A cucurbit androecy gene reveals how unisexual flowers develop and dioecy emerges

A nuclear-encoded endonuclease governs the paternal transmission of mitochondria in Cucumis plants

Non-Mendelian transmission of mitochondria has been well established across most eukaryotes, however the genetic mechanism that governs this uniparental inheritance remains unclear. Plants in the genus Cucumis, specifically melon and cucumber, exhibit paternal transmission of the mitochondrial (mt) DNA, making them excellent models for exploring the molecular mechanisms underlying mitochondrial transmission. Here, we develop a toolkit to screen for mutants in mitochondrial inheritance (mti), and use fine mapping to successfully identify a mitochondrially targeted endonuclease gene (MTI1) controlling mitochondrial transmission. Knockout of MTI1 results in a shift from paternal to bi-parental inheritance of the mtDNA, confirming the crucial role of MTI1 in uniparental inheritance of mitochondria. Moreover, we demonstrate that MTI1 exhibits robust endonuclease activity both in vitro and in vivo, specifically expresses in mitochondria of the fertilized ovule within 24 h of pollination. Collectively, this study reveals that a nuclear-encoded but mitochondria-targeted gene plays a causative role in governing the non-Mendelian mitochondrial inheritance, revolutionizing our knowledge about mitochondrial DNA transmission.

The development of ideal insertion and deletion (InDel) markers and initial indel map variation in cucumber using re-sequenced data

BACKGROUND

InDels are the most common type of length polymorphism and play a critical role in the genetic traits of many important phenotypes in both plants and animals, making them an ideal source for length polymorphism molecular markers. However, in the process of cucumber breeding, researchers still face deficiencies in the identification of InDel loci and the development of genomic-wide molecular markers.

RESULTS

In this study, we conducted InDel identification on 115 cucumber re-sequencing datasets, identifying a total of 7,842,946 InDels, with lengths ranging from 1 to 59 bp and an average density of one InDel every 2.8 kb on the chromosomes. The InDel variations were classified into four main categories, and 81 InDel hotspots were identified, serving as the foundation for constructing a cucumber InDel variation map. Additionally, we utilized an electronic PCR strategy to develop genome-wide InDel markers for cucumber, resulting in the selection of 22,442 InDel primers exhibiting high polymorphism (PIC ≥ 0.5) and major allele differences of ≥ 3 bp. We experimentally validated 50 randomly selected InDel primers, and the results showed that all markers exhibited high polymorphism.

CONCLUSIONS

The construction of the cucumber genome InDel variation map aids in understanding the genetic basis of key traits in cucumber derived from InDel variations. The ideal InDel markers developed in this study may enhance the efficiency of cucumber breeding for resistance to both biotic and abiotic stresses, as well as scientific research.

Fine mapping and identification of CqMYB62 as the subgynoecy gene in chieh-qua (Benincasa hispida Cogn. var. Chieh-qua How)

KEY MESSAGE

It was hypothesized that Bch08G003160 (CqMYB62), located in the 51.08 Kb region on chromosome 08, might be an important candidate gene for the subgynoecy trait in chieh-qua, based on BSA-seq and linkage mapping approaches. In cucurbit crops, the use of female lines can greatly increase the yield of a single plant and is especially important for the production of hybrid generation seeds, thus being of great interest to breeders. To identify genes regulating sex differentiation in chieh-qua, genetic analysis of the subgynoecy trait was conducted using a chieh-qua F2 population. Initial localization of the locus was done using BSA-seq, followed by fine mapping with a large F2 population (n = 2,741). The locus was ultimately narrowed down to a 51.08 Kb region on Chr08, revealing a single gene Bch08G003160 (CqMYB62) in this region. Further analysis revealed that the presence of two variant loci (SNP_416 and SNP_317) in the coding region resulted in premature termination of the codon and loss of function of the structural domain of the PLN03212 superfamily. Moreover, our research indicated that the subgynoecy trait mediated by CqMYB62 in chieh-qua is potentially regulated by gibberellic acid (GA). Two efficient dCAPS markers were developed to distinguish subgynoecy. In summary, these findings highlight the critical role of CqMYB62 in subgynoecy trait regulation, offering potential implications for chieh-qua breeding programs.

Transcriptome profiling reveals the mechanism of fruit navel development in melon (Cucumis melo L.)

BACKGROUND

Melon is an important horticultural crop cultivated extensively worldwide. The size of the fruit navel, the terminal region of melon fruits, significantly influences the appearance quality of the fruit. However, the regulatory factors and molecular mechanisms governing the fruit navel development remain poorly understood in melon.

RESULTS

In this study, the regulators and mechanisms underlying fruit navel development were investigated through phenotypic analysis, RNA sequencing (RNA-seq) and RT-qPCR methods. The inbred line 'T03' and a big fruit navel mutant 'BFN' of melon were used as experimental materials. RNA-seq analysis identified 116 differentially expressed genes (DEGs), including 54 up-regulated and 62 down-regulated genes, in both the green bud (GB) and ovary at anthesis (OA) stages of the 'BFN' melon compared to the 'T03' melon. Functional enrichment analysis revealed that these 116 DEGs were significantly associated with "Sesquiterpenoid and triterpenoid biosynthesis", "Circadian rhythm-plant", "Galactose metabolism" and "Biosynthesis of various alkaloids" pathways. There were three (AP2/ERF, MYB and C2H2 types) and eight (AP2/ERF, MADS-box, homeobox domain and bZIP types) transcription factors presented in up-regulated and down-regulated DEGs, and their putative target genes were predicted. Based on KEGG and expression analyses, two terpene cyclase/mutase genes (MELO3 C001812 and MELO3 C004329) were identified as being involved in the "Sesquiterpenoid and triterpenoid biosynthesis" pathway, and their transcripts were significantly downregulated in all detected development stages (EGB, GB, GYB, YB and OA) of 'BFN' fruits compared with 'T03' fruits.

CONCLUSIONS

The findings of this study elucidate a fundamental regulatory mechanism underlying fruit navel formation, and identify two key negative regulators, MELO3C001812 and MELO3C004329, involved in the development of the fruit navel in melon.

The MADS-box transcription factor CmFYF promotes the production of male flowers and inhibits the fruit development in melon (Cucumis melo L.)

