RGL2 controls flower development, ovule number and fertility in Arabidopsis

When Size Matters: New Insights on How Seed Size Can Contribute to the Early Stages of Plant Development

The seed habit is the most complex and successful method of sexual reproduction in vascular plants. It represents a remarkable moment in the evolution of plants that afterward spread on land. In particular, seed size had a pivotal role in evolutionary success and agronomic traits, especially in the field of crop domestication. Given that crop seeds constitute one of the primary products for consumption, it follows that seed size represents a fundamental determinant of crop yield. This adaptative feature is strictly controlled by genetic traits from both maternal and zygotic tissues, although seed development and growth are also affected by environmental cues. Despite being a highly exploited topic for both basic and applied research, there are still many issues to be elucidated for developmental biology as well as for agronomic science. This review addresses a number of open questions related to cues that influence seed growth and size and how they influence seed germination. Moreover, new insights on the genetic-molecular control of this adaptive trait are presented.

DELLA proteins positively regulate seed size in Arabidopsis

Human and animal nutrition is mainly based on seeds. Seed size is a key factor affecting seed yield and has thus been one of the primary objectives of plant breeders since the domestication of crop plants. Seed size is coordinately regulated by signals of maternal and zygotic tissues that control the growth of the seed coat, endosperm and embryo. Here, we provide previously unreported evidence for the role of DELLA proteins, key repressors of gibberellin responses, in the maternal control of seed size. The gain-of-function della mutant gai-1 produces larger seeds as a result of an increase in the cell number in ovule integuments. This leads to an increase in ovule size and, in turn, to an increase in seed size. Moreover, DELLA activity promotes increased seed size by inducing the transcriptional activation of AINTEGUMENTA, a genetic factor that controls cell proliferation and organ growth, in the ovule integuments of gai-1. Overall, our results indicate that DELLA proteins are involved in the control of seed size and suggest that modulation of the DELLA-dependent pathway could be used to improve crop yield.

Genome-wide identification, evolution and expression profiles analysis of bHLH gene family in Castanea mollissima

The basic helix-loop-helix (bHLH) transcription factors (TFs) gene family is an important gene family in plants, and participates in regulation of plant apical meristem growth, metabolic regulation and stress resistance. However, its characteristics and potential functions have not been studied in chestnut (Castanea mollissima), an important nut with high ecological and economic value. In the present study, 94 CmbHLHs were identified in chestnut genome, of which 88 were unevenly distributed on chromosomes, and other six were located on five unanchored scaffolds. Almost all CmbHLH proteins were predicted in the nucleus, and subcellular localization demonstrated the correctness of the above predictions. Based on the phylogenetic analysis, all of the CmbHLH genes were divided into 19 subgroups with distinct features. Abundant cis-acting regulatory elements related to endosperm expression, meristem expression, and responses to gibberellin (GA) and auxin were identified in the upstream sequences of CmbHLH genes. This indicates that these genes may have potential functions in the morphogenesis of chestnut. Comparative genome analysis showed that dispersed duplication was the main driving force for the expansion of the CmbHLH gene family inferred to have evolved through purifying selection. Transcriptome analysis and qRT-PCR experiments showed that the expression patterns of CmbHLHs were different in different chestnut tissues, and revealed some members may have potential functions in chestnut buds, nuts, fertile/abortive ovules development. The results from this study will be helpful to understand the characteristics and potential functions of the bHLH gene family in chestnut.

Ovule initiation: the essential step controlling offspring number in Arabidopsis

Seed is the offspring of angiosperms. Plants produce large numbers of seeds to ensure effective reproduction and survival in varying environments. Ovule is a fundamentally important organ and is the precursor of the seed. In Arabidopsis and other plants characterized by multi-ovulate ovaries, ovule initiation determines the maximal ovule number, thus greatly affecting seed number per fruit and seed yield. Investigating the regulatory mechanism of ovule initiation has both scientific and economic significance. However, the genetic and molecular basis underlying ovule initiation remains unclear due to technological limitations. Very recently, rules governing the multiple ovules initiation from one placenta have been identified, the individual functions and crosstalk of phytohormones in regulating ovule initiation have been further characterized, and new regulators of ovule boundary are reported, therefore expanding the understanding of this field. In this review, we present an overview of current knowledge in ovule initiation and summarize the significance of ovule initiation in regulating the number of plant offspring, as well as raise insights for the future study in this field that provide potential routes for the improvement of crop yield.

