BABY BOOM regulates early embryo and endosperm development

Transcriptome Analysis Revealed the Regulatory Mechanism of DIMBOA Affecting Early Somatic Embryogenesis in Dimocarpus longan Lour

Dimocarpus longan Lour. is an evergreen tree of the genus Longan in the Sapindaceae family, native to tropical and subtropical regions. Longan embryonic development is closely related to fruit set and fruit quality. An in-depth study of the mechanism of longan embryonic development could therefore contribute to the development of the longan industry. DIMBOA is the principal compound representing benzoxazinoids (BXs), and is closely linked to auxin biosynthesis and signal transduction. Auxin is one of the crucial hormones for inducing somatic embryogenesis (SE) in plants. Previous research has shown that DIMBOA promotes morphogenesis in the early somatic embryogenesis of longan, but the specific regulatory mechanism has not yet been clarified. To elucidate the molecular mechanism by which DIMBOA affects early somatic embryogenesis in longan, we chose longan embryogenic cultures grown under 0 mg/L DIMBOA as the control group (the check, CK), and longan embryogenic cultures grown under 0.1 mg/L DIMBOA as the treatment group (D) to be analyzed by transcriptomic sequencing. A total of 478 differentially expressed genes (DEGs) are detected in check vs. D, of which 193 are upregulated and 285 are downregulated. These DEGs are significantly enriched in the biosynthetic and metabolic functions of various substances such as vitamin B6 (VB6) biosynthesis, phenylpropanoid pathways, and carbohydrate metabolism. DIMBOA affects SE processes in longan via TFs, including MYB, ZF, bHLH, LBD, NAC, WRKY, etc. After DIMBOA treatment, the expression of most of the key genes for IAA synthesis was significantly downregulated, VB6 content was significantly reduced, and H2O2 content was significantly increased. Therefore, it is suggested that DIMBOA directly or indirectly affects the H2O2 content through the VB6 metabolic pathway, thereby regulating the endogenous IAA level to modulate the early SE morphogenesis of longan.

To infinity and beyond: recent progress, bottlenecks, and potential of clonal seeds by apomixis

Apomixis - clonal seed production in plants - is a rare yet phylogenetically widespread trait that has recurrently evolved in plants to fix hybrid genotypes over generations. Apomixis is absent from major crop species and has been seen as a holy grail of plant breeding due to its potential to propagate hybrid vigor in perpetuity. Here we exhaustively review recent progress, bottlenecks, and potential in the individual components of gametophytic apomixis (avoidance of meiosis, skipping fertilization by parthenogenesis, autonomous endosperm development), and sporophytic apomixis. The Mitosis instead of Meiosis system has now been successfully set up in three species (Arabidopsis, rice, and tomato), yet significant hurdles remain for universal bioengineering of clonal gametes. Parthenogenesis has been engineered in even more species, yet incomplete penetrance still remains an issue; we discuss the choice of parthenogenesis genes (BABY BOOM, PARTHENOGENESIS, WUSCHEL) and also how to drive egg cell-specific expression. The identification of pathways to engineer autonomous endosperm development would allow fully autonomous seed production, yet here significant challenges remain. The recent achievements in the engineering of synthetic apomixis in rice at high penetrance show great potential and the remaining obstacles toward implementation in this crop are addressed. Overall, the recent practical examples of synthetic apomixis suggest the field is flourishing and implementation in agricultural systems could soon take place.

Regulation of cell cycle in plant gametes: when is the right time to divide?

Cell division is a fundamental process shared across diverse life forms, from yeast to humans and plants. Multicellular organisms reproduce through the formation of specialized types of cells, the gametes, which at maturity enter a quiescent state that can last decades. At the point of fertilization, signalling lifts the quiescent state and triggers cell cycle reactivation. Studying how the cell cycle is regulated during plant gamete development and fertilization is challenging, and decades of research have provided valuable, yet sometimes contradictory, insights. This Review summarizes the current understanding of plant cell cycle regulation, gamete development, quiescence, and fertilization-triggered reactivation.

