigenetic regulator roles in seed development in castor bean and other important crops.

Seeds as natural capital

Halting and reversing the current loss of biodiversity and habitats will be facilitated by a comprehensive valuation of all nature's contributions to people (NCPs), on which we rely. In this context, we explore the full natural capital value of seeds to reveal how this extends far beyond their economic value associated with mainstream agriculture and forestry. Seeds represent the main assets for nature-based solutions at species (i.e., unlocking neglected species properties and via seed banking) and ecosystem level (i.e., ecological restoration). Challenges remain to enhance their sustainable use in nature conservation and in supporting a sustainable development model. Such advances will depend on the comprehensive valuation of the natural capital value of seeds, which has so far been grossly underestimated.

Receptor-like protein kinases in plant reproduction: Current understanding and future perspectives

Reproduction is a crucial process in the life span of flowering plants, and directly affects human basic requirements in agriculture, such as grain yield and quality. Typical receptor-like protein kinases (RLKs) are a large family of membrane proteins sensing extracellular signals to regulate plant growth, development, and stress responses. In Arabidopsis thaliana and other plant species, RLK-mediated signaling pathways play essential roles in regulating the reproductive process by sensing different ligand signals. Molecular understanding of the reproductive process is vital from the perspective of controlling male and female fertility. Here, we summarize the roles of RLKs during plant reproduction at the genetic and molecular levels, including RLK-mediated floral organ development, ovule and anther development, and embryogenesis. In addition, the possible molecular regulatory patterns of those RLKs with unrevealed mechanisms during reproductive development are discussed. We also point out the thought-provoking questions raised by the research on these plant RLKs during reproduction for future investigation.

Evolutionary divergence in embryo and seed coat development of U's Triangle Brassica species illustrated by a spatiotemporal transcriptome atlas

The economically valuable Brassica species include the six related members of U's Triangle. Despite the agronomic and economic importance of these Brassicas, the impacts of evolution and relatively recent domestication events on the genetic landscape of seed development have not been comprehensively examined in these species. Here we present a 3D transcriptome atlas for the six species of U's Triangle, producing a unique resource that captures gene expression data for the major subcompartments of the seed, from the unfertilized ovule to the mature embryo and seed coat. This comprehensive dataset for seed development in tetraploid and ancestral diploid Brassicas provides new insights into evolutionary divergence and expression bias at the gene and subgenome levels during the domestication of these valued crop species. Comparisons of gene expression associated with regulatory networks and metabolic pathways operating in the embryo and seed coat during seed development reveal differences in storage reserve accumulation and fatty acid metabolism among the six Brassica species. This study illustrates the genetic underpinnings of seed traits and the selective pressures placed on seed production, providing an immense resource for continued investigation of Brassica polyploid biology, genomics and evolution.

CWIN-sugar transporter nexus is a key component for reproductive success

Reproductive development is critical for completion of plant life cycle and realization of crop yield potential. Reproductive organs comprise multiple distinctive or even transgenerational tissues, which are symplasmically disconnected from each other for protection and better control of nutrition and development. Cell wall invertases (CWINs) and sugar transporters are often specifically or abundantly expressed in these apoplasmic interfaces to provide carbon nutrients and sugar signals to developing pollens, endosperm and embryo. Emerging evidence shows that some of those genes were indeed targeted for selection during crop domestication. In this Opinion paper, I discuss the functional significance of the localized expression of CWINs and sugar transporters in reproductive organs followed by an analysis on how their spatial patterning may be regulated at the molecular levels and how the localized CWIN activity may be exploited for improvement of reproductive output.