The FOREVER YOUNG FLOWER (FYF/AGL42) gene plays an important role in regulating the flower development especially the flowering time, and senescence and abscission of floral organs. Melon is an important horticultural crop, and the flower development has an important influence on pollination, fertilization and final fruit yield. However, the function of FYF homolog is still unknown in melon. In this study, the characteristic of melon CmFYF was analyzed combining with molecular biology, developmental biology and biochemical tools. CmFYF was present in all detected tissues of melon, but its expression level was significantly higher in shoot apex of lateral branches and male flowers than that in other tissues. Subcellular localization revealed that CmFYF was located in the nucleus. CmFYF was able to respond to multiple hormone and environmental signals including GA3, SA, MeJA, cold and drought. Ectopic expression of CmFYF in Arabidopsis resulted in the early flowering phenotype and increased plant height, but had no effect on the flower organs or fruits development. In melon, overexpression of CmFYF increased the number of male flowers, but inhibited the size of fruit. These results suggested that CmFYF of melon was partially equivalent to AtFYF of Arabidopsis. Further biochemical analyses indicated that CmFYF directly interacted with CmAGb (a homolog of Arabidopsis AGAMOUS), CmKNAT7 (KNOTTED-LIKE HOMEOBOX OF ARABIDOPSIS THALIANA 7) and itself at the protein level. Therefore, this study enriched the function of FYF homologs and revealed a preliminary molecular mechanism underlying the male flower production and fruit development in melon.

Developmental innovation of inferior ovaries and flower sex orchestrated by KNOX1 in cucurbits

In flowering plants, inferior ovaries are key morphological innovations that evolved multiple times from superior ovaries to protect female parts of the flower. However, the developmental mechanisms underlying inferior ovary formation remain largely unknown. Comparative spatial transcriptome mapping and cell lineage reconstructions in developing floral buds of cucumber and tomato, which have inferior and superior ovaries, respectively, revealed that inferior ovaries develop from accelerated receptacle growth resulting from the continuous activity of meristematic stems cells at the base of the cucumber floral organs. Genetic knockout of a receptacle-specific KNOX1 transcription factor in cucumber caused arrest in receptacle growth and yielded bisexual flowers with superior ovaries similar to those of tomato. Here we provide developmental and mechanistic insights into inferior ovary formation and sex determination in cucurbits.

Unraveling the Hormonal and Molecular Mechanisms Shaping Fruit Morphology in Plants

The importance of fruit shape studies extends beyond fundamental plant biology, as it holds significant implications for breeding. Understanding the genetic and hormonal regulation of fruit morphology can facilitate targeted breeding strategies to enhance yield, quality, and stress resistance, ultimately contributing to sustainable farming and nutrition security. The diversity in fruit shapes is the result of complex hormone regulation and molecular pathways that affect key traits, including carpel number, fruit length, and weight. Fruit shape is a quality attribute that directly influences consumer preference, marketability and the ease of post-harvest processing. This article focuses on investigations carried out on molecular, genetic and hormonal regulation mechanisms of fruit shape, color, maturation in fruit plants and key genetic pathways such as CLV-WUS and OVATE, as well as their roles in shaping non-climacteric fruits such as strawberries, grapes and raspberries. Plant hormones, especially abscisic acid (ABA) and indole-3-acetic acid (IAA), play a crucial role in enhancing desirable traits such as color and taste, while regulating anthocyanin synthesis and growth time. In addition, the dynamic interactions between auxin, gibberellin, and ethylene are crucial for the ripening process. Jasmonate enhances stress response, brassinosteroids promote ripening and cytokinins promote early fruit development. In addition, this review also studied the fruit morphology of species such as tomatoes and cucumbers, emphasizing the importance of the CLV-WUS pathway, which regulates the number of carpels through genes such as WUSCHEL (WUS), FRUITFULL1 (FUL1), and auxin response factor 14 (ARF14). The weight of fresh fruit is affected by microRNAs such as miRNA156, which emphasizes the importance of post transcriptional regulation. The involvement of transcription factors such as SISHN1, CaOvate, and CISUN25-26-27a further emphasizes the complexity of hormone regulation. Understanding these regulatory mechanisms can enhance our understanding of fruit development and have a profound impact on agricultural practices and crop improvement strategies aimed at meeting the growing global demand for high-quality agricultural products.

S-RNase evolution in self-incompatibility: Phylogenomic insights into synteny with Class I T2 RNase genes

S-RNases are essential in the gametophytic self-incompatibility (GSI) system of many flowering plants, where they act as stylar-S determinants. Despite their prominence, the syntenic genomic origin and evolutionary trajectory of S-RNase genes in eudicots have remained largely unclear. Here, we performed large-scale phylogenetic and microsynteny network analyses of T2 RNase genes across 130 angiosperm genomes, encompassing 35 orders and 56 families. S-like RNase genes in Cucurbitaceae species phylogenetically grouped with functionally characterized S-RNases in various species. Additionally, Cucurbitaceae S-like RNase genes showed conserved synteny with Class I T2 RNase genes. From this, we inferred that the well-characterized S-RNase genes (belonging to Class III-A genes) and Class I T2 RNase genes (located on duplicated genomic blocks) likely derived from the gamma triplication event shared by core eudicots. Additionally, we identified frequent lineage-specific gene transpositions of S-RNases and S-like RNases across diverse angiosperm lineages, including Rosaceae, Solanaceae, and Rutaceae families, accompanied by a significant increase in transposable element activity near these genes. Our findings delineate the genomic origin and evolutionary path of eudicot S-RNase genes, enhancing our understanding of the evolution of the S-RNase-based GSI system.

The Monochoria genome provides insights into the molecular mechanisms underlying floral heteranthery

Heteranthery, the occurrence of functionally and structurally distinct stamens within a flower, represents a striking example of convergent evolution among diverse animal-pollinated lineages. Although the ecological basis of this somatic polymorphism is understood, the developmental and molecular mechanisms are largely unknown. To address this knowledge gap, we selected Monochoria elata (Pontederiaceae) as our study system due to its typical heterantherous floral structure. We constructed a chromosome-level genome assembly of M. elata, conducted transcriptomic analyses and target phytohormone metabolome analysis to explore gene networks and hormones associated with heteranthery. We focused on three key stamen characteristics-colour, spatial patterning, and filament elongation-selected for their significant roles in stamen differentiation and their relevance to the functional diversity observed in heterantherous species. Our analyses suggest that gene networks involving MelLEAFY3, MADS-box, and TCP genes regulate stamen identity, with anthocyanin influencing colour, and lignin contributing to filament elongation. Additionally, variation in jasmonic acid and abscisic acid concentration between feeding and pollinating anthers appears to contribute to their morphological divergence. Our findings highlight gene networks and hormones associated with intra-floral stamen differentiation and indicate that whole genome duplications have likely facilitated the evolution of heteranthery during divergence from other Pontederiaceae without heteranthery.