Transcriptional engineering for value enhancement of oilseed crops: a forward perspective

Plant-derived oils provide 20%-35% of dietary calories and are a primary source of essential omega-6 (linoleic) and omega-3 (α-linolenic) fatty acids. While traditional breeding has significantly increased yields in key oilseed crops like soybean, sunflower, canola, peanut, and cottonseed, overall gains have plateaued over the past few decades. Oilseed crops also experience substantial yield losses in both prime and marginal agricultural areas due to biotic and abiotic stresses and shifting agro-climates. Recent genomic, transcriptomic, and metabolomics research has expanded our understanding of the genetic and physiological control of fatty acid biosynthesis and composition. Many oilseed species have inherent stress-combating mechanisms, including transcription factor regulation. Advances in genome editing tools like CRISPR/Cas9 offer precise genetic modifications, targeting transcription factors and binding sites to enhance desirable traits, such as the nutritional profile and chemical composition of fatty acids. This review explores the application of genome editing in oilseed improvement, covering recent progress, challenges, and future potential to boost yield and oil content. These advancements could play a transformative role in developing resilient, nutritious crop varieties essential for sustainable food security in a changing climate.

Genome-Wide Identification and Evolutionary Analysis of Functional BBM-like Genes in Plant Species

Background/Objectives: BABY BOOM (BBM), a transcription factor from the APETALA2 (AP2) protein family, plays a critical role in somatic embryo induction and apomixis. BBM has now been widely applied to induce apomixis or enhance plant transformation and regeneration efficiency through overexpression or ectopic expression. However, the structural and functional evolutionary history of BBM genes in plants is still not well understood. Methods: The protein sequences of 10 selected plant species were used to locate the branch of BBM-Like by key domain identification and phylogenetic tree construction. The identified BBML genes were used for further conserved motif identification, gene structural analysis, miRNA binding site prediction, cis-acting element prediction, collinear analysis, protein-protein interaction network construction, three-dimensional structure modeling, molecular docking, and expression pattern analysis. Results: A total of 24 BBML proteins were identified from 10 representative plant species. Phylogenetic relationship analysis displayed that BBML proteins from eudicots and monocots were divided into two clusters, with monocots exhibiting a higher number of BBMLs. Gene duplication events indicated that whole genome/segmental duplication were the primary drivers of BBML genes' evolution in the tested species, with purifying selection playing a key role during evolution processes. Comparative analysis of motif, domains, and gene structures revealed that most BBMLs were highly evolutionarily conserved. The expression patterns of BBML genes revealed significant tissue specificity, particularly in the root and embryo. We also constructed protein-protein interaction networks and molecular docking models to identify functional pathways and key amino acid residues of BBML proteins. The functions of BBMLs may differ between monocots and eudicots, as suggested by the functional enrichment of interacting proteins. Conclusions: Our research delved into the molecular mechanism, evolutionary relationships, functional differentiation, and expression patterns of BBML genes across plants, laying the groundwork for further investigations into the molecular properties and biological roles of BBMLs.

Efficient sorghum and maize transformation using a ternary vector system combined with morphogenic regulators

Sorghum bicolor (sorghum) is a vital C4 monocotyledon crop cultivated in arid regions worldwide, valued for its significance in both human and animal nutrition. Despite its agricultural prominence, sorghum research has been hindered by low transformation frequency. In this study, we examined sorghum transformation using the pVS1-VIR2 ternary vector system for Agrobacterium, combined with the morphogenic genes BABY BOOM and WUSCHEL2 and selection using G418. We optimized Agrobacterium-mediated infection, targeting key parameters such as bacterial optical density, co-cultivation time, and temperature. Additionally, an excision-based transformation system enabled us to generate transgenic plants free of morphogenic regulators. The method yielded remarkable transformation frequencies, reaching up to 164.8% based on total isolated plantlets. The same combination of ternary vector, morphogenic genes and geneticin-based selection also resulted in a marked increase in transformation efficiency of the Zea mays (maize) inbred line B104. The potential for genomic editing using this approach positions it as a valuable tool for the development of sorghum and maize varieties that comply with evolving European regulations. Our work marks a significant stride in sorghum biotechnology and holds promise for addressing global food security challenges in a changing climate.