Seed development in Paeonia ostii (Paeoniaceae), with particular reference to embryogeny

BACKGROUND

Seeds of Paeonia ostii have been proposed as a source of raw material for the production of edible oil; however, lack of information about the developmental biology of the seeds hampers our ability to use them. Our aim was to investigate development of the seed coat, endosperm and embryo of P. ostii in relation to timing of accumulation of nutrient reserves from pollination to seed maturity. Ovules and developing seeds of P. ostii were collected at various stages of development from zygote to maturity. Seed fresh mass, dry mass, germination, moisture, soluble sugars, starch, protein and oil content were determined. Ontogeny of seeds including embryo, endosperm and seed coat were analyzed histologically.

RESULTS

The ovule of P. ostii is anatropous, crassinucellate and bitegmic. The zygote begins to divide at about 5 days after pollination (DAP), and the division is not accompanied by cell wall formation. By 25 DAP, the proembryo begins to cellularize. Thereafter, several embryo primordia appear at the surface of the cellularized proembryo, but only one matures. Endosperm development follows the typical nuclear type. The seed coat is derived from the outer integument. During seed development, soluble sugars, starch and crude fat content increased and then decreased, with maximum contents at 60, 80 and 100 DAP, respectively. Protein content was relatively low compared with soluble sugars and crude fat, but it increased throughout seed development.

CONCLUSIONS

During seed development in P. ostii, the seed coat acts as a temporary storage tissue. Embryo development of P. ostii can be divided into two stages: a coenocytic proembryo from zygote (n + n) that degenerates and a somatic embryo from peripheral cells of the proembryo (2n → 2n). This pattern of embryogeny differs from that of all other angiosperms, but it is similar to that of gymnosperms.

Endosperm-Embryo Communications: Recent Advances and Perspectives

Seed maturation depends on well-coordinated communications between the processes of endosperm and embryo development. The endosperm is considered to be destined to support embryo development and the timing of endosperm cellularization is critical for embryo growth. Recent findings suggest that the endosperm development and the onset of embryo maturation are two independent processes during seed development. Meanwhile, it is lately reported that several mobile regulators originating from the endosperm are needed to ensure proper embryo growth and seed maturation. In this opinion article, we highlight processes on how endosperm communicates with embryo during seed development and discuss some intriguing questions in light of the latest advancements.

Genome-wide association study and population structure analysis of seed-bound amino acids and total protein in watermelon

BACKGROUND

Watermelon seeds are a powerhouse of value-added traits such as proteins, free amino acids, vitamins, and essential minerals, offering a paleo-friendly dietary option. Despite the availability of substantial genetic variation, there is no sufficient information on the natural variation in seed-bound amino acids or proteins across the watermelon germplasm. This study aimed to analyze the natural variation in watermelon seed amino acids and total protein and explore underpinning genetic loci by genome-wide association study (GWAS).

METHODS

The study evaluated the distribution of seed-bound free amino acids and total protein in 211 watermelon accessions of Citrullus spp, including 154 of Citrullus lanatus, 54 of Citrullus mucosospermus (egusi) and three of Citrullus amarus. We used the GWAS approach to associate seed phenotypes with 11,456 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS).

RESULTS

Our results demonstrate a significant natural variation in different free amino acids and total protein content across accessions and geographic regions. The accessions with high protein content and proportion of essential amino acids warrant its use for value-added benefits in the food and feed industries via biofortification. The GWAS analysis identified 188 SNPs coinciding with 167 candidate genes associated with watermelon seed-bound amino acids and total protein. Clustering of SNPs associated with individual amino acids found by principal component analysis was independent of the speciation or cultivar groups and was not selected during the domestication of sweet watermelon. The identified candidate genes were involved in metabolic pathways associated with amino acid metabolism, such as Argininosuccinate synthase, explaining 7% of the variation in arginine content, which validate their functional relevance and potential for marker-assisted analysis selection. This study provides a platform for exploring potential gene loci involved in seed-bound amino acids metabolism, useful in genetic analysis and development of watermelon varieties with superior seed nutritional values.