The calcium-dependent protein kinase CmaCPK4 regulates sex determination in pumpkin (Cucurbita maxima D.)

Pumpkin (Cucurbita maxima D.) is typically monoecious with individual male and female flowers, and its yield is associated with the degree of femaleness, i.e. the ratio of female to male flowers produced by the plant. Subgynoecy represents a sex form with a high degree of femaleness, but the regulatory mechanisms in pumpkin remain poorly understood. In this study, using the F2 population crossed from the subgynoecious line 2013-12 and the monoecious line 9-6, we initially identified a recessive locus to control the subgynoecious trait and named it sg1. After bulked segregant analysis with whole-genome resequencing and molecular marker linkage analysis, the sg1 locus was mapped to pumpkin Chromosome 2. Genetic sequence analysis found a pumpkin calcium-dependent protein kinase (CPK) gene, CmaCPK4, in the mapping interval as the candidate gene. A retrotransposon insertion identified within the promoter elevated CmaCPK4 expression in 2013-12. Morphological characterization of near-isogenic lines containing the sg1 allele showed increases in the ratio of female flowers and high ethylene contents in terminal buds compared with the receptor parent. Heterologous overexpression of CmaCPK4 significantly increased the ratio of female flowers in cucumber (Cucumis sativus). Furthermore, CmaCPK4 directly interacts with and phosphorylates 1-aminocyclopropane-1-carboxylate synthase 5 (CmaACS5) and 1-aminocyclopropane-1-carboxylate synthase 7 (CmaACS7), resulting in increased ethylene content in 2013-12, which affected pumpkin sex determination. These findings provide insights into the role of the CmaCPK4-CmaACS5/CmaACS7 module in ethylene-induced sex determination in pumpkin.

SpMS1, a male sterility factor, interacts with SpAP1 to regulate unisexual flower development in dioecious spinach

The emergence of unisexual flower is an important event during plant evolution. The molecular mechanism underlying the formation of unisexual flowers remains unclear in dioecious spinach. In this study, we identified the spinach MALE STERILITY1 gene, SpMS1, which serves as a masculine factor to regulate male fertility and sex reversion. Silencing SpMS1 led to stamen sterility in male flowers and the development of masculine traits in female flowers. Overexpression of SpMS1 in wild-type Arabidopsis resulted in sterile stamens and irregular pollen exine. Notably, ectopic expression of SpMS1 in Arabidopsis ms1 mutants restored pollen viability and flower fertility. Furthermore, our findings demonstrate that SpMS1 interacts with MADS-box transcription factor SpAP1 to regulate unisexual flower development. Thus, SpMS1 exhibits a conserved function in pollen fertility akin to bisexual flowers, while also acting as a key regulator of unisexual flower development in spinach. This study sheds light on the mechanism of sex differentiation in dioecious plants and also provides valuable insights for manipulating male sterility in plant breeding programs.

Female flowers with short ovaries in 'Lemon' cucumber (Cucumis sativus) plants and their progeny carrying the mm genotype (CS-ACS2 genes with c.97G > T mutations): a novel trimonoecious phenotype

Analysis of the sex expression in 10 'Lemon' (mmff) cucumber plants (Cucumis sativus L.), known to be andromonoecious, revealed that 3 plants produced female flowers with short ovaries, resembling bisexual flowers, after producing male and bisexual flowers. To investigate the heredity pattern governing these aberrant female flowers with short ovaries, F1 hybrid plants (MmFf) were generated through a cross between 'Dokanari-sennari' (MMFF) and 'Lemon' (mmff), and #4 (mmff) and #45 (mmFF) were meticulously selected from a pool of 45 F2 segregants. Analysis of the sex expression in both 10 F5 plants (mmff) derived from the #4 (mmff) and 10 F4 plants (mmFF) derived from the #45 (mmFF) revealed that 8-9 plants produced female flowers with short ovaries after producing male and bisexual flowers. Notably, no female flowers with short ovaries were produced in the plants carrying the M gene, such as 'Dokanari-sennari' (MMFF), 8 F1 hybrid plants (MmFf), and the 29 F2 segregants (M-F-,M-ff). Thus, female flowers with short ovaries may be produced in some 'Lemon' (mmff) cucumber plants and their progeny, particularly those carrying the mm genotype (CS-ACS2 genes with c.97G > T mutations), after the production of male and bisexual flowers. However, no clear genetic rules governing the occurrence of these female flowers with short ovaries were observed. This is the first report on trimonoecious cucumber plants displaying male flowers, bisexual flowers with short ovaries, and female flowers with short ovaries, all on the same plant, under the influence of the mm genotype (CS-ACS2 genes with c.97G > T mutations).

Revisit and explore the ethylene-independent mechanism of sex expression in cucumber (Cucumis sativus)

KEY MESSAGE

This review provides a thorough and comprehensive perspective on the topic of cucumber sexual expression. Specifically, insights into sex expression mediated by pathways other than ethylene are highlighted. Cucumber (Cucumis sativus L.) is a common and important commercial crop that is cultivated and consumed worldwide. Additionally, this species is commonly used as a model for investigating plant sex expression. Cucumbers exhibit a variety of floral arrangements, comprising male, female, and hermaphroditic (bisexual) flowers. Generally, cucumber plants that produce female flowers are typically preferred due to their significant impact on the overall output. Various environmental conditions, such as temperature, light quality, and photoperiod, have been also shown to influence the sex expression in this species. Multiple lines of evidence indicate that ethylene and its biosynthesis genes are crucial in regulating cucumber sex expression. Gibberellins, another well-known phytohormone, can similarly influence cucumber sex expression via an ethylene-independent route. Further studies employing the next-generation sequencing technology also visualized a deeper slice of the molecular mechanism such as the role of the cell cycle program in the cucumber sex expression. This review aims to provide an overview of the sex expression of cucumber including its underlying molecular mechanism and regulatory aspects based on recent investigations.