An epiQTL underlying asexual seed formation in Arabidopsis

KEY MESSAGE

The DNA methylation status at an epigenetic quantitative trait locus in the Arabidopsis chromosome 2 is linked to the formation of apomictic-like endosperms. Seed development in most angiosperms is coupled to fertilization of the maternal gametes by two sperm cells. However, apomictic species can reproduce asexually via seeds. This trait is of great agricultural interest, as it would fix complex genotypes and allow for pollen-independent seed production. However, engineering full apomixis requires three independent processes: apomeiosis, parthenogenesis and autonomous endosperm development. While the first two have been successfully engineered in some crops, the formation of autonomous endosperms remains a challenge. Although it is known that this trait is under epigenetic control, such as of DNA methylation, the underlying mechanisms remain mostly undiscovered. Here, using epigenetic recombinant inbred lines, we identified an epigenetic quantitative trait locus in the Arabidopsis chromosome 2, which correlates with permissiveness for the formation of asexual seeds: hypomethylation at this genomic region allows the formation of larger autonomous endosperms. Importantly, the methylation at this locus only correlates with asexual seed size, and not to the size of sexual seeds or that of other organs. With this, we aim to show that screening for epialleles is a promising strategy to uncover loci underlying relevant traits and could pave the way to identifying genes necessary for the engineering of apomixis.

Transcription factor ZmNAC19 promotes embryo development in Arabidopsis thaliana

KEY MESSAGE

Overexpression of ZmNAC19, a NAC transcription factor gene from maize, improves embryo development in transgenic Arabidopsis. NAC proteins are plant-specific transcription factors that are involved in multiple aspects of plant growth, development and stress response. Although functions of many NAC transcription factors have been elucidated, little is known about their roles in seed development. In this study, we report the function of a maize NAC transcription factor ZmNAC19 in seed development. ZmNAC19 is highly expressed in embryos of developing maize seeds. ZmNAC19 localizes to nucleus and exhibits transactivation activity in yeast cells. Overexpression of ZmNAC19 in Arabidopsis significantly increases seed size and seed yield. During 3 to 7 days after flowering, embryos of ZmNAC19-overexpression Arabidopsis lines developed faster compared to Col-0, while no visible differences were detected for their endosperms. Furthermore, overexpression of ZmNAC19 in Arabidopsis leads to increased transcription levels of two embryo development-related genes YUC1 and RGE1, and several elements proven to be binding sites of NAC transcription factors were observed in promoters of these two genes. Taken together, these results suggest that ZmNAC19 acts as a positive regulator in plant embryo development.

Unveiling the imprinted dance: how parental genomes orchestrate seed development and hybrid success

Parental epigenetic asymmetries, which contribute to the monoallelic expression of genes known as imprints, play a critical role in seed development in flowering plants. Primarily, differential DNA methylation patterns and histone modifications on parental alleles form the molecular basis of gene imprinting. Plants predominantly exhibit this non-Mendelian inheritance phenomenon in the endosperm and the early embryo of developing seeds. Imprinting is crucial for regulating nutrient allocation, maintaining seed development, resolving parental conflict, and facilitating evolutionary adaptation. Disruptions in imprinted gene expression, mediated by epigenetic regulators and parental ploidy levels, can lead to endosperm-based hybridization barriers and hybrid dysfunction, ultimately reducing genetic diversity in plant populations. Conversely, imprinting helps maintain genetic stability within plant populations. Imprinted genes likely influence seed development in various ways, including ensuring proper endosperm development, influencing seed dormancy, and regulating seed size. However, the functions of most imprinted genes, the evolutionary significance of imprinting, and the long-term consequences of imprinting disruptions on plant development and adaptation need further exploration. Thus, it is clear that research on imprinting has immense potential for improving our understanding of plant development and ultimately enhancing key agronomic traits. This review decodes the possible genetic and epigenetic regulatory factors underpinning genomic imprinting and their positive and negative consequences on seed development. This study also forecasts the potential implications of exploiting gene imprinting for crop improvement programs.

Haploid induction: an overview of parental factor manipulation during seed formation

In plants, in vivo haploid induction has gained increasing attention for its significant potential applications in crop breeding and genetic research. This strategy reduces the chromosome number in progeny after fertilization, enabling the rapid production of homozygous plants through double haploidization, contrasting with traditional inbreeding over successive generations. Haploidy typically initiates at the onset of seed development, with several key genes identified as paternal or maternal factors that play critical roles during meiosis, fertilization, gamete communication, and chromosome integrity maintenance. The insights gained have led to the development of efficient haploid inducer lines. However, the molecular and genetic mechanisms underlying these factors vary considerably, making it challenging to create broadly applicable haploidy induction systems for plants. In this minireview, we summarize recent discoveries and advances in paternal and maternal haploid induction factors, examining their current understanding and functionalities to further develop efficient haploid inducer systems through the application of parental factor manipulation.