Genome-wide analysis of genomic imprinting in the endosperm and allelic variation in flax

Genomic imprinting is an epigenetic phenomenon that causes biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in the triploid endosperm and plays a vital role in seed development. In this study, we identified 248 candidate imprinted genes including 114 maternally expressed imprinted genes (MEGs) and 134 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. These imprinted genes were neither clustered in specific chromosomal regions nor well conserved among flax and other plant species. MEGs tended to be expressed specifically in the endosperm, whereas the expression of PEGs was not tissue-specific. Imprinted single nucleotide polymorphisms differentiated 200 flax cultivars into the oil flax, oil-fiber dual purpose flax and fiber flax subgroups, suggesting that genomic imprinting contributed to intraspecific variation in flax. The nucleotide diversity of imprinted genes in the oil flax subgroup was significantly higher than that in the fiber flax subgroup, indicating that some imprinted genes underwent positive selection during flax domestication from oil flax to fiber flax. Moreover, imprinted genes that underwent positive selection were related to flax functions. Thirteen imprinted genes related to flax seed size and weight were identified using a candidate gene-based association study. Therefore, our study provides information for further exploration of the function and genomic variation of imprinted genes in the flax population.

Temporal Control of Seed Development in Dicots: Molecular Bases, Ecological Impact and Possible Evolutionary Ramifications

In flowering plants, seeds serve as organs of both propagation and dispersal. The developing seed passes through several consecutive stages, following a conserved general outline. The overall time needed for a seed to develop, however, may vary both within and between plant species, and these temporal developmental properties remain poorly understood. In the present paper, we summarize the existing data for seed development alterations in dicot plants. For genetic mutations, the reported cases were grouped in respect of the key processes distorted in the mutant specimens. Similar phenotypes arising from the environmental influence, either biotic or abiotic, were also considered. Based on these data, we suggest several general trends of timing alterations and how respective mechanisms might add to the ecological plasticity of the families considered. We also propose that the developmental timing alterations may be perceived as an evolutionary substrate for heterochronic events. Given the current lack of plausible models describing timing control in plant seeds, the presented suggestions might provide certain insights for future studies in this field.

The genetics underlying metabolic signatures in a brown rice diversity panel and their vital role in human nutrition

Brown rice (Oryza sativa) possesses various nutritionally dense bioactive phytochemicals exhibiting a wide range of antioxidant, anti-cancer, and anti-diabetic properties known to promote various human health benefits. However, despite the wide claims made about the importance of brown rice for human nutrition the underlying metabolic diversity has not been systematically explored. Non-targeted metabolite profiling of developing and mature seeds of a diverse genetic panel of 320 rice cultivars allowed quantification of 117 metabolites. The metabolite genome-wide association study (mGWAS) detected genetic variants influencing diverse metabolic targets in developing and mature seeds. We further interlinked genetic variants on chromosome 7 (6.06-6.43 Mb region) with complex epistatic genetic interactions impacting multi-dimensional nutritional targets, including complex carbohydrate starch quality, the glycemic index, antioxidant catechin, and rice grain color. Through this nutrigenomics approach rare gene bank accessions possessing genetic variants in bHLH and IPT5 genes were identified through haplotype enrichment. These variants were associated with a low glycemic index, higher catechin levels, elevated total flavonoid contents, and heightened antioxidant activity in the whole grain with elevated anti-cancer properties being confirmed in cancer cell lines. This multi-disciplinary nutrigenomics approach thus allowed us to discover the genetic basis of human health-conferring diversity in the metabolome of brown rice.