Constitutive expression of cucumber CsACS2 in Arabidopsis Thaliana disrupts anther dehiscence through ethylene signaling and DNA methylation pathways

KEY MESSAGE

Constitutive expression of cucumber CsACS2 in Arabidopsis disrupts anther dehiscence and male fertility via ethylene signaling and DNA methylation, revealing new avenues for enhancing crop reproductive traits. The cucumber gene CsACS2, encoding ACC (1-aminocyclopropane-1-carboxylic acid) synthase, plays a pivotal role in ethylene biosynthesis and sex determination. This study investigates the effects of constitutive CsACS2 expression in Arabidopsis thaliana on anther development and male fertility. Transgenic Arabidopsis plants overexpressing CsACS2 exhibited male sterility due to inhibited anther dehiscence, which was linked to suppressed secondary cell wall thickening. RNA-Seq analysis revealed upregulation of ethylene signaling pathway genes and downregulation of secondary cell wall biosynthesis genes, with gene set enrichment analysis indicating the involvement of DNA methylation. Rescue experiments demonstrated that silver nitrate (AgNO₃) effectively restored fertility, while 5-azacytidine (5-az) partially restored it, highlighting the roles of ethylene signaling and DNA methylation in this process. Constitutive CsACS2 expression in Arabidopsis disrupts anther development through ethylene signaling and DNA methylation pathways, providing new insights into the role of ethylene in plant reproductive development and potential applications in crop improvement.

Parthenocarpy, a pollination-independent fruit set mechanism to ensure yield stability

Fruit development is essential for flowering plants' reproduction and a significant food source. Climate change threatens fruit yields due to its impact on pollination and fertilization processes, especially vulnerable to extreme temperatures, insufficient light, and pollinator decline. Parthenocarpy, the development of fruit without fertilization, offers a solution, ensuring yield stability in adverse conditions and enhancing fruit quality. Parthenocarpic fruits not only secure agricultural production but also exhibit improved texture, appearance, and shelf life, making them desirable for food processing and other applications. Recent research unveils the molecular mechanisms behind parthenocarpy, implicating transcription factors (TFs), noncoding RNAs, and phytohormones such as auxin, gibberellin (GA), and cytokinin (CK). Here we review recent findings, construct regulatory models, and identify areas for further research.

Ethylene in fruits: beyond ripening control

Fruits are a rich source of nutrients, minerals, and dietary fibers for both humans and animals. While the gaseous phytohormone ethylene is well-known for its role in controlling fruit ripening, there is growing evidence that ethylene also plays crucial roles in regulating other developmental processes of fruits, such as sex determination, fruit set, and fruit growth. In this review, we aim to revisit these findings from various species like cucumber, melon, tomato, rice, maize, and more. These studies not only enhance our understanding of ethylene's function in fruits but also highlight the potential for manipulating ethylene to improve crops. Furthermore, we discuss recent studies that show the ethylene precursor ACC (1-AMINOCYCLOPROPANE-1-CARBOXYLATE), and the ethylene signaling components EIN2 (ETHYLENE INSENSITIVE2) and EIN3 (ETHYLENE INSENSITIVE3) have ethylene-independent function in specific conditions. This phenomenon, combined with findings of dosage-dependent ethylene functions in certain conditions, highlights the importance of analyzing mutants with completely blocked ethylene pathways in different species at specific developmental stages and tissue types. Overall, this review offers a timely and essential summary of ethylene's role in sex determination, fruit formation, and fruit growth, which could be beneficial for horticulture crop breeding.

Exploring ethylene-related genes in Cannabis sativa: implications for sexual plasticity

KEY MESSAGE

Presented here are model Yang cycle, ethylene biosynthesis and signaling pathways in Cannabis sativa. C. sativa floral transcriptomes were used to predict putative ethylene-related genes involved in sexual plasticity in the species. Sexual plasticity is a phenomenon, wherein organisms possess the ability to alter their phenotypic sex in response to environmental and physiological stimuli, without modifying their sex chromosomes. Cannabis sativa L., a medically valuable plant species, exhibits sexual plasticity when subjected to specific chemicals that influence ethylene biosynthesis and signaling. Nevertheless, the precise contribution of ethylene-related genes (ERGs) to sexual plasticity in cannabis remains unexplored. The current study employed Arabidopsis thaliana L. as a model organism to conduct gene orthology analysis and reconstruct the Yang Cycle, ethylene biosynthesis, and ethylene signaling pathways in C. sativa. Additionally, two transcriptomic datasets comprising male, female, and chemically induced male flowers were examined to identify expression patterns in ERGs associated with sexual determination and sexual plasticity. These ERGs involved in sexual plasticity were categorized into two distinct expression patterns: floral organ concordant (FOC) and unique (uERG). Furthermore, a third expression pattern, termed karyotype concordant (KC) expression, was proposed, which plays a role in sex determination. The study revealed that CsERGs associated with sexual plasticity are dispersed throughout the genome and are not limited to the sex chromosomes, indicating a widespread regulation of sexual plasticity in C. sativa.

One-factor sex determination evolves without linkage between feminizing and masculinizing mutations

The evolution of separate sexes from cosexuality requires at least two mutations: a feminizing allele to cause female development and a masculinizing allele to cause male development. Classically, the double mutant is assumed to be sterile, which leads to two-factor sex determination where male and female sex chromosomes differ at two loci. However, several species appear to have one-factor sex determination where sexual development depends on variation at a single locus. We show that one-factor sex determination evolves when the double mutant develops as a male or a female. The feminizing allele fixes when the double mutant is male, and the masculinizing allele fixes when the double mutant is female. The other locus then gives XY or ZW sex determination based on dominance: for example, a dominant masculinizer becomes a Y chromosome. Although the resulting sex determination system differs, the conditions required for feminizers and masculinizers to spread are the same as in classical models, with the important difference that the two alleles do not need to be linked. Thus, we reveal alternative pathways for the evolution of sex determination and discuss how they can be distinguished using new data on the genetics of sex determination.