Integrating QTL mapping and transcriptomics to decipher the genetic architecture of sterol metabolism in Brassica napus L

Sterols are secondary metabolites commonly found in rapeseed that play crucial physiological roles in plants and also benefit human health. Consequently, unraveling the genetic basis of sterol synthesis in rapeseed is highly important. In this study, 21 individual sterols as well as total sterol (TS) content were detected in a double haploid (DH) population of Brassica napus, and a total of 24 quantitative trait loci (QTL) and 157 mQTL were identified that were associated with TS and different individual sterols. Time-series transcriptomic analysis showed that the differentially expressed genes (DEGs) involved in sterol and lipid biosynthesis pathways were enriched. Additionally, a regulatory network between sterol-related DEGs and transcription factors (TFs) was established using coexpression analysis. Some candidate genes were identified with the integration of transcriptomic analysis and QTL mapping, and the key candidate gene BnSQS1.C03 was selected for further functional analysis. BnSQS1.C03 demonstrated squalene synthase activity in vitro and increased the TS by 3.8% when overexpressed in Arabidopsis. The present results provide new insights into sterol regulatory pathways and a valuable genetic basis for breeding rapeseed varieties with high sterol content in the future.

LAFL Factors in Seed Development and Phase Transitions

Development is a chain reaction in which one event leads to another until the completion of a life cycle. Phase transitions are milestone events in the cycle of life. LEAFY COTYLEDON1 (LEC1), ABA INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 proteins, collectively known as LAFL, are master transcription factors (TFs) regulating seed and other developmental processes. Since the initial characterization of the LAFL genes, more than three decades of active research has generated tremendous amounts of knowledge about these TFs, whose roles in seed development and germination have been comprehensively reviewed. Recent advances in cell biology with genetic and genomic tools have allowed the characterization of the LAFL regulatory networks in previously challenging tissues at a higher throughput and resolution in reference species and crops. In this review, we provide a holistic perspective by integrating advances at the epigenetic, transcriptional, posttranscriptional, and protein levels to exemplify the spatiotemporal regulation of the LAFL networks in Arabidopsis seed development and phase transitions, and we briefly discuss the evolution of these TF networks.

AtRKD5 inhibits the parthenogenic potential mediated by AtBBM

Parthenogenesis, the development of unfertilized egg cells into embryos, is a key component of apomixis. AtBBM (BABY BOOM), a crucial regulator of embryogenesis in Arabidopsis, possesses the capacity to shift nutritional growth toward reproductive growth. However, the mechanisms underlying AtBBM-induced parthenogenesis remain largely unexplored in dicot plants. Our findings revealed that in order to uphold the order of sexual reproduction, the embryo-specific promoter activity of AtBBM as well as repressors that inhibit its expression in egg cells combine to limiting its ability to induce parthenogenesis. Notably, AtRKD5, a RWP-RK domain-containing (RKD) transcription factor, binds to the 3' end of AtBBM and is identified as one of the inhibitory factors for AtBBM expression in the egg cell. In the atrkd5 mutant, we successfully achieved enhanced ectopic expression of AtBBM in egg cells, resulting in the generation of haploid offspring via parthenogenesis at a rate of 0.28%. Furthermore, by introducing chimeric Arabidopsis and rice BBM genes into the egg cell, we achieved a significant 4.6-fold enhancement in haploid induction through the atdmp8/9 mutant. These findings lay a strong foundation for further exploration of the BBM-mediated parthenogenesis mechanism and the improvement of haploid breeding efficiency mediated by the dmp8/9 mutant.

