Integration of epigenetic and genetic controls of seed size by cytokinin in Arabidopsis

Insights into dynamic coenocytic endosperm development: Unraveling molecular, cellular, and growth complexity

The endosperm, a product of double fertilization, is one of the keys to the evolution and success of angiosperms in conquering the land. While there are differences in endosperm development among flowering plants, the most common form is coenocytic growth, where the endosperm initially undergoes nuclear division without cytokinesis and eventually becomes cellularized. This complex process requires interplay among networks of transcription factors such as MADS-box, auxin response factors (ARFs), and phytohormones. The role of cytoskeletal elements in shaping the coenocytic endosperm and influencing seed growth also becomes evident. This review offers a recent understanding of the molecular and cellular dynamics in coenocytic endosperm development and their contributions to the final seed size.

OsLCD3 interacts with OsSAMS1 to regulate grain size via ethylene/polyamine homeostasis control

A fundamental question in developmental biology is how to regulate grain size to improve crop yields. Despite this, little is still known about the genetics and molecular mechanisms regulating grain size in crops. Here, we provide evidence that a putative protein kinase-like (OsLCD3) interacts with the S-adenosyl-L-methionine synthetase 1 (OsSAMS1) and determines the size and weight of grains. OsLCD3 mutation (lcd3) significantly increased grain size and weight by promoting cell expansion in spikelet hull, whereas its overexpression caused negative effects, suggesting that grain size was negatively regulated by OsLCD3. Importantly, lcd3 and OsSAMS1 overexpression (SAM1OE) led to large and heavy grains, with increased ethylene and decreased polyamines production. Based on genetic analyses, it appears that OsLCD3 and OsSAMS1 control rice grain size in part by ethylene/polyamine homeostasis. The results of this study provide a genetic and molecular understanding of how the OsLCD3-OsSAMS1 regulatory module regulates grain size, suggesting that ethylene/polyamine homeostasis is an appropriate target for improving grain size and weight.

MtPIN4 plays critical roles in amino acid biosynthesis and metabolism of seed in Medicago truncatula

The regulation of seed development is critical for determining crop yield. Auxins are vital phytohormones that play roles in various aspects of plant growth and development. However, its role in amino acid biosynthesis and metabolism in seeds is not fully understood. In this study, we identified a mutant with small seeds through forward genetic screening in Medicago truncatula. The mutated gene encodes MtPIN4, an ortholog of PIN1. Using molecular approaches and integrative omics analyses, we discovered that auxin and amino acid content significantly decreased in mtpin4 seeds, highlighting the role of MtPIN4-mediated auxin distribution in amino acid biosynthesis and metabolism. Furthermore, genetic analysis revealed that the three orthologs of PIN1 have specific and overlapping functions in various developmental processes in M. truncatula. Our findings emphasize the significance of MtPIN4 in seed development and offer insights into the molecular mechanisms governing the regulation of seed size in crops. This knowledge could be applied to enhance crop quality by targeted manipulation of seed protein regulatory pathways.

Phenotypic characterization and candidate gene analysis of a short kernel and brassinosteroid insensitive mutant from hexaploid oat (Avena sativa)

In an ethyl methanesulfonate oat (Avena sativa) mutant population we have found a mutant with striking differences to the wild-type (WT) cv. Belinda. We phenotyped the mutant and compared it to the WT. The mutant was crossed to the WT and mapping-by-sequencing was performed on a pool of F2 individuals sharing the mutant phenotype, and variants were called. The impacts of the variants on genes present in the reference genome annotation were estimated. The mutant allele frequency distribution was combined with expression data to identify which among the affected genes was likely to cause the observed phenotype. A brassinosteroid sensitivity assay was performed to validate one of the identified candidates. A literature search was performed to identify homologs of genes known to be involved in seed shape from other species. The mutant had short kernels, compact spikelets, altered plant architecture, and was found to be insensitive to brassinosteroids when compared to the WT. The segregation of WT and mutant phenotypes in the F2 population was indicative of a recessive mutation of a single locus. The causal mutation was found to be one of 123 single-nucleotide polymorphisms (SNPs) spanning the entire chromosome 3A, with further filtering narrowing this down to six candidate genes. In-depth analysis of these candidate genes and the brassinosteroid sensitivity assay suggest that a Pro303Leu substitution in AVESA.00010b.r2.3AG0419820.1 could be the causal mutation of the short kernel mutant phenotype. We identified 298 oat proteins belonging to orthogroups of previously published seed shape genes, with AVESA.00010b.r2.3AG0419820.1 being the only of these affected by a SNP in the mutant. The AVESA.00010b.r2.3AG0419820.1 candidate is functionally annotated as a GSK3/SHAGGY-like kinase with homologs in Arabidopsis, wheat, barley, rice, and maize, with several of these proteins having known mutants giving rise to brassinosteroid insensitivity and shorter seeds. The substitution in AVESA.00010b.r2.3AG0419820.1 affects a residue with a known gain-of function substitution in Arabidopsis BRASSINOSTEROID-INSENSITIVE2. We propose a gain-of-function mutation in AVESA.00010b.r2.3AG0419820.1 as the most likely cause of the observed phenotype, and name the gene AsGSK2.1. The findings presented here provide potential targets for oat breeders, and a step on the way towards understanding brassinosteroid signaling, seed shape and nutrition in oats.

Two imprinted genes primed by DEMETER in the central cell and activated by WRKY10 in the endosperm

The early development of the endosperm is crucial for balancing the allocation of maternal nutrients to offspring. This process is believed to be evolutionarily associated with genomic imprinting, resulting in parentally biased allelic gene expression. Beyond FertilizationIndependentSeed (FIS) genes, the number of imprinted genes involved in early endosperm development and seed size determination remains limited. This study introduces two early endosperm-expressed HAIKU (IKU) downstream Candidate F-box 1 (ICF1) and ICF2, as maternally expressed imprinted genes (MEGs). Although these genes are also demethylated by DEMETER (DME) in the central cell, their activation differs from the direct DME-mediated activation seen in classical MEGs such as the FIS genes. Instead, ICF maternal alleles carry pre-established hypomethylation in their promoters, priming them for activation by the WRKY10 transcription factor in the endosperm. On the contrary, paternal alleles are predominantly suppressed by CG methylation. Furthermore, we find that ICF genes partially contribute to the small seed size observed in iku mutants. Our discovery reveals a two-step regulatory mechanism that highlights the important role of conventional transcription factors in the activation of imprinted genes, which was previously not fully recognized. Therefore, the mechanism provides a new dimension to understand the transcriptional regulation of imprinting in plant reproduction and development.

Analysis of Genetic Diversity in Adzuki Beans (Vigna angularis): Insights into Environmental Adaptation and Early Breeding Strategies for Yield Improvement

Adzuki beans are widely cultivated in East Asia and are one of the earliest domesticated crops. In order to gain a deeper understanding of the genetic diversity and domestication history of adzuki beans, we conducted Genotyping by Sequencing (GBS) analysis on 366 landraces originating from Korea, China, and Japan, resulting in 6586 single-nucleotide polymorphisms (SNPs). Population structure analysis divided these 366 landraces into three subpopulations. These three subpopulations exhibited distinctive distributions, suggesting that they underwent extended domestication processes in their respective regions of origin. Phenotypic variance analysis of the three subpopulations indicated that the Korean-domesticated subpopulation exhibited significantly higher 100-seed weights, the Japanese-domesticated subpopulation showed significantly higher numbers of grains per pod, and the Chinese-domesticated subpopulation displayed significantly higher numbers of pods per plant. We speculate that these differences in yield-related traits may be attributed to varying emphases placed by early breeders in these regions on the selection of traits related to yield. A large number of genes related to biotic/abiotic stress resistance and defense were found in most quantitative trait locus (QTL) for yield-related traits using genome-wide association studies (GWAS). Genomic sliding window analysis of Tajima's D and a genetic differentiation coefficient (Fst) revealed distinct domestication selection signatures and genotype variations on these QTLs within each subpopulation. These findings indicate that each subpopulation would have been subjected to varied biotic/abiotic stress events in different origins, of which these stress events have caused balancing selection differences in the QTL of each subpopulation. In these balancing selections, plants tend to select genotypes with strong resistance under biotic/abiotic stress, but reduce the frequency of high-yield genotypes to varying degrees. These biotic/abiotic stressors impact crop yield and may even lead to selection purging, resulting in the loss of several high-yielding genotypes among landraces. However, this also fuels the flow of crop germplasms. Overall, balancing selection appears to have a more significant impact on the three yield-related traits compared to breeder-driven domestication selection. These findings are crucial for understanding the impact of domestication selection history on landraces and yield-related traits, aiding in the improvement of adzuki bean varieties.