Harbinger transposon insertion in ethylene signaling gene leads to emergence of new sexual forms in cucurbits

In flowering plants, the predominant sexual morph is hermaphroditism, and the emergence of unisexuality is poorly understood. Using Cucumis melo (melon) as a model system, we explore the mechanisms driving sexual forms. We identify a spontaneous mutant exhibiting a transition from bisexual to unisexual male flower, and identify the causal mutation as a Harbinger transposon impairing the expression of Ethylene Insensitive 2 (CmEIN2) gene. Genetics and transcriptomic analysis reveal a dual role of CmEIN2 in both sex determination and fruit shape formation. Upon expression of CmACS11, EIN2 is recruited to repress the expression of the carpel inhibitor, CmWIP1. Subsequently, EIN2 is recruited to mediate stamina inhibition. Following the sex determination phase, EIN2 promotes fruit shape elongation. Genome-wide analysis reveals that Harbinger transposon mobilization is triggered by environmental cues, and integrates preferentially in active chromatin, particularly within promoter regions. Characterization of a large collection of melon germplasm points to active transpositions in the wild, compared to cultivated accessions. Our study underscores the association between chromatin dynamics and the temporal aspects of mobile genetic element insertions, providing valuable insights into plant adaptation and crop genome evolution.

The transcription factor CpMYB62 controls the genetic network that leads to the determination of female flowers in Cucurbita pepo

In monoecious species, female flowering constitutes the developmental process that determines the onset and production of fruit and is therefore closely related to crop yield. This article presents the identification and phenotypic and molecular characterization of myb62, an ethylmethane sulfonate loss-of-function mutation that completely blocks the female floral transition, converting all female flowers into male flowers. BSA-seq analysis coupled with WGS showed that myb62 corresponds to a C>T transition in the coding region of the gene CpMYB62, generating a premature stop codon and a truncated transcription factor without its N-terminal effector domain. The myb62 phenotype was partially rescued by exogenous ethylene application, indicating that the function of CpMYB62 is mediated by ethylene. Different evidence supports this conclusion: first, the reduced ethylene production of the mutant, and second, the male flower productive phenotype of the double mutant between myb62 and the ethylene-insensitive mutant etr2b, which demonstrated that myb62 is epistatic over etr2b. Furthermore, transcriptomic analysis of WT and myb62 apical shoots confirmed that CpMYB62 regulates master sex-determining genes, upregulating those encoding the ethylene biosynthesis enzymes CpACO2B and CpACS27A and those encoding for transcription factors that promote the development of carpels(CpCRC), but downregulating those involved in the arrest of carpels (CpWIP1), In the gene network controlling sex determination in cucurbits, CpMYB62 occupies the most upstream position, activating ethylene and other sex determining genes involved in female flower determination in Cucurbita  pepo.

Gene co-expression network analysis in areca floral organ and the potential role of the AcMADS17 and AcMADS23 in transgenic Arabidopsis

Areca catechu L., a monocot belonging to the palm family, is monoecious, with female and male flowers separately distributed on the same inflorescence. To discover the molecular mechanism of flower development in Areca, we sequenced different floral samples to generate tissue-specific transcriptomic profiles. We conducted a comparative analysis of the transcriptomic profiles of apical sections of the inflorescence with male flowers and the basal section of the inflorescence with female flowers. Based on the RNA sequencing dataset, we applied weighted gene co-expression network analysis (WGCNA) to identify sepal, petal, stamen, stigma and other specific modules as well as hub genes involved in specific floral organ development. The syntenic and expression patterns of AcMADS-box genes were analyzed in detail. Furthermore, we analyzed the open chromatin regions and transcription factor PI binding sites in male and female flowers by assay for transposase-accessible chromatin sequencing (ATAC-seq) assay. Heterologous expression revealed the important role of AcMADS17 and AcMADS23 in floral organ development. Our results provide a valuable genomic resource for the functional analysis of floral organ development in Areca.

ACC SYNTHASE4 inhibits gibberellin biosynthesis and FLOWERING LOCUS T expression during citrus flowering

Flowering is an essential process in fruit trees. Flower number and timing have a substantial impact on the yield and maturity of fruit. Ethylene and gibberellin (GA) play vital roles in flowering, but the mechanism of coordinated regulation of flowering in woody plants by GA and ethylene is still unclear. In this study, a lemon (Citrus limon L. Burm) 1-aminocyclopropane-1-carboxylic acid synthase gene (CiACS4) was overexpressed in Nicotiana tabacum and resulted in late flowering and increased flower number. Further transformation of citrus revealed that ethylene and starch content increased, and soluble sugar content decreased in 35S:CiACS4 lemon. Inhibition of CiACS4 in lemon resulted in effects opposite to that of 35S:CiACS4 in transgenic plants. Overexpression of the CiACS4-interacting protein ETHYLENE RESPONSE FACTOR3 (CiERF3) in N. tabacum resulted in delayed flowering and more flowers. Further experiments revealed that the CiACS4-CiERF3 complex can bind the promoters of FLOWERING LOCUS T (CiFT) and GOLDEN2-LIKE (CiFE) and suppress their expression. Moreover, overexpression of CiFE in N. tabacum led to early flowering and decreased flowers, and ethylene, starch, and soluble sugar contents were opposite to those in 35S:CiACS4 transgenic plants. Interestingly, CiFE also bound the promoter of CiFT. Additionally, GA3 and 1-aminocyclopropanecarboxylic acid (ACC) treatments delayed flowering in adult citrus, and treatment with GA and ethylene inhibitors increased flower number. ACC treatment also inhibited the expression of CiFT and CiFE. This study provides a theoretical basis for the application of ethylene to regulate flower number and mitigate the impacts of extreme weather on citrus yield due to delayed flowering.

Developmental stages and episode-specific regulatory genes in andromonoecious melon flower development

BACKGROUND AND AIMS

Given the lack of specific studies on floral development in melon (Cucumis melo L.), we carried out an extensive study involving morphological and transcriptomic analyses to characterize floral development in this species.

METHODS

Using an andromonoecious line, we analysed the development of floral buds in male and hermaphrodite flowers with both light microscopy and scanning electron microscopy. Based on flower lengths, we established a correlation between the developmental stages and four main episodes of floral development and conducted an extensive RNA sequencing analysis of these episodes.

KEY RESULTS

We identified 12 stages of floral development, from the appearance of the floral meristems to anthesis. The main structural differences between male and hermaphrodite flowers appeared between stages 6 and 7; later stages of development leading to the formation of organs and structures in both types of flowers were also described. We analysed the gene expression patterns of the four episodes in flower development to find the genes that were specific to each given episode. Among others, we identified genes that defined the passage from one episode to the next according to the ABCDE model of floral development.

CONCLUSIONS

This work combines a detailed morphological analysis and a comprehensive transcriptomic study to enable characterization of the structural and molecular mechanisms that determine the floral development of an andromonoecious genotype in melon. Taken together, our results provide a first insight into gene regulation networks in melon floral development that are crucial for flowering and pollen formation, highlighting potential targets for genetic manipulation to improve crop yield of melon in the future.