PLETHORA transcription factors promote early embryo development through induction of meristematic potential

Plants are dependent on divisions of stem cells to establish cell lineages required for growth. During embryogenesis, early division products are considered to be stem cells, whereas during post-embryonic development, stem cells are present in meristems at the root and shoot apex. PLETHORA/AINTEGUMENTA-LIKE (PLT/AIL) transcription factors are regulators of post-embryonic meristem function and are required to maintain stem cell pools. Despite the parallels between embryonic and post-embryonic stem cells, the role of PLTs during early embryogenesis has not been thoroughly investigated. Here, we demonstrate that the PLT regulome in the zygote, and apical and basal cells is in strong congruence with that of post-embryonic meristematic cells. We reveal that out of all six PLTs, only PLT2 and PLT4/BABY BOOM (BBM) are expressed in the zygote, and that these two factors are essential for progression of embryogenesis beyond the zygote stage and first divisions. Finally, we show that other PLTs can rescue plt2 bbm defects when expressed from the PLT2 and BBM promoters, establishing upstream regulation as a key factor in early embryogenesis. Our data indicate that generic PLT factors facilitate early embryo development in Arabidopsis by induction of meristematic potential.

Application of Developmental Regulators for Enhancing Plant Regeneration and Genetic Transformation

Establishing plant regeneration systems and efficient genetic transformation techniques plays a crucial role in plant functional genomics research and the development of new crop varieties. The inefficient methods of transformation and regeneration of recalcitrant species and the genetic dependence of the transformation process remain major obstacles. With the advancement of plant meristematic tissues and somatic embryogenesis research, several key regulatory genes, collectively known as developmental regulators, have been identified. In the field of plant genetic transformation, the application of developmental regulators has recently garnered significant interest. These regulators play important roles in plant growth and development, and when applied in plant genetic transformation, they can effectively enhance the induction and regeneration capabilities of plant meristematic tissues, thus providing important opportunities for improving genetic transformation efficiency. This review focuses on the introduction of several commonly used developmental regulators. By gaining an in-depth understanding of and applying these developmental regulators, it is possible to further enhance the efficiency and success rate of plant genetic transformation, providing strong support for plant breeding and genetic engineering research.

Autonomous differentiation of transgenic cells requiring no external hormone application: the endogenous gene expression and phytohormone behaviors

The ectopic overexpression of developmental regulator (DR) genes has been reported to improve the transformation in recalcitrant plant species because of the promotion of cellular differentiation during cell culture processes. In other words, the external plant growth regulator (PGR) application during the tissue and cell culture process is still required in cases utilizing DR genes for plant regeneration. Here, the effect of Arabidopsis BABY BOOM (BBM) and WUSCHEL (WUS) on the differentiation of tobacco transgenic cells was examined. We found that the SRDX fusion to WUS, when co-expressed with the BBM-VP16 fusion gene, significantly influenced the induction of autonomous differentiation under PGR-free culture conditions, with similar effects in some other plant species. Furthermore, to understand the endogenous background underlying cell differentiation toward regeneration, phytohormone and RNA-seq analyses were performed using tobacco leaf explants in which transgenic cells were autonomously differentiating. The levels of active auxins, cytokinins, abscisic acid, and inactive gibberellins increased as cell differentiation proceeded toward organogenesis. Gene Ontology terms related to phytohormones and organogenesis were identified as differentially expressed genes, in addition to those related to polysaccharide and nitrate metabolism. The qRT-PCR four selected genes as DEGs supported the RNA-seq data. This differentiation induction system and the reported phytohormone and transcript profiles provide a foundation for the development of PGR-free tissue cultures of various plant species, facilitating future biotechnological breeding.

New improvements in grapevine genome editing: high efficiency biallelic homozygous knock-out from regenerated plantlets by using an optimized zCas9i

BACKGROUND

For ten years, CRISPR/cas9 system has become a very useful tool for obtaining site-specific mutations on targeted genes in many plant organisms. This technology opens up a wide range of possibilities for improved plant breeding in the future. In plants, the CRISPR/Cas9 system is mostly used through stable transformation with constructs that allow for the expression of the Cas9 gene and sgRNA. Numerous studies have shown that site-specific mutation efficiency can vary greatly between different plant species due to factors such as plant transformation efficiency, Cas9 expression, Cas9 nucleotide sequence, the addition of intronic sequences, and many other parameters. Since 2016, when the first edited grapevine was created, the number of studies using functional genomic approaches in grapevine has remained low due to difficulties with plant transformation and gene editing efficiency. In this study, we optimized the process to obtain site-specific mutations and generate knock-out mutants of grapevine (Vitis vinifera cv. 'Chardonnay'). Building on existing methods of grapevine transformation, we improved the method for selecting transformed plants at chosen steps of the developing process using fluorescence microscopy.