ZjWRKY23 and ZjWRKY40 Promote Fruit Size Enlargement by Targeting and Downregulating Cytokinin Oxidase/Dehydrogenase 5 Expression in Chinese Jujube

Fruit size is crucial for fruit trees, as it contributes to both quality and yield. However, the underlying mechanism of fruit size regulation remains largely unknown. Taking advantage of using a fruit double-sized bud mutant of Chinese jujube, "Jinkuiwang" and its wild type, "Jinsixiaozao", we carried out a comprehensive study on the mechanism of fruit size development in jujube. Using weighted gene coexpression network analyses, a number of candidate regulators for fruit size including those involved in hormonal signaling pathways, transcription factors, and heat shock proteins were identified. A hub gene named cytokinin oxidase/dehydrogenase 5 (ZjCKX5), responsible for cytokinin degradation, was found to play a negative role in regulating fruit size development, and overexpressing ZjCKX5 in tomato and Arabidopsis resulted in much smaller fruits and dwarf plants. Furthermore, another two hub genes, ZjWRKY23 and ZjWRKY40 transcription factors, were found to participate in fruit size regulation by targeting and downregulating the ZjCKX5 expression. Overexpressing ZjWRKY23 or ZjWRKY40 in tomato led to much larger fruits and promoted plant architecture. Based on these results, a molecular framework for jujube fruit size regulation, namely, ZjWRKY-ZjCKX5 module, was proposed. This study provides a new insight into the molecular networks underlying fruit size regulation.

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.

The transcription factor BnaWRKY10 regulates cytokinin dehydrogenase BnaCKX2 to control cytokinin distribution and seed size in Brassica napus

Cytokinins (CKs) are phytohormones that promote cell division and differentiation. However, the regulation of CK distribution and homeostasis in Brassica napus is poorly understood. Here, the endogenous CKs were first quantified by LC-ESI-MS/MS in rapeseed tissues and visualized by TCSn::GUS reporter lines. Interestingly, the cytokinin oxidase/dehydrogenase BnaCKX2 homologs were mainly expressed in reproductive organs. Subsequently, the quadruple mutants of the four BnaCKX2 homologs were generated. Endogenous CKs were increased in the seeds of the BnaCKX2 quadruple mutants, resulting in a significantly reduced seed size. In contrast, overexpression of BnaA9.CKX2 resulted in larger seeds, probably by delaying endosperm cellularization. Furthermore, the transcription factor BnaC6.WRKY10b, but not BnaC6.WRKY10a, positively regulated BnaA9.CKX2 expression by binding directly to its promoter region. Overexpression of BnaC6.WRKY10b rather than BnaC6.WRKY10a resulted in lower concentration of CKs and larger seeds by activating BnaA9.CKX2 expression, indicating that the functional differentiation of BnaWRKY10 homologs might have occurred during B. napus evolution or domestication. Notably, the haploid types of BnaA9.CKX2 were associated with 1000-seed weight in the natural B. napus population. Overall, the study reveals the distribution of CKs in B. napus tissues, and shows that BnaWRKY10-mediated BnaCKX2 expression is essential for seed size regulation, providing promising targets for oil crop improvement.

Histone methylation readers MRG1/MRG2 interact with the transcription factor TCP14 to positively modulate cytokinin sensitivity in Arabidopsis

Cytokinins influence many aspects of plant growth and development. Although cytokinin biosynthesis and signaling have been well studied in planta, little is known about the regulatory effects of epigenetic modifications on the cytokinin response. Here, we reveal that mutations to Morf Related Gene (MRG) proteins MRG1/MRG2, which are readers of trimethylated histone H3 lysine 4 and lysine 36 (H3K4me3 and H3K36me3), result in cytokinin hyposensitivity during various developmental processes, including callus induction and root and seedling growth inhibition. Similar to the mrg1 mrg2 mutant, plants with a defective AtTCP14, which belongs to the TEOSINTE BRANCHED, CYCLOIDEA, AND PROLIFERATING CELL FACTOR (TCP) transcription factor family, are insensitive to cytokinin. Furthermore, the transcription of several genes related to cytokinin signaling pathway is altered. Specifically, the expression of Arabidopsis thalianaHISTIDINE-CONTAINING PHOSPHOTRANSMITTER PROTEIN 2 (AHP2) decreases significantly in the mrg1 mrg2 and tcp14-2 mutants. We also confirm the interaction between MRG2 and TCP14 in vitro and in vivo. Thus, MRG2 and TCP14 can be recruited to AHP2 after recognizing H3K4me3/H3K36me3 markers and promote the histone-4 lysine-5 acetylation to further enhance AHP2 expression. In summary, our research elucidate a previously unknown mechanism mediating the effects of MRG proteins on the magnitude of the cytokinin response.

Laser capture microdissection-based spatiotemporal transcriptomes uncover regulatory networks during seed abortion in seedless Ponkan (Citrus reticulata)

Seed abortion is an important process in the formation of seedless characteristics in citrus fruits. However, the molecular regulatory mechanism underlying citrus seed abortion is poorly understood. Laser capture microdissection-based RNA-seq combined with Pacbio-seq was used to profile seed development in the Ponkan cultivars 'Huagan No. 4' (seedless Ponkan) (Citrus reticulata) and 'E'gan No. 1' (seeded Ponkan) (C. reticulata) in two types of seed tissue across three developmental stages. Through comparative transcriptome and dynamic phytohormone analyses, plant hormone signal, cell division and nutrient metabolism-related processes were revealed to play critical roles in the seed abortion of 'Huagan No. 4'. Moreover, several genes may play indispensable roles in seed abortion of 'Huagan No. 4', such as CrWRKY74, CrWRKY48 and CrMYB3R4. Overexpression of CrWRKY74 in Arabidopsis resulted in severe seed abortion. By analyzing the downstream regulatory network, we further determined that CrWRKY74 participated in seed abortion regulation by inducing abnormal programmed cell death. Of particular importance is that a preliminary model was proposed to depict the regulatory networks underlying seed abortion in citrus. The results of this study provide novel insights into the molecular mechanism across citrus seed development, and reveal the master role of CrWRKY74 in seed abortion of 'Huagan No. 4'.

Molecular Network for Regulation of Seed Size in Plants

The size of seeds is particularly important for agricultural development, as it is a key trait that determines yield. It is controlled by the coordinated development of the integument, endosperm, and embryo. Large seeds are an important way of improving the ultimate "sink strength" of crops, providing more nutrients for early plant growth and showing certain tolerance to abiotic stresses. There are several pathways for regulating plant seed size, including the HAIKU (IKU) pathway, ubiquitin-proteasome pathway, G (Guanosine triphosphate) protein regulatory pathway, mitogen-activated protein kinase (MAPK) pathway, transcriptional regulators pathway, and phytohormone regulatory pathways including the auxin, brassinosteroid (BR), gibberellin (GA), jasmonic acid (JA), cytokinin (CK), Abscisic acid (ABA), and microRNA (miRNA) regulatory pathways. This article summarizes the seed size regulatory network and prospective ways of improving yield. We expect that it will provide a valuable reference to researchers in related fields.