An miR164-resistant mutation in the transcription factor gene CpCUC2B enhances carpel arrest and ectopic boundary specification in Cucurbita pepo flower development

The sex determination process in cucurbits involves the control of stamen or carpel development during the specification of male or female flowers from a bisexual floral meristem, a function coordinated by ethylene. A gain-of-function mutation in the miR164-binding site of CpCUC2B, ortholog of the Arabidopsis transcription factor gene CUC2, not only produced ectopic floral meristems and organs, but also suppressed the development of carpels and promoted the development of stamens. The cuc2b mutation induced the transcription of CpCUC2B in the apical shoots of plants after female flowering but repressed other CUC genes regulated by miR164, suggesting a conserved functional redundancy of these genes in the development of squash flowers. The synergistic androecious phenotype of the double mutant between cuc2b and etr2b, an ethylene-insensitive mutation that enhances the production of male flowers, demonstrated that CpCUC2B arrests the development of carpels independently of ethylene and CpWIP1B. The transcriptional regulation of CpCUC1, CpCUC2, and ethylene genes in cuc2b and ethylene mutants also confirms this conclusion. However, the epistasis of cuc2b over aco1a, a mutation that suppresses stamen arrest in female flowers, and the down-regulation of CpACS27A in cuc2b female apical shoots, indicated that CpCUC2B promotes stamen development by suppressing the late ethylene production.

Striking a growth-defense balance: Stress regulators that function in maize development

Maize (Zea mays) cultivation is strongly affected by both abiotic and biotic stress, leading to reduced growth and productivity. It has recently become clear that regulators of plant stress responses, including the phytohormones abscisic acid (ABA), ethylene (ET), and jasmonic acid (JA), together with reactive oxygen species (ROS), shape plant growth and development. Beyond their well established functions in stress responses, these molecules play crucial roles in balancing growth and defense, which must be finely tuned to achieve high yields in crops while maintaining some level of defense. In this review, we provide an in-depth analysis of recent research on the developmental functions of stress regulators, focusing specifically on maize. By unraveling the contributions of these regulators to maize development, we present new avenues for enhancing maize cultivation and growth while highlighting the potential risks associated with manipulating stress regulators to enhance grain yields in the face of environmental challenges.

Possibility of genome editing for melon breeding

Genome editing technologies are promising for conventional mutagenesis breeding, which takes a long time to remove unnecessary mutations through backcrossing and create new lines because they directly modify the target genes of elite strains. In particular, this technology has advantages for traits caused by the loss of function. Many efforts have been made to utilize this technique to introduce valuable features into crops, including maize, soybeans, and tomatoes. Several genome-edited crops have already been commercialized in the US and Japan. Melons are an important vegetable crop worldwide, produced and used in various areas. Therefore, many breeding efforts have been made to improve its fruit quality, resistance to plant diseases, and stress tolerance. Quantitative trait loci (QTL) analysis was performed, and various genes related to important traits were identified. Recently, several studies have shown that the CRISPR/Cas9 system can be applied to melons, resulting in its possible utilization as a breeding technique. Focusing on two productivity-related traits, disease resistance, and fruit quality, this review introduces the progress in genetics, examples of melon breeding through genome editing, improvements required for breeding applications, and the possibilities of genome editing in melon breeding.

Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant

Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigated in animals and brown algae, less is known about evolutionary forces in dioecious angiosperms. In this study, we separately compared the expression of sex-biased genes between female and male floral buds and between female and male flowers at anthesis in dioecious Trichosanthes pilosa (Cucurbitaceae). In floral buds, sex-biased gene expression was pervasive, and had significantly different roles in sexual dimorphism such as physiology. We observed higher rates of sequence evolution for male-biased genes in floral buds compared to female-biased and unbiased genes. Male-biased genes under positive selection were mainly associated with functions to abiotic stress and immune responses, suggesting that high evolutionary rates are driven by adaptive evolution. Additionally, relaxed purifying selection may contribute to accelerated evolution in male-biased genes generated by gene duplication. Our findings, for the first time in angiosperms, suggest evident rapid evolution of male-biased genes, advance our understanding of the patterns and forces driving the evolution of sexual dimorphism in dioecious plants.

Young evolutionary origins of dioecy in the genus Asparagus

PREMISE

Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking.

METHODS

We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature.

RESULTS

We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers.

CONCLUSIONS

Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.

High-quality Momordica balsamina genome elucidates its potential use in improving stress resilience and therapeutic properties of bitter gourd

Introduction

Momordica balsamina is the closest wild species that can be crossed with an important fruit vegetable crop, Momordica charantia, has immense medicinal value, and placed under II subclass of primary gene pool of bitter gourd. M. balsamina is tolerant to major biotic and abiotic stresses. Genome characterization of Momordica balsamina as a wild relative of bitter gourd will contribute to the knowledge of the gene pool available for improvement in bitter gourd. There is potential to transfer gene/s related to biotic resistance and medicinal importance from M. balsamina to M. charantia to produce high-quality, better yielding and stress tolerant bitter gourd genotypes.

Methods

The present study provides the first and high-quality chromosome-level genome assembly of M. balsamina with size 384.90 Mb and N50 30.96 Mb using sequence data from 10x Genomics, Nanopore, and Hi-C platforms.

Results

A total of 6,32,098 transposons elements; 2,15,379 simple sequence repeats; 5,67,483 transcription factor binding sites; 3,376 noncoding RNA genes; and 41,652 protein-coding genes were identified, and 4,347 disease resistance, 67 heat stress-related, 05 carotenoid-related, 15 salt stress-related, 229 cucurbitacin-related, 19 terpenes-related, 37 antioxidant activity, and 06 sex determination-related genes were characterized.

Conclusion

Genome sequencing of M. balsamina will facilitate interspecific introgression of desirable traits. This information is cataloged in the form of webgenomic resource available at http://webtom.cabgrid.res.in/mbger/. Our finding of comparative genome analysis will be useful to get insights into the patterns and processes associated with genome evolution and to uncover functional regions of cucurbit genomes.

Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce

The naturally occurring bisexual cone of gymnosperms has long been considered a possible intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in the conifer Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-class, C-class and LEAFY genes, supporting the out of male model. GGM7 could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of key genes in cone development, including PcDAL12, PcDAL10, PcNEEDLY, and PcHDG5. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the evolution of bisexuality.