Overexpression of ABI5 Binding Proteins Suppresses Inhibition of Germination Due to Overaccumulation of DELLA Proteins

Abscisic acid (ABA) and gibberellic acid (GA) antagonistically regulate many aspects of plant growth, including seed dormancy and germination. The effects of these hormones are mediated by a complex network of positive and negative regulators of transcription. The DELLA family of proteins repress GA response, and can promote an ABA response via interactions with numerous regulators, including the ABA-insensitive (ABI) transcription factors. The AFP family of ABI5 binding proteins are repressors of the ABA response. This study tested the hypothesis that the AFPs also interact antagonistically with DELLA proteins. Members of these protein families interacted weakly in yeast two-hybrid and bimolecular fluorescence complementation studies. Overexpression of AFPs in sleepy1, a mutant that over-accumulates DELLA proteins, suppressed DELLA-induced overaccumulation of storage proteins, hyperdormancy and hypersensitivity to ABA, but did not alter the dwarf phenotype of the mutant. The interaction appeared to reflect additive effects of the AFPs and DELLAs, consistent with action in convergent pathways.

Gibberellins regulate ovule number through a DELLA-CUC2 complex in Arabidopsis

Ovule development is a key process for plant reproduction, helping to ensure correct seed production. Several molecular factors and plant hormones such as gibberellins are involved in ovule initiation and development. Gibberellins control ovule development by the destabilization of DELLA proteins, whereas DELLA activity has been shown to act as a positive factor for ovule primordia emergence. But the molecular mechanism by which DELLA acts in ovule primordia initiation remained unknown. In this study we report that DELLA proteins participate in ovule initiation by the formation of a protein complex with the CUC2 transcription factor. The DELLA protein GAI requires CUC2 to promote ovule primordia formation, through the direct GAI-CUC2 interaction in placental cells that would determine the boundary regions between ovules during pistil development. Analysis of GAI-CUC2 interaction and co-localization in the placenta supports this hypothesis. Moreover, molecular analysis identified a subset of the loci for which the GAI protein may act as a transcriptional co-regulator in a CUC2-dependent manner. The DELLA-CUC2 complex is a component of the gene regulatory network controlling ovule primordia initiation in Arabidopsis.

Gynoecium and fruit development in Arabidopsis

Flowering plants produce flowers and one of the most complex floral structures is the pistil or the gynoecium. All the floral organs differentiate from the floral meristem. Various reviews exist on molecular mechanisms controlling reproductive development, but most focus on a short time window and there has been no recent review on the complete developmental time frame of gynoecium and fruit formation. Here, we highlight recent discoveries, including the players, interactions and mechanisms that govern gynoecium and fruit development in Arabidopsis. We also present the currently known gene regulatory networks from gynoecium initiation until fruit maturation.

Resequencing and genome-wide association studies of autotetraploid potato

Potato is the fourth most important food crop in the world. Although with a long history for breeding approaches, genomic information and association between genes and agronomic traits remain largely unknown particularly in autotetraploid potato cultivars, which limit the molecular breeding progression. By resequencing the genome of 108 main cultivar potato accessions with rich genetic diversity and population structure from International Potato Center, with approximate 20-fold coverage, we revealed more than 27 million Single Nucleotide Polymorphisms and ~ 3 million Insertion and Deletions with high quality and accuracy. Domestication analysis and genome-wide association studies (GWAS) identified candidate loci related to photoperiodic flowering time and temperature sensitivity as well as disease resistance, providing informative insights into the selection and domestication of cultivar potato. In addition, GWAS with GWASploy for 25 agronomic traits identified candidate loci by association signals, especially those related to tuber size, small-sized tuber weight and tuber thickness that was also validated by transcriptome analysis. Our study provides a valuable resource that facilitates the elucidation of domestication process as well as the genetic studies and agronomic improvement of autotetraploid potato.

Molecular Network for Regulation of Ovule Number in Plants

In seed-bearing plants, the ovule ("small egg") is the organ within the gynoecium that develops into a seed after fertilization. The gynoecium located in the inner compartment of the flower turns into a fruit. The number of ovules in the ovary determines the upper limit or the potential of seed number per fruit in plants, greatly affecting the final seed yield. Ovule number is an important adaptive characteristic for plant evolution and an agronomic trait for crop improvement. Therefore, understanding the mechanism and pathways of ovule number regulation becomes a significant research aspect in plant science. This review summarizes the ovule number regulators and their regulatory mechanisms and pathways. Specially, an integrated molecular network for ovule number regulation is constructed, in which phytohormones played a central role, followed by transcription factors, enzymes, other protein and micro-RNA. Of them, AUX, BR and CK are positive regulator of ovule number, whereas GA acts negatively on it. Interestingly, many ovule number regulators have conserved functions across several plant taxa, which should be the targets of genetic improvement via breeding or gene editing. Many ovule number regulators identified to date are involved in the diverse biological process, such as ovule primordia formation, ovule initiation, patterning, and morphogenesis. The relations between ovule number and related characteristics/traits especially of gynoecium/fruit size, ovule fertility, and final seed number, as well as upcoming research questions, are also discussed. In summary, this review provides a general overview of the present finding in ovule number regulation, which represents a more comprehensive and in-depth cognition on it.