Control of ovule development in Vitis vinifera by VvMADS28 and interacting genes

Seedless grapes are increasingly popular throughout the world, and the development of seedless varieties is a major breeding goal. In this study, we demonstrate an essential role for the grapevine MADS-box gene VvMADS28 in morphogenesis of the ovule. We found that VvMADS28 mRNA accumulated in the ovules of a seeded cultivar, 'Red Globe', throughout the course of ovule and seed development, especially within the integument/seed coat. In contrast, in the seedless cultivar 'Thompson Seedless', VvMADS28 was expressed only weakly in ovules, and this was associated with increased levels of histone H3 lysine 27 trimethylation (H3K27me3) within the VvMADS28 promoter region. RNAi-mediated transient suppression of VvMADS28 expression in 'Red Globe' led to reduced seed size associated with inhibition of episperm and endosperm cell development. Heterologous overexpression of VvMADS28 in transgenic tomatoes interfered with sepal development and resulted in smaller fruit but did not obviously affect seed size. Assays in yeast cells showed that VvMADS28 is subject to regulation by the transcription factor VvERF98, and that VvMADS28 could interact with the Type I/ Mβ MADS-domain protein VvMADS5. Moreover, through DNA-affinity purification-sequencing (DAP-seq), we found that VvMADS28 protein specifically binds to the promoter of the grapevine WUSCHEL (VvWUS) gene, suggesting that maintenance of the VvMADS28-VvMADS5 dimer and VvWUS expression homeostasis influences seed development. Taken together, our results provide insight into regulatory mechanisms of ovule and seed development associated with VvMADS28.

Functions of WRKYs in plant growth and development

As sessile organisms, plants must overcome various stresses. Accordingly, they have evolved several plant-specific growth and developmental processes. These plant processes may be related to the evolution of plant-specific protein families. The WRKY transcription factors originated in eukaryotes and expanded in plants, but are not present in animals. Over the past two decades, there have been many studies on WRKYs in plants, with much of the research concentrated on their roles in stress responses. Nevertheless, recent findings have revealed that WRKYs are also required for seed dormancy and germination, postembryonic morphogenesis, flowering, gametophyte development, and seed production. Thus, WRKYs may be important for plant adaptations to a sessile lifestyle because they simultaneously regulate stress resistance and plant-specific growth and development.

Genetic Localization and Homologous Genes Mining for Barley Grain Size

Grain size is an important agronomic trait determining barley yield and quality. An increasing number of QTLs (quantitative trait loci) for grain size have been reported due to the improvement in genome sequencing and mapping. Elucidating the molecular mechanisms underpinning barley grain size is vital for producing elite cultivars and accelerating breeding processes. In this review, we summarize the achievements in the molecular mapping of barley grain size over the past two decades, highlighting the results of QTL linkage analysis and genome-wide association studies. We discuss the QTL hotspots and predict candidate genes in detail. Moreover, reported homologs that determine the seed size clustered into several signaling pathways in model plants are also listed, providing the theoretical basis for mining genetic resources and regulatory networks of barley grain size.

Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity

Both phytohormone signaling and epigenetic mechanisms have long been known to play crucial roles in plant development and plasticity in response to ambient stimuli. Indeed, diverse signaling pathways mediated by phytohormones and epigenetic processes integrate multiple upstream signals to regulate various plant traits. Emerging evidence indicates that phytohormones and epigenetic processes interact at multiple levels. In this review, we summarize the current knowledge of the interplay between phytohormones and epigenetic processes from the perspective of phytohormone biology. We also review chemical regulators used in epigenetic studies and propose strategies for developing novel regulators using multidisciplinary approaches.

Integration of Auxin, Brassinosteroid and Cytokinin in the Regulation of Rice Yield

Crop varieties with a high yield are most desirable in the present context of the ever-growing human population. Mostly, the yield traits are governed by a complex of numerous molecular and genetic facets modulated by various quantitative trait loci (QTLs). With the identification and molecular characterizations of yield-associated QTLs over recent years, the central role of phytohormones in regulating plant yield is becoming more apparent. Most often, different groups of phytohormones work in close association to orchestrate yield attributes. Understanding this cross talk would thus provide new venues for phytohormone pyramiding by editing a single gene or QTL(s) for yield improvement. Here, we review a few important findings to integrate the knowledge on the roles of auxin, brassinosteroid and cytokinin and how a single gene or a QTL could govern cross talk among multiple phytohormones to determine the yield traits.

Fruit shape loci sun, ovate, fs8.1 and their interactions affect seed size and shape in tomato

Seed size and shape are not only critical for plant reproduction and dispersal, but also important agronomic traits. Tomato fruit shape loci sun, ovate and fs8.1 regulate the morphology of fruit, flower, leaf and stem, and recently their functions in seed morphogenesis have also been noticed. However, mechanism underlying seed morphology variation has not been systematically investigated yet. Thus, using the near isogenic lines (NILs) harboring one, two or three of the fruit shape loci, histological, physiological and transcriptional bases of seed morphology change have been studied. sun and ovate showed potential abilities in decreasing seed size, whereas, fs8.1 had a potential ability in increasing this parameter. Interactions between two loci and the interaction among three loci all led to significant decrease of seed size. All the loci significantly down-regulated seed shape index (SSI), except for sun/fs8.1 double NIL, which resulted in the reductions in both seed length and width and finally led to a decreased trend of SSI. Histologically, seed morphological changes were mainly attributed to the cell number variations. Transcriptional and physiological analyses discovered that phytohormone-, cytoskeleton- as well as sugar transportation- and degradation-related genes were involved in the regulation of seed morphology by the fruit shape loci.

Role of cytokinins in seed development in pulses and oilseed crops: Current status and future perspective

Cytokinins constitutes a vital group of plant hormones regulating several developmental processes, including growth and cell division, and have a strong influence on grain yield. Chemically, they are the derivatives of adenine and are the most complex and diverse group of hormones affecting plant physiology. In this review, we have provided a molecular understanding of the role of cytokinins in developing seeds, with special emphasis on pulses and oilseed crops. The importance of cytokinin-responsive genes including cytokinin oxidases and dehydrogenases (CKX), isopentenyl transferase (IPT), and cytokinin-mediated genetic regulation of seed size are described in detail. In addition, cytokinin expression in germinating seeds, its biosynthesis, source-sink dynamics, cytokinin signaling, and spatial expression of cytokinin family genes in oilseeds and pulses have been discussed in context to its impact on increasing economy yields. Recently, it has been shown that manipulation of the cytokinin-responsive genes by mutation, RNA interference, or genome editing has a significant effect on seed number and/or weight in several crops. Nevertheless, the usage of cytokinins in improving crop quality and yield remains significantly underutilized. This is primarily due to the multigene control of cytokinin expression. The information summarized in this review will help the researchers in innovating newer and more efficient ways of manipulating cytokinin expression including CKX genes with the aim to improve crop production, specifically of pulses and oilseed crops.