Comparative RNA-Seq Analysis between Monoecious and Androecious Plants Reveals Regulatory Mechanisms Controlling Female Flowering in Cucurbita pepo

In the monoecious Cucurbita pepo, the transition to female flowering is the time at which the plant starts the production of female flowers after an initial male phase of development. Ethylene plays an essential role in this process since some ethylene deficient and ethylene-insensitive mutants are androecious and only produce male flowers. To gain insight into the molecular mechanisms regulating the specification and early development of female flowers, we have compared the transcriptomic changes occurring in the shoot apices of WT and androecious ethylene-insensitive etr1b mutant plants upon female flowering transition. There were 1160 female flowering-specific DEGs identified in WT plants upon female flowering, and 284 of them were found to be modulated by the ethylene-insensitive etr1b mutation. The function of these DEGs indicated that female flower specification depends on the adoption of a transcriptional program that includes previously identified sex-determining genes in the ethylene pathway, but also genes controlling the biosynthesis and signaling pathways of other phytohormones, and those encoding for many different transcription factors. The transcriptomic changes suggested that gibberellins play a negative role in female flowering, while ethylene, auxins, ABA and cytokinins are positive regulators. Transcription factors from 34 families, including NAC, ERF, bHLH, bZIP, MYB and C2H2/CH3, were found to be regulating female flowering in an ethylene-dependent or -independent manner. Our data open a new perspective of the molecular mechanisms that control the specification and development of female flowers in C. pepo.

Multi-Omics Analysis Reveals Intricate Gene Networks Involved in Female Development in Melon

Sexual differentiation is an important developmental phenomenon in cucurbits that directly affects fruit yield. The natural existence of multiple flower types in melon offers an inclusive structure for studying the molecular basis of sexual differentiation. The current study aimed to identify and characterize the molecular network involved in sex determination and female development in melon. Male and female pools separated by the F2 segregated generation were used for sequencing. The comparative multi-omics data revealed 551 DAPs and 594 DEGs involved in multiple pathways of melon growth and development, and based on functional annotation and enrichment analysis, we summarized four biological process modules, including ethylene biosynthesis, flower organ development, plant hormone signaling, and ubiquitinated protein metabolism, that are related to female development. Furthermore, the detailed analysis of the female developmental regulatory pathway model of ethylene biosynthesis, signal transduction, and target gene regulation identified some important candidates that might have a crucial role in female development. Two CMTs ((cytosine-5)-methyltransferase), one AdoHS (adenosylhomocysteinase), four ACSs (1-aminocyclopropane-1-carboxylic acid synthase), three ACOs (ACC oxidase), two ARFs (auxin response factor), four ARPs (auxin-responsive protein), and six ERFs (Ethylene responsive factor) were identified based on various female developmental regulatory models. Our data offer new and valuable insights into female development and hold the potential to offer a deeper comprehension of sex differentiation mechanisms in melon.

Evolution of sex-determination in dioecious plants: From active Y to X/A balance?

Sex chromosomes in plants have been known for a century, but only recently have we begun to understand the mechanisms behind sex determination in dioecious plants. Here, we discuss evolution of sex determination, focusing on Silene latifolia, where evolution of separate sexes is consistent with the classic "two mutations" model-a loss of function male sterility mutation and a gain of function gynoecium suppression mutation, which turned an ancestral hermaphroditic population into separate males and females. Interestingly, the gynoecium suppression function in S. latifolia evolved via loss of function in at least two sex-linked genes and works via gene dosage balance between sex-linked, and autosomal genes. This system resembles X/A-ratio-based sex determination systems in Drosophila and Rumex, and could represent a steppingstone in the evolution of X/A-ratio-based sex determination from an active Y system.

Ethylene produced in carpel primordia controls CmHB40 expression to inhibit stamen development

Sex determination evolved to control the development of unisexual flowers. In agriculture, it conditions how plants are cultivated and bred. We investigated how female flowers develop in monoecious cucurbits. We discovered in melon, Cucumis melo, a mechanism in which ethylene produced in the carpel is perceived in the stamen primordia through spatially differentially expressed ethylene receptors. Subsequently, the CmEIN3/CmEIL1 ethylene signalling module, in stamen primordia, activates the expression of CmHB40, a transcription factor that downregulates genes required for stamen development and upregulates genes associated with organ senescence. Investigation of melon genetic biodiversity revealed a haplotype, originating in Africa, altered in EIN3/EIL1 binding to CmHB40 promoter and associated with bisexual flower development. In contrast to other bisexual mutants in cucurbits, CmHB40 mutations do not alter fruit shape. By disentangling fruit shape and sex-determination pathways, our work opens up new avenues in plant breeding.

Form and contour: breeding and genetics of organ shape from wild relatives to modern vegetable crops

Shape is a primary determinant of consumer preference for many horticultural crops and it is also associated with many aspects of marketing, harvest mechanics, and postharvest handling. Perceptions of quality and preference often map to specific shapes of fruits, tubers, leaves, flowers, roots, and other plant organs. As a result, humans have greatly expanded the palette of shapes available for horticultural crops, in many cases creating a series of market classes where particular shapes predominate. Crop wild relatives possess organs shaped by natural selection, while domesticated species possess organs shaped by human desires. Selection for visually-pleasing shapes in vegetable crops resulted from a number of opportunistic factors, including modification of supernumerary cambia, allelic variation at loci that control fundamental processes such as cell division, cell elongation, transposon-mediated variation, and partitioning of photosynthate. Genes that control cell division patterning may be universal shape regulators in horticultural crops, influencing the form of fruits, tubers, and grains in disparate species. Crop wild relatives are often considered less relevant for modern breeding efforts when it comes to characteristics such as shape, however this view may be unnecessarily limiting. Useful allelic variation in wild species may not have been examined or exploited with respect to shape modifications, and newly emergent information on key genes and proteins may provide additional opportunities to regulate the form and contour of vegetable crops.