A novel Arabidopsis gene RGAT1 is required for GA-mediated tapetum and pollen development

The phytohormone gibberellin (GA) is critical for anther development. RGA, a member of the DELLA family of proteins that are central GA signalling repressors, is a key regulator of male fertility in plants. However, the downstream genes in GA-RGA-mediated anther development remain to be characterised. We identified RGA Target 1 (RGAT1), a novel Arabidopsis gene, that functions as an important RGA-regulated target in pollen development. RGAT1 is predominantly expressed in the tapetum and microspores during anther stages 8-11, and can be directly activated by RGA and suppressed by GA in inflorescence apices. Both loss of function and gain of function of RGAT1 led to abnormal tapetum development, resulting in abortive pollen and short siliques. In RGAT1-knockdown and overexpression lines, pollen abortion occurred at stage 10. Loss of RGAT1 function induced the premature degeneration of tapetal cells with defective ER-derived tapetosomes, while RGAT1 overexpression delayed tapetum degeneration. TUNEL assay confirmed that RGAT1 participates in timely tapetal programmed cell death. Moreover, reducing RGAT1 expression partially rescued the tapetal developmental defects in GA-deficient ga1-3 mutant. Our findings revealed that RGAT1 is a direct target of RGA and plays an essential role in GA-mediated tapetum and pollen development.

Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat

GRAS transcription factors play important roles in many processes of plant development as well as abiotic and biotic stress responses. However, little is known about this gene family in bread wheat (Triticum aestivum), one of the most important crops worldwide. The completion of a quality draft genome allows genome-wide detection and evolutionary analysis of the GRAS gene family in wheat. In this study, 188 TaGRAS genes were detected and divided into 12 subfamilies based on phylogenetic analyses: DELLA, DLT, HAM, LISCL, SCL3, SCL4/7, SCR, SHR, PAT1, Os19, Os4 and LAS. Tandem and segmental duplications are the main contributors to the expansion of TaGRAS, which may contribute to the adaptation of wheat to various environmental conditions. A high rate of homoeolog retention during hexaploidization was detected, suggesting the nonredundancy and biological importance of TaGRAS homoeologs. Systematic analyses of TaGRAS indicated the conserved expression pattern and function of the same subfamily during evolution. In addition, we detected five genes belonging to the LISCL subfamily induced by both biotic and abiotic stresses and they may be potential targets for further research through gene editing. Using degradome and ChIP-seq data, we identified the targets of miR171 and histone modifications and further analyzed the contribution of epigenetic modification to the subfunctionalization of TaGRAS. This study laid a foundation for further functional elucidation of TaGRAS genes.

Genome-wide Identification, Evolution and Expression Analysis of Basic Helix-loop-helix (bHLH) Gene Family in Barley (Hordeum vulgare L.)

Background

The basic helix-loop-helix (bHLH) transcription factor is one of the most important gene families in plants, playing a key role in diverse metabolic, physiological, and developmental processes. Although it has been well characterized in many plants, the significance of the bHLH family in barley is not well understood at present.

Methods

Through a genome-wide search against the updated barley reference genome, the genomic organization, evolution and expression of the bHLH family in barley were systematically analyzed.

Results

We identified 141 bHLHs in the barley genome (HvbHLHs) and further classified them into 24 subfamilies based on phylogenetic analysis. It was found that HvbHLHs in the same subfamily shared a similar conserved motif composition and exon-intron structures. Chromosome distribution and gene duplication analysis revealed that segmental duplication mainly contributed to the expansion of HvbHLHs and the duplicated genes were subjected to strong purifying selection. Furthermore, expression analysis revealed that HvbHLHs were widely expressed in different tissues and also involved in response to diverse abiotic stresses. The co-expression network was further analyzed to underpin the regulatory function of HvbHLHs. Finally, 25 genes were selected for qRT-PCR validation, the expression profiles of HvbHLHs showed diverse patterns, demonstrating their potential roles in relation to stress tolerance regulation.

Conclusion

This study reported the genome organization, evolutionary characteristics and expression profile of the bHLH family in barley, which not only provide the targets for further functional analysis, but also facilitate better understanding of the regulatory network bHLH genes involved in stress tolerance in barley.

miR169 and PmRGL2 synergistically regulate the NF-Y complex to activate dormancy release in Japanese apricot (Prunus mume Sieb. et Zucc.)