Ancestral function but divergent epigenetic regulation of HAIKU2 reveals routes of seed developmental evolution

Evolution is driven by various mechanisms. A directional increase in the embryo to endosperm ratio is an evolutionary trend within the angiosperms. The endosperm constitutes a major portion of the seed volume in Poales and some dicots. However, in other dicots such as Arabidopsis and soybean, the endosperm proliferates early, followed by embryo growth to replace the endosperm. The Arabidopsis leucine-rich repeat receptor protein kinase AtHAIKU2 (AtIKU2) is a key regulator of early endosperm proliferation. In this study, we found that IKU2s from Brachypodium, rice, and soybean can complement the abnormal seed developmental phenotype of Atiku2, while AtIKU2 also rescues the defective endosperm proliferation in the Brachypodium BdIKU2 knockout mutant seeds. AtIKU2 and soybean GmIKU2 are actively expressed a few days after fertilization. Thereafter, expression of AtIKU2 is suppressed by the FIS-PRC2 complex-mediated H3K27me3. The soybean GmIKU2 locus is also enriched with H3K27me3 marks. The histone methyltransferase AtMEA is unique to Brassicaceae, but one GmSWN in soybean plays a similar role in seed development as AtMEA. By contrast, the BdIKU2 and rice OsIKU2 loci are continuously expressed and are devoid of H3K27me3 marks. Taken together, these results suggest that IKU2 genes retain an ancestral function, but the duration of their expression that is controlled by PRC2-mediated epigenetic silencing contributes to silenced or persistent endosperm proliferation in different species. Our study reveals an epigenetic mechanism that drives the development of vastly different seed ontogenies.

Transcriptome characteristics during cell wall formation of endosperm cellularization and embryo differentiation in Arabidopsis

Embryonic and endosperm development are important biological events during Arabidopsis seed development, and are controlled by dynamic changes in a range of gene expression. Nevertheless, the regulatory mechanisms of endosperm cellularization and embryo differentiation remain unclear. Here, we characterized the early embryo and endosperm development of the naa15 mutant that had abnormal embryo differentiation and incomplete endosperm cellularization compared to WT of Arabidopsis, and comparatively investigated the changes of gene expressions in WT seeds at 3, 4, and 5 days after pollination (3W, 4W, and 5W) and the white homozygous aborted naa15 seeds at 5, 6, and 7 DAP (5M, 6M, and 7M) from naa15-1/+ siliques using RNA sequencing and qPCR assays. The transcriptome analyses showed that there were 2040 and 3630 differentially expressed genes (DEGs) in 4W (at endosperm cellularization initiation stage and heart embryo stage) vs 3W (at syncytium stage and globular embryo stage), and 5W (at end of endosperm cellularization stage and torpedo embryo stage) vs 4W, respectively. The KEGG and GO analyses showed that lipid metabolic processes and transmembrane transport related to cell wall biogenesis, cell division and differentiation, the plant hormone signaling pathway, photosynthesis, and transcription regulator activity were evidently enriched in WT and naa15. The heatmap and qPCR analyses showed that auxin response genes (ARFs), auxin transport genes (PINs) cytokinin synthesis genes (LOGs), cytokinin dehydrogenase genes (CKXs), cytokinin receptor, transcription factors (MYB, bHLH, MADS-box, and ERF) were significantly downregulated in naa15 compared to WT. A series of cell wall genes annotated to xyloglucan endotransglycosylase/hydrolase, pectin methyl esterase, and pectin methyl esterase inhibitor were also identified in these DEGs. Moreover, using an immunofluorescent assay, the features of cell walls displayed that cellulose fluorescence signals in the embryo and endosperm of naa15 were significantly decreased, and the signals of low- and high- methyl esterification of pectin were also obviously decreased in the endosperm of naa15. In summary, we identified a large number of DEGs and investigated the features of cell walls during endosperm cellularization and embryonic differentiation, which provided important information on transcription and gene expression to reveal their regulatory mechanisms.

Genome-wide identification and analysis of the cytokinin oxidase/dehydrogenase (ckx) gene family in finger millet (Eleusine coracana)

Cytokinin dehydrogenase/oxidase (CKX) enzymes play a key role in regulating cytokinin (CK) levels in plants by degrading the excess of this phytohormone. CKX genes have proven an attractive target for genetic engineering, as their silencing boosts cytokinin accumulation in various tissues, thereby contributing to a rapid increase in biomass and overall plant productivity. We previously reported a similar effect in finger millet (Eleusine coracana) somaclonal lines, caused by downregulation of EcCKX1 and EcCKX2. However, the CKX gene family has numerous representatives, especially in allopolyploid crop species, such as E. coracana. To date, the entire CKX gene family of E. coracana and its related species has not been characterized. We offer here, for the first time, a comprehensive genome-wide identification and analysis of a panel of CKX genes in finger millet. The functional genes identified in the E. coracana genome are compared with the previously-identified genes, EcCKX1 and EcCKX2. Exon-intron structural analysis and motif analysis of FAD- and CK-binding domains are performed. The phylogeny of the EcCKX genes suggests that CKX genes are divided into several distinct groups, corresponding to certain isotypes. Finally, the phenotypic effect of EcCKX1 and EcCKX2 in partially silencing the SE7 somaclonal line is investigated, showing that lines deficient in CKX-expression demonstrate increased grain yield and greater bushiness, enhanced biomass accumulation, and a shorter vegetation cycle.

Transcriptome analysis reveals cell cycle-related transcripts as key determinants of varietal differences in seed size of Brassica juncea

Brassica juncea is an important oilseed crop, widely grown as a source of edible oil. Seed size is a pivotal agricultural trait in oilseed Brassicas. However, the regulatory mechanisms underlying seed size determination are poorly understood. To elucidate the transcriptional dynamics involved in the determination of seed size in B. juncea, we performed a comparative transcriptomic analysis using developing seeds of two varieties, small-seeded Early Heera2 (EH2) and bold-seeded Pusajaikisan (PJK), at three distinct stages (15, 30 and 45 days after pollination). We detected 112,550 transcripts, of which 27,186 and 19,522 were differentially expressed in the intra-variety comparisons and inter-variety comparisons, respectively. Functional analysis using pathway, gene ontology, and transcription factor enrichment revealed that cell cycle- and cell division-related transcripts stay upregulated during later stages of seed development in the bold-seeded variety but are downregulated at the same stage in the small-seeded variety, indicating that an extended period of cell proliferation in the later stages increased seed weight in PJK as compared to EH2. Further, k-means clustering and candidate genes-based analyses unravelled candidates for employing in seed size improvement of B. juncea. In addition, candidates involved in determining seed coat color, oil content, and other seed traits were also identified.

OsCKX2 regulates phosphate deficiency tolerance by modulating cytokinin in rice

Cytokinin oxidase/dehydrogenases (CKXs) are key enzymes that degrade cytokinins (CTKs) and play an essential role in plant growth and development. The present study analyzed the phenotypic and physiological characteristics of OsCKX2 overexpressing (OE) and knockout (KO) rice plants after exposure to phosphate (Pi) deficiency and the transcriptome and metabolome to investigate the function of OsCKX2 in response to Pi deficiency. OsCKX2 KO plants demonstrated higher endogenous CTK levels than wild-type (WT) under Pi deficiency. Further analysis indicated more robust tolerance of OsCKX2 KO plants to Pi deficiency, which exhibited higher phosphorus concentration, larger shoot biomass, and lesser leaf yellowing under Pi deficiency; whereas the opposite was observed for OsCKX2 OE plants. Transcriptome and metabolome analyses revealed that overexpression of OsCKX2 downregulated the transcriptional levels of genes related to Pi transporters, membrane lipid metabolism, and glycolysis, and reduced the consumption of metabolites in membrane lipid metabolism and glycolysis. On the contrary, knockout of OsCKX2 upregulated the expression of Pi transporters, and increased the consumption of metabolites in membrane lipid metabolism and glycolysis. These results indicated that OsCKX2 impacted Pi uptake, recycling, and plant growth via Pi transporters, phospholipid hydrolysis, and glycolysis under Pi deficiency. Overall, OsCKX2 negatively regulated Pi deficiency tolerance by modulating CTKs in rice.

Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks

The limited knowledge of genomic diversity and functional genes associated with the traits of soybean varieties has resulted in slow progress in breeding. In this study, we sequenced the genomes of 250 soybean landraces and cultivars from China, America, and Europe, and investigated their population structure, genetic diversity and architecture, and the selective sweep regions of these accessions. Five novel agronomically important genes were identified, and the effects of functional mutations in respective genes were examined. The candidate genes GSTT1, GL3, and GSTL3 associated with the isoflavone content, CKX3 associated with yield traits, and CYP85A2 associated with both architecture and yield traits were found. The phenotype-gene network analysis revealed that hub nodes play a crucial role in complex phenotypic associations. This study describes novel agronomic trait-associated genes and a complex genetic network, providing a valuable resource for future soybean molecular breeding.