RESULTS

By comparison of two different Cas9 gene and two different promoters, we increased site-specific mutation efficiency using a maize-codon optimized Cas9 containing 13 introns (zCas9i), achieving up to 100% biallelic mutation in grapevine plantlets cv. 'Chardonnay'. These results are directly correlated with Cas9 expression level.

CONCLUSIONS

Taken together, our results highlight a complete methodology for obtaining a wide range of homozygous knock-out mutants for functional genomic studies and future breeding programs in grapevine.

Haploid rhapsody: the molecular and cellular orchestra of in vivo haploid induction in plants

In planta haploid induction (HI), which reduces the chromosome number in the progeny after fertilization, has garnered increasing attention for its significant potential in crop breeding and genetic research. Despite the identification of several natural and synthetic HI systems in different plant species, the molecular and cellular mechanisms underlying these HI systems remain largely unknown. This review synthesizes the current understanding of HI systems in plants (with a focus on genes and molecular mechanisms involved), including the molecular and cellular interactions which orchestrate the HI process. As most HI systems can function across taxonomic boundaries, we particularly discuss the evidence for conserved mechanisms underlying the process. These include mechanisms involved in preserving chromosomal integrity, centromere function, gamete communication and/or fusion, and maintenance of karyogamy. While significant discoveries and advances on haploid inducer systems have arisen over the past decades, we underscore gaps in understanding and deliberate on directions for further research for a more comprehensive understanding of in vivo HI processes in plants.

Involvement of 5mC DNA demethylation via 5-aza-2'-deoxycytidine in regulating gene expression during early somatic embryo development in white spruce (Picea glauca)

DNA methylation plays a crucial role in the development of somatic embryos (SEs) through the regulation of gene expression. To examine the impact of DNA methylation on gene expression during early SE development in Picea glauca, the demethylation reagent 5-aza-dC (5-aza-2'-deoxycytidine) was employed to modify DNA methylation regions and levels during the pre-maturation stage of somatic embryogenesis. The application of 2.0 µM 5-aza-dC did not induce toxicity to SEs in early development. Following treatment, the global DNA methylation level decreased significantly on the 7th day of pre-maturation and the 1st week of maturation. Methylated DNA immunoprecipitation (MeDIP) sequencing revealed that differentially methylated regions, as analyzed through Gene Ontology (GO), were related to plant development and reproduction and that they were hypomethylated on the 3rd day but hypermethylated on the 7th day in 5-aza-dC-treated embryogenic tissues. These findings indicate that 5-aza-dC treatment positively impacts early SE development, which was inhibited following 7 d of treatment. The expression of MSH7, JMJ14, and CalS10 was associated with DNA methylation, epigenetic regulation, and somatic embryogenesis. Further analysis of methylated regions revealed that the expression profiles of MSH7, JMJ14, and CalS10 were correlated with altered DNA methylation, suggesting DNA methylation at 5 mC may play a role in controlling the expression of these genes and regulating the early development of SEs in P. glauca. This study offers new insights into the regulation of somatic embryogenesis in conifers.

Mutation in Polycomb repressive complex 2 gene OsFIE2 promotes asexual embryo formation in rice

Prevention of autonomous division of the egg apparatus and central cell in a female gametophyte before fertilization ensures successful reproduction in flowering plants. Here we show that rice ovules of Polycomb repressive complex 2 (PRC2) Osfie1 and Osfie2 double mutants exhibit asexual embryo and autonomous endosperm formation at a high frequency, while ovules of single Osfie2 mutants display asexual pre-embryo-like structures at a lower frequency without fertilization. Earlier onset, higher penetrance and better development of asexual embryos in the double mutants compared with those in Osfie2 suggest that the autonomous endosperm facilitated asexual embryo development. Transcriptomic analysis showed that male genome-expressed OsBBM1 and OsWOX8/9 were activated in the asexual embryos. Similarly, the maternal alleles of the paternally expressed imprinted genes were activated in the autonomous endosperm, suggesting that the egg apparatus and central cell convergently adopt PRC2 to maintain the non-dividing state before fertilization, possibly through silencing of the maternal alleles of male genome-expressed genes.