This study is the first to demonstrate that GA₄-induced dormancy release is associated with the NF-Y complex, which interacts with gibberellin inhibitor RGL2 in Japanese apricot. Seasonal dormancy is not only vital for the survival in cold winter but also affects flowering of temperate fruit trees and the dormancy release depends on the accumulation of the cold temperatures (Chilling requirement-CR). To understand the mechanism of dormancy release in deciduous fruit crops, we compared miRNA sequencing data during the transition stage from paradormancy to dormancy release in the Japanese apricot and found that the miR169 family showed significant differentially up-regulated expression during dormancy induction and was down-regulated during the dormancy release periods. The 5' RACE assay and RT-qPCR validated its target gene NUCLEAR FACTOR-Y subunit A (NF-YA), which exhibited the opposite expression pattern. Further study showed that exogenous GA₄ could inhibit the expression of the gibberellic acid (GA) signal transduction suppressor PmRGL2 (RGA-LIKE 2) and promote the expression of NF-Y. Moreover, the interaction between the NF-Y family and GA inhibitor PmRGL2 was verified by the yeast-two-hybrid (Y2H) system and a bimolecular fluorescence complementarity (BiFC) experiment. These results suggest that synergistic regulation of the NF-Y and PmRGL2 complex leads to the activation of dormancy release induced by GA₄. These findings will help to elucidate the functional and regulatory roles of miR169 and NF-Y complex in seasonal bud dormancy induced by GA in Japanese apricot and provide new insights for the discovery of dormancy release mechanisms in woody plants.

Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis

Ovule development is essential for plant survival, as it allows correct embryo and seed development upon fertilization. The female gametophyte is formed in the central area of the nucellus during ovule development, in a complex developmental programme that involves key regulatory genes and the plant hormones auxins and brassinosteroids. Here we provide novel evidence of the role of gibberellins (GAs) in the control of megagametogenesis and embryo sac development, via the GA-dependent degradation of RGA-LIKE1 (RGL1) in the ovule primordia. YPet-rgl1Δ17 plants, which express a dominant version of RGL1, showed reduced fertility, mainly due to altered embryo sac formation that varied from partial to total ablation. YPet-rgl1Δ17 ovules followed normal development of the megaspore mother cell, meiosis, and formation of the functional megaspore, but YPet-rgl1Δ17 plants had impaired mitotic divisions of the functional megaspore. This phenotype is RGL1-specific, as it is not observed in any other dominant mutants of the DELLA proteins. Expression analysis of YPet-rgl1Δ17 coupled to in situ localization of bioactive GAs in ovule primordia led us to propose a mechanism of GA-mediated RGL1 degradation that allows proper embryo sac development. Taken together, our data unravel a novel specific role of GAs in the control of female gametophyte development.

Phytohormone signaling mechanisms and genetic methods for their modulation and detection

Phytohormones enable plants to regulate their development, growth and physiology according to the environmental requirements. Knowledge about the underlying signaling mechanisms, combined with the ability to pharmacologically or genetically manipulate phytohormone responses is steadily being incorporated into modern plant biology research and agriculture. This knowledge also enabled the development of genetically encoded phytohormone indicators that allow the tracking of spatiotemporal phytohormone dynamics and signaling processes in vivo. This review aims to provide an overview about core phytohormone signaling mechanisms, and about genetic tools for the manipulation and in vivo tracking of phytohormone actions.

Gynoecium size and ovule number are interconnected traits that impact seed yield

Angiosperms form the largest group of land plants and display an astonishing diversity of floral structures. The development of flowers greatly contributed to the evolutionary success of the angiosperms as they guarantee efficient reproduction with the help of either biotic or abiotic vectors. The female reproductive part of the flower is the gynoecium (also called pistil). Ovules arise from meristematic tissue within the gynoecium. Upon fertilization, these ovules develop into seeds while the gynoecium turns into a fruit. Gene regulatory networks involving transcription factors and hormonal communication regulate ovule primordium initiation, spacing on the placenta, and development. Ovule number and gynoecium size are usually correlated and several genetic factors that impact these traits have been identified. Understanding and fine-tuning the gene regulatory networks influencing ovule number and pistil length open up strategies for crop yield improvement, which is pivotal in light of a rapidly growing world population. In this review, we present an overview of the current knowledge of the genes and hormones involved in determining ovule number and gynoecium size. We propose a model for the gene regulatory network that guides the developmental processes that determine seed yield.