The APETALA2 transcription factor LsAP2 regulates seed shape in lettuce

Seeds are major vehicles of propagation and dispersal in plants. A number of transcription factors, including APETALA2 (AP2), play crucial roles during the seed development process in various plant species. However, genes essential for seed development and the regulatory networks that operate during seed development remain unclear in lettuce. Here, we identified a lettuce AP2 (LsAP2) gene that was highly expressed during the early stages of seed development. LsAP2 knockout plants obtained by the CRISPR/Cas9 system were used to explore the biological function of LsAP2. Compared with the wild type, the seeds of Lsap2 mutant plants were longer and narrower, and developed an extended tip at the seed top. After further investigating the structural characteristics of the seeds of Lsap2 mutant plants, we proposed a new function of LsAP2 in seed dispersal. Moreover, we identified several interactors of LsAP2. Our results showed that LsAP2 directly interacted with the lettuce homolog of BREVIPEDICELLUS (LsBP) and promoted the expression of LsBP. Transcriptome analysis revealed that LsAP2 might also be involved in brassinosteroid biosynthesis and signaling pathways. Taken together, our data indicate that LsAP2 has a significant function in regulating seed shape in lettuce.

The B3 domain-containing transcription factor ZmABI19 coordinates expression of key factors required for maize seed development and grain filling

Grain filling in maize (Zea mays) is regulated by a group of spatiotemporally synchronized transcription factors (TFs), but the factors that coordinate their expression remain unknown. We used the promoter of the grain filling-specific TF gene Opaque2 (O2) to screen upstream regulatory factors and identified a B3 domain TF, ZmABI19, that directly binds to the O2 promoter for transactivation. zmabi19 mutants displayed developmental defects in the endosperm and embryo, and mature kernels were opaque and reduced in size. The accumulation of zeins, starch and lipids dramatically decreased in zmabi19 mutants. RNA sequencing revealed an alteration of the nutrient reservoir activity and starch and sucrose metabolism in zmabi19 endosperms, and plant phytohormone signal transduction and lipid metabolism in zmabi19 embryos. Chromatin immunoprecipitation followed by sequencing coupled with differential expression analysis identified 106 high-confidence direct ZmABI19 targets. ZmABI19 directly regulates multiple key grain filling TFs including O2, Prolamine-box binding factor 1, ZmbZIP22, NAC130, and Opaque11 in the endosperm and Viviparous1 in the embryo. A number of phytohormone-related genes were also bound and regulated by ZmABI19. Our results demonstrate that ZmABI19 functions as a grain filling initiation regulator. ZmABI19 roles in coupling early endosperm and embryo development are also discussed.

Genomic imprinted genes in reciprocal hybrid endosperm of Brassica napus

BACKGROUND

Genomic imprinting results in the expression of parent-of-origin-specific alleles in the offspring. Brassica napus is an oil crop with research values in polyploidization. Identification of imprinted genes in B. napus will enrich the knowledge of genomic imprinting in dicotyledon plants.

RESULTS

In this study, we performed reciprocal crosses between B. napus L. cultivars Yangyou 6 (Y6) and Zhongshuang 11 (ZS11) to collect endosperm at 20 and 25 days after pollination (DAP) for RNA-seq. In total, we identified 297 imprinted genes, including 283 maternal expressed genes (MEGs) and 14 paternal expressed genes (PEGs) according to the SNPs between Y6 and ZS11. Only 36 genes (35 MEGs and 1 PEG) were continuously imprinted in 20 and 25 DAP endosperm. We found 15, 2, 5, 3, 10, and 25 imprinted genes in this study were also imprinted in Arabidopsis, rice, castor bean, maize, B. rapa, and other B. napus lines, respectively. Only 26 imprinted genes were specifically expressed in endosperm, while other genes were also expressed in root, stem, leaf and flower bud of B. napus. A total of 109 imprinted genes were clustered on rapeseed chromosomes. We found the LTR/Copia transposable elements (TEs) were most enriched in both upstream and downstream of the imprinted genes, and the TEs enriched around imprinted genes were more than non-imprinted genes. Moreover, the expression of 5 AGLs and 6 pectin-related genes in hybrid endosperm were significantly changed comparing with that in parent endosperm.

CONCLUSION

This research provided a comprehensive identification of imprinted genes in B. napus, and enriched the gene imprinting in dicotyledon plants, which would be useful in further researches on how gene imprinting regulates seed development.