Transcriptional regulation of plant seed development

Plant seeds, which are unique reproductive organs of gymnosperms and angiosperms, are used for edible, medicinal, and industrial purposes. Transcription factors (TFs) are master regulators of plant growth, development, and stress responses. This review describes, in detail, the functions of TFs in regulating seed development. Different TFs, or even different TF families, may have similar functions in seed development. For example, WUSCHEL-related homeobox, LEC2/FUS3/ABI3, and HEME ACTIVATOR PROTEIN3 families can control plant seed embryonic initiation and development. In contrast, some members of the same TF family may have completely opposite roles. For instance, AtMYB76 and AtMYB89 inhibit the accumulation of seed oil, whereas AtMYB96 promotes seed fatty acid accumulation in Arabidopsis thaliana. Compared with the number of studies that have addressed regulation by single TFs, only a few have focused on multiple-TF regulatory networks. This review should be useful as a reference for future studies on regulatory networks of TF complexes.

Genome-wide association study for candidate genes controlling seed yield and its components in rapeseed (Brassica napus subsp. napus)

Genetic improvement of seed yield per plant (SY) is one of the major objectives in Brassica napus breeding programme. SY, being a complex quantitative trait is directly and indirectly influenced by yield-component traits such as siliqua length (SL), number of seeds per siliqua (NSS), and thousand seed weight (TSW). Therefore, concurrent improvement in SL, NSS and TSW can lead to higher SY in B. napus. This study was conducted to identify significant SNPs and putative candidate genes governing SY and its component traits (SL, NSS, TSW). All these traits were evaluated in a diverse set of 200 genotypes representing diversity from wide geographical locations. Of these, a set of 125 genotypes were chosen based on pedigree diversity and multi-location trait variation for genotyping by sequencing (GBS). Best linear unbiased predictors (BLUPs) of all the traits were used for genome-wide association study (GWAS) with 85,126 SNPs obtained from GBS. A total of 16, 18, 27 and 18 SNPs were found to be significantly associated for SL, NSS, TSW and SY respectively. Based on linkage disequilibrium decay analysis, 150 kb genomic region flanking the SNP was used for the identification of underlying candidate genes for each test trait. Important candidate genes involved in phytohormone signaling (WAT1, OSR1, ARR8, CKX1, REM7, REM9, BG1) and seed storage proteins (Cruciferin) were found to have significant influence on seed weight and yield. Genes involved in sexual reproduction and fertilization (PERK7, PERK13, PRK3, GATA15, NFD6) were found to determine the number of seeds per siliqua. Several genes found in this study namely ATS3A, CKX1, SPL2, SPL6, SPL9, WAT1 showed pleiotropic effect with yield component traits. Significant SNPs and putative candidate genes identified for SL, NSS, TSW and SY could be used in marker-assisted breeding for improvement of crop yield in B. napus. Genotypes identified with high SL, NSS, TSW and SY could serve as donors in crop improvement programs in B. napus.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01060-9.

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.

Cross Inhibition of MPK10 and WRKY10 Participating in the Growth of Endosperm in Arabidopsis thaliana

The product of double fertilization produces seed, which contains three components: triploid endosperm, diploid embryo, and maternal seed coat. Amongst them, the endosperm plays a crucial role in coordinating seed growth. Mitogen-activated protein kinase (MAPK) cascades are conserved in eukaryotes and involved in signal transduction of plant development. MPK3, MPK6, and MPK10 form a small group of MPKs family in Arabidopsis thaliana. MPK3 and MPK6 are extensively studied and were found to be involved in diverse processes including plant reproduction. However, less is known about the function of MPK10. Here, we found WRKY10/MINI3, a member of HAIKU (IKU) pathway engaging in endosperm development, and MPK10 is high-specifically expressed in the early developmental endosperm but with opposite gradients. We further proved that MPK10 and WRKY10 cross-inhibit the expression of each other. The inhibition effect of MPK10 on gene expression of WRKY10 and the downstream targets is supported by the fact that MPK10 interacts with WRKY10 and suppresses the transcriptional activity of WRKY10. Constantly, mpk10 mutants produce big seeds while WRKY10/MINI3 positively regulate seed growth. Altogether, our data provides a model of WRKY10 and MPK10 regulating endosperm development with a unique cross inhibitory mechanism.

Cytokinin oxidase/dehydrogenase OsCKX11 coordinates source and sink relationship in rice by simultaneous regulation of leaf senescence and grain number

The flag leaf and grain belong to the source and sink, respectively, of cereals, and both have a bearing on final yield. Premature leaf senescence significantly reduces the photosynthetic rate and severely lowers crop yield. Cytokinins play important roles in leaf senescence and determine grain number. Here, we characterized the roles of the rice (Oryza sativa L.) cytokinin oxidase/dehydrogenase OsCKX11 in delaying leaf senescence, increasing grain number, and coordinately regulating source and sink. OsCKX11 was predominantly expressed in the roots, leaves, and panicles and was strongly induced by abscisic acid and leaf senescence. Recombinant OsCKX11 protein catalysed the degradation of various types of cytokinins but showed preference for trans-zeatin and cis-zeatin. Cytokinin levels were significantly increased in the flag leaves of osckx11 mutant compared to those of the wild type (WT). In the osckx11 mutant, the ABA-biosynthesizing genes were down-regulated and the ABA-degrading genes were up-regulated, thereby reducing the ABA levels relative to the WT. Thus, OsCKX11 functions antagonistically between cytokinins and ABA in leaf senescence. Moreover, osckx11 presented with significantly increased branch, tiller, and grain number compared with the WT. Collectively, our findings reveal that OsCKX11 simultaneously regulates photosynthesis and grain number, which may provide new insights into leaf senescence and crop molecular breeding.

The Cytokinin Status of the Epidermis Regulates Aspects of Vegetative and Reproductive Development in Arabidopsis thaliana

The epidermal cell layer of plants has important functions in regulating plant growth and development. We have studied the impact of an altered epidermal cytokinin metabolism on Arabidopsis shoot development. Increased epidermal cytokinin synthesis or breakdown was achieved through expression of the cytokinin synthesis gene LOG4 and the cytokinin-degrading CKX1 gene, respectively, under the control of the epidermis-specific AtML1 promoter. During vegetative growth, increased epidermal cytokinin production caused an increased size of the shoot apical meristem and promoted earlier flowering. Leaves became larger and the shoots showed an earlier juvenile-to-adult transition. An increased cytokinin breakdown had the opposite effect on these phenotypic traits indicating that epidermal cytokinin metabolism can be a factor regulating these aspects of shoot development. The phenotypic consequences of abbreviated cytokinin signaling in the epidermis achieved through expression of the ARR1-SRDX repressor were generally milder or even absent indicating that the epidermal cytokinin acts, at least in part, cell non-autonomously. Enhanced epidermal cytokinin synthesis delayed cell differentiation during leaf development leading to an increased cell proliferation and leaf growth. Genetic analysis showed that this cytokinin activity was mediated mainly by the AHK3 receptor and the transcription factor ARR1. We also demonstrate that epidermal cytokinin promotes leaf growth in a largely cell-autonomous fashion. Increased cytokinin synthesis in the outer layer of reproductive tissues and in the placenta enhanced ovule formation by the placenta and caused the formation of larger siliques. This led to a higher number of seeds in larger pods resulting in an increased seed yield per plant. Collectively, the results provide evidence that the cytokinin metabolism in the epidermis is a relevant parameter determining vegetative and reproductive plant growth and development.