Cryptochrome-mediated hypocotyl phototropism was regulated antagonistically by gibberellic acid and sucrose in Arabidopsis

Both phototropins (phot1 and phot2) and cryptochromes (cry1 and cry2) were proven as the Arabidopsis thaliana blue light receptors. Phototropins predominately function in photomovement, and cryptochromes play a role in photomorphogenesis. Although cryptochromes have been proposed to serve as positive modulators of phototropic responses, the underlying mechanism remains unknown. Here, we report that depleting sucrose from the medium or adding gibberellic acids (GAs) can partially restore the defects in phototropic curvature of the phot1 phot2 double mutants under high-intensity blue light; this restoration does not occur in phot1 phot2 cry1 cry2 quadruple mutants and nph3 (nonphototropic hypocotyl 3) mutants which were impaired phototropic response in sucrose-containing medium. These results indicate that GAs and sucrose antagonistically regulate hypocotyl phototropism in a cryptochromes dependent manner, but it showed a crosstalk with phototropin signaling on NPH3. Furthermore, cryptochromes activation by blue light inhibit GAs synthesis, thus stabilizing DELLAs to block hypocotyl growth, which result in the higher GAs content in the shade side than the lit side of hypocotyl to support the asymmetric growth of hypocotyl. Through modulation of the abundance of DELLAs by sucrose depletion or added GAs, it revealed that cryptochromes have a function in mediating phototropic curvature.

Manipulating Gibberellin Control Over Growth and Fertility as a Possible Target for Managing Wild Radish Weed Populations in Cropping Systems

Wild radish is a major weed of Australian cereal crops. A rapid establishment, fast growth, and abundant seed production are fundamental to its success as an invasive species. Wild radish has developed resistance to a number of commonly used herbicides increasing the problem. New innovative approaches are needed to control wild radish populations. Here we explore the possibility of pursuing gibberellin (GA) biosynthesis as a novel molecular target for controlling wild radish, and in doing so contribute new insights into GA biology. By characterizing ga 3-oxidase (ga3ox) mutants in Arabidopsis, a close taxonomic relative to wild radish, we showed that even mild GA deficiencies cause considerable reductions in growth and fecundity. This includes an explicit requirement for GA biosynthesis in successful female fertility. Similar defects were reproducible in wild radish via chemical inhibition of GA biosynthesis, confirming GA action as a possible new target for controlling wild radish populations. Two possible targeting approaches are considered; the first would involve developing a species-specific inhibitor that selectively inhibits GA production in wild radish over cereal crops. The second, involves making crop species insensitive to GA repression, allowing the use of existing broad spectrum GA inhibitors to control wild radish populations. Toward the first concept, we cloned and characterized two wild radish GA3OX genes, identifying protein differences that appear sufficient for selective inhibition of dicot over monocot GA3OX activity. We developed a novel yeast-based approach to assay GA3OX activity as part of the molecular characterization, which could be useful for future screening of inhibitory compounds. For the second approach, we demonstrated that a subset of GA associated sln1/Rht-1 overgrowth mutants, recently generated in cereals, are insensitive to GA reductions brought on by the general GA biosynthesis inhibitor, paclobutrazol. The location of these mutations within sln1/Rht-1, offers additional insight into the functional domains of these important GA signaling proteins. Our early assessment suggests that targeting the GA pathway could be a viable inclusion into wild radish management programs that warrants further investigation. In drawing this conclusion, we provided new insights into GA regulated reproductive development and molecular characteristics of GA metabolic and signaling proteins.

An Improved Recombineering Toolset for Plants

Gene functional studies often rely on the expression of a gene of interest as transcriptional and translational fusions with specialized tags. Ideally, this is done in the native chromosomal contexts to avoid potential misexpression artifacts. Although recent improvements in genome editing have made it possible to directly modify the target genes in their native chromosomal locations, classical transgenesis is still the preferred experimental approach chosen in most gene tagging studies because of its time efficiency and accessibility. We have developed a recombineering-based tagging system that brings together the convenience of the classical transgenic approaches and the high degree of confidence in the results obtained by direct chromosomal tagging using genome-editing strategies. These simple, scalable, customizable recombineering toolsets and protocols allow a variety of genetic modifications to be generated. In addition, we developed a highly efficient recombinase-mediated cassette exchange system to facilitate the transfer of the desired sequences from a bacterial artificial chromosome clone to a transformation-compatible binary vector, expanding the use of the recombineering approaches beyond Arabidopsis (Arabidopsis thaliana). We demonstrated the utility of this system by generating more than 250 whole-gene translational fusions and 123 Arabidopsis transgenic lines corresponding to 62 auxin-related genes and characterizing the translational reporter expression patterns for 14 auxin biosynthesis genes.