The phenomenon of autonomous endosperm in sexual and apomictic plants

Endosperm is a key nutritive tissue that supports the developing embryo or seedling, and serves as a major nutritional source for human and livestock feed. In sexually-reproducing flowering plants, it generally develops after fertilization. However, autonomous endosperm (AE) formation (i.e. independent of fertilization) is also possible. Recent findings of AE loci/ genes and aberrant imprinting in native apomicts, together with a successful initiation of parthenogenesis in rice and lettuce, have enhanced our understanding of the mechanisms bridging sexual and apomictic seed formation. However, the mechanisms driving AE development are not well understood. This review presents novel aspects related to AE development in sexual and asexual plants underlying stress conditions as the primary trigger for AE. Both application of hormones to unfertilized ovules and mutations that impair epigenetic regulation lead to AE development in sexual Arabidopsis thaliana, which may point to a common pathway for both phenomena. Apomictic-like AE development under experimental conditions can take place due to auxin-dependent gene expression and/or DNA methylation.

Engineering apomixis in crops

Apomixis is an asexual mode of reproduction through seeds where progeny are clones of the mother plants. Naturally apomictic modes of reproduction are found in hundreds of plant genera distributed across more than 30 plant families, but are absent in major crop plants. Apomixis has the potential to be a breakthrough technology by allowing the propagation through seed of any genotype, including F1 hybrids. Here, we have summarized the recent progress toward synthetic apomixis, where combining targeted modifications of both the meiosis and fertilization processes leads to the production of clonal seeds at high frequencies. Despite some remaining challenges, the technology has approached a level of maturity that allows its consideration for application in the field.

Somatic embryo initiation by rice BABY BOOM1 involves activation of zygote-expressed auxin biosynthesis genes

Plant embryogenesis results from the fusion of male and female gametes but can also be induced in somatic cells. The molecular pathways for embryo initiation are poorly understood, especially in monocots. In rice, the male gamete expressed BABY BOOM1 (OsBBM1) transcription factor functions as an embryogenic trigger in the zygote and can also promote somatic embryogenesis when ectopically expressed in somatic tissues. We used gene editing, transcriptome profiling, and chromatin immunoprecipitation to determine the molecular players involved in embryo initiation downstream of OsBBM1. We identify OsYUCCA (OsYUC) auxin biosynthesis genes as direct targets of OsBBM1. Unexpectedly, these OsYUC targets in zygotes are expressed only from the maternal genome, whereas the paternal genome exclusively provides functional OsBBM1 to initiate embryogenesis. Induction of somatic embryogenesis by exogenous auxin requires OsBBM genes and downstream OsYUC targets. Ectopic OsBBM1 initiates somatic embryogenesis without exogenous auxins but requires functional OsYUC genes. Thus, an OsBBM-OsYUC module is a key player for both somatic and zygotic embryogenesis in rice. Zygotic embryo initiation involves a partnership of male and female genomes, through which paternal OsBBM1 activates maternal OsYUC genes. In somatic embryogenesis, exogenous auxin triggers OsBBM1 expression, which then activates endogenous auxin biosynthesis OsYUC genes.

Behavior of Male Gamete Fusogen GCS1/HAP2 and the Regulation in Arabidopsis Double Fertilization

In the sexual reproduction of flowering plants, two independent fertilization events occur almost simultaneously: two identical sperm cells fuse with either the egg cell or the central cell, resulting in embryo and endosperm development to produce a seed. GCS1/HAP2 is a sperm cell membrane protein essential for plasma membrane fusion with both female gametes. Other sperm membrane proteins, DMP8 and DMP9, are more important for egg cell fertilization than that of the central cell, suggesting its regulatory mechanism in GCS1/HAP2-driving gamete membrane fusion. To assess the GCS1/HAP2 regulatory cascade in the double fertilization system of flowering plants, we produced Arabidopsis transgenic lines expressing different GCS1/HAP2 variants and evaluated the fertilization in vivo. The fertilization pattern observed in GCS1_RNAi transgenic plants implied that sperm cells over the amount of GCS1/HAP2 required for fusion on their surface could facilitate membrane fusion with both female gametes. The cytological analysis of the dmp8dmp9 sperm cell arrested alone in an embryo sac supported GCS1/HAP2 distribution on the sperm surface. Furthermore, the fertilization failures with both female gametes were caused by GCS1/HAP2 secretion from the egg cell. These results provided a possible scenario of GCS1/HAP2 regulation, showing a potential scheme for capturing additional GCS1/HAP2-interacting proteins.