The Importance of Cytokinins during Reproductive Development in Arabidopsis and Beyond

Fertilization and seed formation are fundamental events in the life cycle of flowering plants. The seed is a functional unit whose main purpose is to propagate the plant. The first step in seed development is the formation of male and female gametophytes and subsequent steps culminate in successful fertilization. The detailed study of this process is highly relevant because it directly impacts human needs, such as protecting biodiversity and ensuring sustainable agriculture to feed the increasing world population. Cytokinins comprise a class of phytohormones that play many important roles during plant growth and development and in recent years, the role of this class of phytohormones during reproduction has become clear. Here, we review the role of cytokinins during ovule, pollen and seed formation at the genetic and molecular levels. The expansion of knowledge concerning the molecular mechanisms that control plant reproduction is extremely important to optimise seed production.

ENO2 Affects the Seed Size and Weight by Adjusting Cytokinin Content and Forming ENO2-bZIP75 Complex in Arabidopsis thaliana

Arabidopsis thaliana ENO2 (AtENO2) encodes two proteins AtENO2 (enolase) and AtMBP-1 (c-Myc binding protein 1-like). The loss of AtENO2 function causes the constitutive developmental defects which are correlated with reduced enolase activity, but not AtMBP-1 transcript abundance. However, the regulation mechanism of AtENO2 on the seed properties is still not clear. In this study, we found that the mutation of AtENO2 reduced the seed size and weight. The level of glucose in seed was significantly elevated but that of starch was decreased in AtENO2 mutants compared to WT plants. We also found that AtENO2 mutation reduced the content of cytokinin which resulted in smaller cotyledons. The RNA-seq data showed that there were 1892 differentially expressed genes and secondary metabolic pathways were significantly enriched. Instead of AtMBP-1, AtENO2 protein interacted with AtbZIP75 which may mediate the secondary metabolism. Therefore, ENO2 alters the size and weight of seeds which is not only regulated by the content of cytokinin and secondary metabolism, but may be affected by the interaction of ENO2 and bZIP57. These results are helpful to understand the novel function of AtENO2 which provide a foundation for further exploration of the key candidate genes for crop breeding.

Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds

BACKGROUND

Brassica rapa is an important oilseed and vegetable crop species and is the A subgenome donor of two important oilseed Brassica crops, Brassica napus and Brassica juncea. Although seed size (SZ), seed color (SC), and oil content (OC) substantially affect seed yield and quality, the mechanisms regulating these traits in Brassica crops remain unclear.

RESULTS

We collected seeds from a pair of B. rapa accessions with significantly different SZ, SC, and OC at seven seed developmental stages (every 7 days from 7 to 49 days after pollination), and identified 28,954 differentially expressed genes (DEGs) from seven pairwise comparisons between accessions at each developmental stage. K-means clustering identified a group of cell cycle-related genes closely connected to variation in SZ of B. rapa. A weighted correlation analysis using the WGCNA package in R revealed two important co-expression modules comprising genes whose expression was positively correlated with SZ increase and negatively correlated with seed yellowness, respectively. Upregulated expression of cell cycle-related genes in one module was important for the G₂/M cell cycle transition, and the transcription factor Bra.A05TSO1 seemed to positively stimulate the expression of two CYCB1;2 genes to promote seed development. In the second module, a conserved complex regulated by the transcription factor TT8 appear to determine SC through downregulation of TT8 and its target genes TT3, TT18, and ANR. In the third module, WRI1 and FUS3 were conserved to increase the seed OC, and Bra.A03GRF5 was revealed as a key transcription factor on lipid biosynthesis. Further, upregulation of genes involved in triacylglycerol biosynthesis and storage in the seed oil body may increase OC. We further validated the accuracy of the transcriptome data by quantitative real-time PCR of 15 DEGs. Finally, we used our results to construct detailed models to clarify the regulatory mechanisms underlying variations in SZ, SC, and OC in B. rapa.

CONCLUSIONS

This study provides insight into the regulatory mechanisms underlying the variations of SZ, SC, and OC in plants based on transcriptome comparison. The findings hold great promise for improving seed yield, quality and OC through genetic engineering of critical genes in future molecular breeding.

Memory of environmental conditions across generations affects the acclimation potential of scots pine

Long generation times have been suggested to hamper rapid genetic adaptation of organisms to changing environmental conditions. We examined if environmental memory of the parental Scots pines (Pinus sylvestris L.) drive offspring survival and growth. We used seeds from trees growing under naturally dry conditions (control), irrigated trees (irrigated from 2003 to 2016), and formerly irrigated trees ("irrigation stop"; irrigated from 2003-2013; control condition since 2014). We performed two experiments, one under controlled greenhouse conditions and one at the experimental field site. In the greenhouse, the offspring from control trees exposed regularly to drought were more tolerant to hot-drought conditions than the offspring from irrigated trees and showed lower mortality even though there was no genetic difference. However, under optimal conditions (high water supply and full sunlight), these offspring showed lower growth and were outperformed by the offspring of the irrigated trees. This different offspring growth, with the offspring of the "irrigation-stop" trees showing intermediate responses, points to the important role of transgenerational memory for the long-term acclimation of trees. Such memory effects, however, may be overridden by climatic extremes during germination and early growth stages such as the European 2018 mega-drought that impacted our field experiment.

The Modular Control of Cereal Endosperm Development

Expansion of the human population demands a significant increase in cereal production. The main component of cereal grains is endosperm, a body of starchy endosperm (SE) cells surrounded by aleurone (AL) cells with transfer cells (TC) at the base and embryo surrounding (ESR) cells adjacent to the embryo. The data reviewed here emphasize the modular nature of endosperm by first suggesting that sucrose promotes development of the fertilized triploid endosperm cell. Next, that the basal syncytial endosperm responds to glucose by turning on TC development. The default endosperm cell fate is SE and ESR differentiation is likely activated by signaling from the embryo. Cells on the exterior surface of the endosperm are specified as AL cells.

Phenotypic, Transcriptomic, and Metabolomic Signatures of Root-Specifically Overexpressed OsCKX2 in Rice

Cytokinins are crucial signaling molecules that regulate plant growth and development. OsCKX2 irreversibly degrades nucleobase cytokinins by encoding cytokinin oxidase/dehydrogenase to control grain production in rice. In this study, OsCKX2 was specifically overexpressed in roots using RCc3 promoter to investigate the effects of root-source cytokinins on the growth of rice. OsCKX2 overexpressed (OE) rice showed retarded growth with lower cytokinin levels and biomass production. Shoot-specific transcriptome analysis between OsCKX2 OE rice and wild type (WT) revealed differentially expressed genes (DEGs) associated with cell division, cell wall structure, phytohormone signaling, and assimilation and catabolism. Metabolome analysis indicated that a majority of differential primary metabolites, such as amino acids and organic acids, increased, while lipids decreased in OsCKX2 OE rice. Integration of transcriptomic and metabolomic data showed that several DEGs and differential metabolites were related to glycolysis and tricarboxylic acid cycle (TCA). To conclude, reduced cytokinin levels via root-specific overexpression of OsCKX2 resulted in developmental defects, which confirmed the importance of root-source cytokinins in plant growth and morphogenesis.

Within-plant heterogeneity in fecundity and herbivory induced by localized DNA hypomethylation in the perennial herb Helleborus foetidus

PREMISE

Phenotypic heterogeneity of reiterated, homologous structures produced by individual plants has ecological consequences for plants and their animal consumers. This paper examines experimentally the epigenetic mosaicism hypothesis, which postulates that within-plant variation in traits of reiterated structures may partly arise from different parts of the same genetic individual differing in patterns or extent of genomic DNA methylation.