The Roads to Haploid Embryogenesis

Although zygotic embryogenesis is usually studied in the field of seed biology, great attention has been paid to the methods used to generate haploid embryos due to their applications in crop breeding. These mainly include two methods for haploid embryogenesis: in vitro microspore embryogenesis and in vivo haploid embryogenesis. Although microspore culture systems and maize haploid induction systems were discovered in the 1960s, little is known about the molecular mechanisms underlying haploid formation. In recent years, major breakthroughs have been made in in vivo haploid induction systems, and several key factors, such as the matrilineal (MTL), baby boom (BBM), domain of unknown function 679 membrane protein (DMP), and egg cell-specific (ECS) that trigger in vivo haploid embryo production in both the crops and Arabidopsis models have been identified. The discovery of these haploid inducers indicates that haploid embryogenesis is highly related to gamete development, fertilization, and genome stability in ealry embryos. Here, based on recent efforts to identify key players in haploid embryogenesis and to understand its molecular mechanisms, we summarize the different paths to haploid embryogenesis, and we discuss the mechanisms of haploid generation and its potential applications in crop breeding. Although these haploid-inducing factors could assist egg cells in bypassing fertilization to initiate embryogenesis or trigger genome elimination in zygotes after fertilization to form haploid embryos, the fertilization of central cells to form endosperms is a prerequisite step for haploid formation. Deciphering the molecular and cellular mechanisms for haploid embryogenesis, increasing the haploid induction efficiency, and establishing haploid induction systems in other crops are critical for promoting the application of haploid technology in crop breeding, and these should be addressed in further studies.

Induction of Somatic Embryogenesis in Plants: Different Players and Focus on WUSCHEL and WUS-RELATED HOMEOBOX (WOX) Transcription Factors

In plants, other cells can express totipotency in addition to the zygote, thus resulting in embryo differentiation; this appears evident in apomictic and epiphyllous plants. According to Haberlandt's theory, all plant cells can regenerate a complete plant if the nucleus and the membrane system are intact. In fact, under in vitro conditions, ectopic embryos and adventitious shoots can develop from many organs of the mature plant body. We are beginning to understand how determination processes are regulated and how cell specialization occurs. However, we still need to unravel the mechanisms whereby a cell interprets its position, decides its fate, and communicates it to others. The induction of somatic embryogenesis might be based on a plant growth regulator signal (auxin) to determine an appropriate cellular environment and other factors, including stress and ectopic expression of embryo or meristem identity transcription factors (TFs). Still, we are far from having a complete view of the regulatory genes, their target genes, and their action hierarchy. As in animals, epigenetic reprogramming also plays an essential role in re-establishing the competence of differentiated cells to undergo somatic embryogenesis. Herein, we describe the functions of WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors in regulating the differentiation-dedifferentiation cell process and in the developmental phase of in vitro regenerated adventitious structures.

Genome-wide characterization of AINTEGUMENTA-LIKE family in Medicago truncatula reveals the significant roles of AINTEGUMENTAs in leaf growth

AINTEGUMENTA-LIKE (AIL) transcription factors are widely studied and play crucial roles in plant growth and development. However, the functions of the AIL family in legume species are largely unknown. In this study, 11 MtAIL genes were identified in the model legume Medicago truncatula, of which four of them are MtANTs. In situ analysis showed that MtANT1 was highly expressed in the shoot apical meristem (SAM) and leaf primordium. Characterization of mtant1 mtant2 mtant3 mtant4 quadruple mutants and MtANT1-overexpressing plants revealed that MtANTs were not only necessary but also sufficient for the regulation of leaf size, and indicated that they mainly function in the regulation of cell proliferation during secondary morphogenesis of leaves in M. truncatula. This study systematically analyzed the MtAIL family at the genome-wide level and revealed the functions of MtANTs in leaf growth. Thus, these genes may provide a potential application for promoting the biomass of legume forages.