METHODS

Leaves of paired ramets borne by field-growing Helleborus foetidus plants were infiltrated periodically over the entire flowering period with either a water solution of the demethylating agent zebularine or just water as the control. The effects of the zebularine treatment were assessed by quantifying genome-wide DNA cytosine methylation in leaves and monitoring inflorescence growth and flower production, number of ovules per flower, pollination success, fruit set, seed set, seed size, and distribution of sap-feeding insects.

RESULTS

Genomic DNA from leaves in zebularine-treated ramets was significantly less methylated than DNA from leaves in control ones. Inflorescences in treated ramets grew smaller and produced fewer flowers, with fewer ovules and lower follicle and seed set, but did not differ from inflorescences in untreated ramets in pollination success or seed size. The zebularine treatment influenced the within-plant distribution of sap-feeding insects.

CONCLUSIONS

Experimental manipulation of genomic DNA methylation level in leaves of wild-growing H. foetidus plants induced considerable within-plant heterogeneity in phenotypic (inflorescences, flowers, fecundity) and ecologically relevant traits (herbivore distribution), which supports the hypothesis that epigenetic mosaicism may partly account for within-plant variation.

Genome Editing to Integrate Seed Size and Abiotic Stress Tolerance Traits in Arabidopsis Reveals a Role for DPA4 and SOD7 in the Regulation of Inflorescence Architecture

Both seed size and abiotic stress tolerance are important agronomic traits in crops. In Arabidopsis, two closely related transcription repressors DPA4 (Development-Related PcG Target in the APEX4)/NGAL3 and SOD7 (Suppressor of da1-1)/NGAL2 (NGATHA-like protein) function redundantly to regulate seed size, which was increased in the dpa4 sod7 double mutants. Whereas ABA-induced transcription repressors (AITRs) are involved in the regulation of ABA signaling and abiotic stress tolerance, Arabidopsis aitr2 aitr5 aitr6 (aitr256) triple mutant showed enhanced tolerance to drought and salt. Here we performed CRISPR/Cas9 genome editing to disrupt DPA4 and SOD7 in aitr256 mutant, trying to integrate seed size and abiotic stress tolerance traits in Arabidopsis, and also to examine whether DPA4 and SOD7 may regulate other aspects of plant growth and development. Indeed, seed size was increased in the dpa4 sod7 aitr256 quintuple mutants, and enhanced tolerance to drought was observed in the mutants. In addition, we found that shoot branching was affected in the dpa4 sod7 aitr256 mutants. The mutant plants failed to produce secondary branches, and flowers/siliques were distributed irregularly on the main stems of the plants. Floral organ number and fertility were also affected in the dpa4 sod7 aitr256 mutant plants. To examine if these phenotypes were dependent on loss-of-function of AITRs, dpa4 sod7 double mutants were generated in Col wild type background, and we found that the dpa4 sod7 mutant plants showed a phenotype similar to the dpa4 sod7 aitr256 quintuple mutants. Taken together, our results indicate that the integration of seed size and abiotic stress tolerance traits by CRISPR/Cas9 editing was successful, and our results also revealed a role of DPA4 and SOD7 in the regulation of inflorescence architecture in Arabidopsis.

Comparative Genomic Analysis Reveals Extensive Genetic Variations of WRKYs in Solanaceae and Functional Variations of CaWRKYs in Pepper

As a conserved protein family, WRKY has been shown to be involved in multiple biological processes in plants. However, the mechanism of functional diversity for WRKYs in pepper has not been well elucidated. Here, a total of 223 WRKY members from solanaceae crops including pepper, tomato and potato, were analyzed using comparative genomics. A tremendous genetic variation among WRKY members of different solanaceous plants or groups was demonstrated by the comparison of some WRKY features, including number/size, group constitution, gene structure, and domain composition. The phylogenetic analysis showed that except for the known WRKY groups (I, IIa/b/c/d/e and III), two extra WRKY subgroups specifically existed in solanaceous plants, which were named group IIf and group IIg in this study, and their genetic variations were also revealed by the characteristics of some group IIf and IIg WRKYs. Except for the extensive genetic variations, certain degrees of conservatism for solanaceae WRKYs were also revealed. Moreover, the variant zinc-finger structure (CX4,7CX22-24HXC) in group III of solanaceae WRKYs was identified. Expression profiles of CaWRKY genes suggested their potential roles in pepper development and stress responses, and demonstrated a functional division pattern for pepper CaWRKYs. Furthermore, functional analysis using virus induced gene silencing (VIGS) revealed critical roles of two CaWRKYs (CaWRKY45 and CaWRKY58) in plant responses to disease and drought, respectively. This study provides a solid foundation for further dissection of the evolutionary and functional diversity of solanaceae WRKYs in crop plants.

Big Grain3, encoding a purine permease, regulates grain size via modulating cytokinin transport in rice

Grain size is an important agronomic trait affecting grain yield, but the underlying molecular mechanisms remain to be elucidated. Here, we isolated a dominant mutant, big grain3 (bg3-D), which exhibits a remarkable increase of grain size caused by activation of the PURINE PERMEASE gene, OsPUP4. BG3/OsPUP4 is predominantly expressed in vascular tissues and is specifically suppressed by exogenous cytokinin application. Hormone profiling revealed that the distribution of different cytokinin forms, in roots and shoots of the bg3-D mutant, is altered. Quantitative reverse transcription-PCR (qRT-PCR) analysis indicated that expression of rice cytokinin type-A RESPONSE REGULATOR (OsRR) genes is enhanced in the roots of the bg3-D mutant. These results suggest that OsPUP4 might contribute to the long-distance transport of cytokinin, by reinforcing cytokinin loading into vascular bundle cells. Furthermore, plants overexpressing OsPUP7, the closest homolog of OsPUP4, also exhibited a similar phenotype to the bg3-D mutant. Interestingly, subcellular localization demonstrated that OsPUP4 was localized on the plasma membrane, whereas OsPUP7 was localized to the endoplasmic reticulum. Based on these findings, we propose that OsPUP4 and OsPUP7 function in a linear pathway to direct cytokinin cell-to-cell transport, affecting both its long-distance movement and local allocation.

Molecular Networks of Seed Size Control in Plants

The size of seeds affects not only evolutionary fitness but also grain yield of crops. Understanding the mechanisms controlling seed size has become an important research field in plant science. Seed size is determined by the integrated signals of maternal and zygotic tissues, which control the coordinated growth of the embryo, endosperm, and seed coat. Recent advances have identified several signaling pathways that control seed size through maternal tissues, including or involving the ubiquitin-proteasome pathway, G-protein signaling, mitogen-activated protein kinase (MAPK) signaling, phytohormone perception and homeostasis, and some transcriptional regulators. Meanwhile, growth of the zygotic tissues is regulated in part by the HAIKU (IKU) pathway and phytohormones. This review provides a general overview of current findings in seed size control and discusses the emerging molecular mechanisms and regulatory networks found to be involved.

Expanding Phaseolus coccineus Genomic Resources: De Novo Transcriptome Assembly and Analysis of Landraces 'Gigantes' and 'Elephantes' Reveals Rich Functional Variation

Beans are one of the most important staple crops in the world. Runner bean (Phaseolus coccineus L.) is a small-scale agriculture crop compared to common bean (Phaseolusvulgaris). Beans have been introduced to Europe from the Central America to Europe and since then they have been scattered to different geographical regions. This has resulted in the generation of numerous local cultivars and landraces with distinguished characters and adaptive potential. To identify and characterize the underlying genomic variation of two very closely related runner bean cultivars, we performed RNA-Seq with de novo transcriptome assembly in two landraces of P. coccineus, 'Gigantes' and 'Elephantes' phenotypically distinct, differing in seed size and shape. The cleaned reads generated 37,379 and 37,774 transcripts for 'Gigantes' and 'Elephantes,' respectively. A total of 1896 DEGs were identified between the two cultivars, 1248 upregulated in 'Elephantes' and 648 upregulated in 'Gigantes.' A significant upregulation of defense-related genes was observed in 'Elephantes,' among those, numerous members of the AP2-EREBP, WRKY, NAC, and bHLH transcription factor families. In total, 3956 and 4322 SSRs were identified in 'Gigantes' and 'Elephantes,' respectively. Trinucleotide repeats were the most dominant repeat motif, accounting for 41.9% in 'Gigantes' and 40.1% in 'Elephantes' of the SSRs identified, followed by dinucleotide repeats (29.1% in both cultivars). Additionally, 19,281 putative SNPs were identified, among those 3161 were non-synonymous, thus having potential functional implications. High-confidence non-synonymous SNPs were successfully validated with an HRM assay, which can be directly adopted for P. coccineus molecular breeding. These results significantly expand the number of polymorphic markers within P. coccineus genus, enabling the robust identification of runner bean cultivars, the construction of high-resolution genetic maps, potentiating genome-wide association studies. They finally contribute to the genetic reservoir for the improvement of the closely related and intercrossable Phaseolus vulgaris.

Enhancing microRNA167A expression in seed decreases the α-linolenic acid content and increases seed size in Camelina sativa

Despite well established roles of microRNAs in plant development, few aspects have been addressed to understand their effects in seeds especially on lipid metabolism. In this study, we showed that overexpressing microRNA167A (miR167OE) in camelina (Camelina sativa) under a seed-specific promoter changed fatty acid composition and increased seed size. Specifically, the miR167OE seeds had a lower α-linolenic acid with a concomitantly higher linoleic acid content than the wild-type. This decreased level of fatty acid desaturation corresponded to a decreased transcriptional expression of the camelina fatty acid desaturase3 (CsFAD3) in developing seeds. MiR167 targeted the transcription factor auxin response factor (CsARF8) in camelina, as had been reported previously in Arabidopsis. Chromatin immunoprecipitation experiments combined with transcriptome analysis indicated that CsARF8 bound to promoters of camelina bZIP67 and ABI3 genes. These transcription factors directly or through the ABI3-bZIP12 pathway regulate CsFAD3 expression and affect α-linolenic acid accumulation. In addition, to decipher the miR167A-CsARF8 mediated transcriptional cascade for CsFAD3 suppression, transcriptome analysis was conducted to implicate mechanisms that regulate seed size in camelina. Expression levels of many genes were altered in miR167OE, including orthologs that have previously been identified to affect seed size in other plants. Most notably, genes for seed coat development such as suberin and lignin biosynthesis were down-regulated. This study provides valuable insights into the regulatory mechanism of fatty acid metabolism and seed size determination, and suggests possible approaches to improve these important traits in camelina.

A new regulator of seed size control in Arabidopsis identified by a genome-wide association study

Organ size in plants is controlled by the interaction between genotype and the environment. Seed size, an important agronomic trait, largely determines yield and is an important focus of research. However, the genetic components underpinning natural variation of seed size in undomesticated species remain largely unidentified. Here we report a genome-wide association study (GWAS) of seed size in Arabidopsis thaliana, which identified 38 significantly associated loci, including one locus associated with CYCB1;4. Natural variations in CYCB1;4, which encodes a cyclin protein involved in the cell cycle, significantly influence seed size in A. thaliana. Transgenic plants with enhanced CYCB1;4 expression show normal development, exhibit increased seed size as a result of an accelerated cell cycle progression, and tend to produce higher yields. By contrast, cycb1;4 mutants have smaller seeds, and the effect is especially pronounced in a large-seed accession. The temporal and spatial expression pattern of CYCB1;4 suggests that this gene may function in both maternal tissues and zygotic tissues to coordinate the final size of seeds. Taken together, our results provide genetic insights into natural variation in seed size in Arabidopsis. Moreover, CYCB1;4 homologs in other crops could have great potential as targets for efforts aimed at yield improvement.

Seeds-An evolutionary innovation underlying reproductive success in flowering plants

"Seeds nourish, seeds unite, seeds endure, seeds defend, seeds travel," explains the science writer Thor Hanson in his book The Triumph of Seeds (2015). The seed is an ultimate product of land plant evolution. The nursing and protective organization of the seed enable a unique parental care of the progeny that has fueled seed plant radiation. Seeds promote dispersal and optimize offspring production and thus reproductive fitness through biological adaptations that integrate environmental and developmental cues. The composite structure of seeds, uniting tissues that originate from three distinct organisms, enables the partitioning of tasks during development, maturation, and storage, while a sophisticated interplay between the compartments allows the fine-tuning of embryonic growth, as well as seed maturation, dormancy, and germination. In this review, we will highlight peculiarities in the development and evolution of the different seed compartments and focus on the molecular mechanisms underlying the interactions between them.

Expansin genes expression in growing ovaries and grains of sunflower are tissue-specific and associate with final grain weight

BACKGROUND

Grain weight (GW) is a key component of sunflower yield and quality, but may be limited by maternal tissues. Cell growth is influenced by expansin proteins that loosen the plant cell wall. This study aimed to identify spatio-temporal expression of EXPN genes in sunflower reproductive organ tissues (ovary, pericarp, and embryo) and evaluate correlations between reproductive organ growth and expansin genes expression. Evaluations involved eight different developmental stages, two genotypes, two source-sink treatments and two experiments. The genotypes evaluated are contrasting in GW (Alybro and confection variety RHA280) under two source-sink treatments (control and shaded) to study the interactions between grain growth and expansin genes expression.

RESULTS

Ovaries and grains were sampled at pre- and post-anthesis, respectively. Final GW differed between genotypes and shading treatments. Shading treatment decreased final GW by 16.4 and 19.5% in RHA280 and Alybro, respectively. Relative expression of eight expansin genes were evaluated in grain tissues. EXPN4 was the most abundant expansin in the ovary tissue, while EXPN10 and EXPN7 act predominantly in ovary and pericarp tissues, and EXPN1 and EXPN15 in the embryo tissues.

CONCLUSIONS

Specific expansin genes were expressed in ovary, pericarp and embryo in a tissue-specific manner. Differential expression among grain tissues was consistent between genotypes, source-sink treatments and experiments. The correlation analysis suggests that EXPN genes could be specifically involved in grain tissue extension, and their expression could be linked to grain size in sunflower.

Quantification of DNA Methylation as Biomarker for Grain Quality

DNA methylation is an important biomarker for gene activity. It contributes to gene silencing and is involved in regulating various seed developmental processes in plants. Many of these processes are involved in important traits associated with aspects of grain quality. A reliable, fast, and cheap method is the estimation of DNA methylation utilizing methylation sensitive restriction enzymes (MSRE) and quantitative real-time PCR (qPCR) for selected candidate regions. The presented method can be used to confirm an effect of RNAi constructs on their target genes or trans-activity. Analysis of promoter regions can contribute to estimation of gene activity and related traits.

Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security

Seeds serve as biochemical factories of nutrition, processing, bio-energy and storage related important bio-molecules and act as a delivery system to transmit the genetic information to the next generation. The research pertaining towards delineating the complex system of regulation of genes and pathways related to seed biology and nutrient partitioning is still under infancy. To understand these, it is important to know the genes and pathway(s) involved in the homeostasis of bio-molecules. In recent past with the advent and advancement of modern tools of genomics and genetic engineering, multi-layered 'omics' approaches and high-throughput platforms are being used to discern the genes and proteins involved in various metabolic, and signaling pathways and their regulations for understanding the molecular genetics of biosynthesis and homeostasis of bio-molecules. This can be possible by exploring systems biology approaches via the integration of omics data for understanding the intricacy of seed development and nutrient partitioning. These information can be exploited for the improvement of biologically important chemicals for large-scale production of nutrients and nutraceuticals through pathway engineering and biotechnology. This review article thus describes different omics tools and other branches that are merged to build the most attractive area of research towards establishing the seeds as biochemical factories for human health and nutrition.