Chemical mutagenesis and thermal selection of coral photosymbionts induce adaptation to heat stress with trait trade-offs

Despite the relevance of heat-evolved microalgal endosymbionts to coral reef restoration, to date, few Symbiodiniaceae strains have been thermally enhanced via experimental evolution. Here, we investigated whether the thermal tolerance of Symbiodiniaceae can be increased through chemical mutagenesis followed by thermal selection. Strains of Durusdinium trenchii, Fugacium kawagutii and Symbiodinium pilosum were exposed to ethyl methanesulfonate to induce random mutagenesis, and then underwent thermal selection at high temperature (31/33°C). After 4.6-5 years of experimental evolution, the in vitro thermal tolerance of these strains was assessed via reciprocal transplant experiments to ambient (27°C) and elevated (31/35°C) temperatures. Growth, photosynthetic efficiency, oxidative stress and nutrient use were measured to compare thermal tolerance between strains. Heat-evolved D. trenchii, F. kawagutii and S. pilosum strains all exhibited increased photosynthetic efficiency under thermal stress. However, trade-offs in growth rates were observed for the heat-evolved D. trenchii lineage at both ambient and elevated temperatures. Reduced phosphate and nitrate uptake rates in F. kawagutii and S. pilosum heat-evolved lineages, respectively, suggest alterations in nutrition resource usage and allocation processes may have occurred. Increased phosphate uptake rates of the heat-evolved D. trenchii strain indicate that experimental evolution resulted in further trade-offs in this species. These findings deepen our understanding of the physiological responses of Symbiodiniaceae cultures to thermal selection and their capacity to adapt to elevated temperatures. The new heat-evolved Symbiodiniaceae developed here may be beneficial for coral reef restoration efforts if their enhanced thermal tolerance can be conferred in hospite.

Impact of Climate Change on Regulation of Genes Involved in Sex Determination and Fruit Production in Cucumber

Environmental changes, both natural and anthropogenic, mainly related to rising temperatures and water scarcity, are clearly visible around the world. Climate change is important for crop production and is a major issue for the growth and productivity of cucumbers. Processes such as sex determination, flower morphogenesis and fruit development in cucumbers are highly sensitive to various forms of stress induced by climatic changes. It is noteworthy that many factors, including genetic factors, transcription factors, phytohormones and miRNAs, are crucial in regulating these processes and are themselves affected by climate change. Changes in the expression and activity of these factors have been observed as a consequence of climatic conditions. This review focuses primarily on exploring the effects of climate change and abiotic stresses, such as increasing temperature and drought, on the processes of sex determination, reproduction, and fruit development in cucumbers at the molecular level. In addition, it highlights the existing research gaps that need to be addressed in order to improve our understanding of the complex interactions between climate change and cucumber physiology. This, in turn, may lead to strategies to mitigate the adverse effects and enhance cucumber productivity in a changing climate.

Genetic Mechanisms for Hybrid Breeding in Vegetable Crops

To address the complex challenges faced by our planet such as rapidly changing climate patterns, food and nutritional insecurities, and the escalating world population, the development of hybrid vegetable crops is imperative. Vegetable hybrids could effectively mitigate the above-mentioned fundamental challenges in numerous countries. Utilizing genetic mechanisms to create hybrids not only reduces costs but also holds significant practical implications, particularly in streamlining hybrid seed production. These mechanisms encompass self-incompatibility (SI), male sterility, and gynoecism. The present comprehensive review is primarily focused on the elucidation of fundamental processes associated with floral characteristics, the genetic regulation of floral traits, pollen biology, and development. Specific attention is given to the mechanisms for masculinizing and feminizing cucurbits to facilitate hybrid seed production as well as the hybridization approaches used in the biofortification of vegetable crops. Furthermore, this review provides valuable insights into recent biotechnological advancements and their future utilization for developing the genetic systems of major vegetable crops.

Understanding Transcription Factors and How They Affect Processes in Cucumber Sex Determination

Plant reproduction is a fundamental process on Earth from the perspective of biodiversity, biomass gain, and crop productivity. It is therefore important to understand the sex determination process, and many researchers are investigating the molecular basis of this phenomenon. However, information on the influence of transcription factors (TFs), genes that encode DNA-binding proteins, on this process is limited, although cucumber is a model plant in this regard. In the present study, based on RNA-seq data for differentially expressed genes (DEGs), we aimed to investigate the regulatory TFs that may influence the metabolic processes in the shoot apex containing the forming flower buds. Therefore, the annotation of the genome of the B10 cucumber line was supplemented with the assigned families of transcription factors. By performing ontology analyses of the DEGs, the processes they participate in were identified, and TFs were located among the results. In addition, TFs that have significantly overrepresented targets among DEGs were detected, and sex-specific interactome network maps were generated, indicating the regulatory TFs based on their effects on DEGs and furthermore, on the processes leading to the formation of different-sex flowers. Among the most overrepresented TF families in the sex comparisons were the NAC, bHLH, MYB, and bZIP families. An interaction network analysis indicated the most abundant families among DEGs' regulatory TFs were MYB, AP2/ERF, NAC, and bZIP, and those with the most significant impact on developmental processes were identified, namely the AP/ERF family, followed by DOF, MYB, MADS, and others. Thus, the networks' central nodes and key regulators were identified with respect to male, female, and hermaphrodite forms. Here, we proposed the first model of the regulatory network of TFs that influences the metabolism of sex development in cucumber. These findings may help us to understand the molecular genetics and functional mechanisms underlying sex determination processes.

Identification of novel sex determination loci in Japanese weedy melon

KEY MESSAGE

Japanese weedy melon exhibits unique sex expression with interactions between previously reported sex determination genes and two novel loci. Sex expression contributes to fruit quality and yield in the Cucurbitaceae. In melon, orchestrated regulation by sex determination genes explains the mechanism of sex expression, resulting in a great variety of sexual morphologies. In this study, we examined the Japanese weedy melon UT1, which does not follow the reported model of sex expression. We conducted QTL analysis using F₂ plants for flower sex on the main stem and the lateral branch and mapped "occurrence of pistil-bearing flower on the main stem" locus on Chr. 3 (Opbf3.1) and "type of pistil-bearing flower" (female or bisexual) loci on Chr. 2 (tpbf2.1) and Chr. 8 (tpbf8.1). The Opbf3.1 included the known sex determination gene CmACS11. Sequence comparison of CmACS11 between parental lines revealed three nonsynonymous SNPs. A CAPS marker developed from one of the SNPs was closely linked to the occurrence of pistil-bearing flowers on the main stem in two F₂ populations with different genetic backgrounds. The UT1 allele on Opbf3.1 was dominant in F₁ lines from crosses between UT1 and diverse cultivars and breeding lines. This study suggests that Opbf3.1 and tpbf8.1 may promote the development of pistil and stamen primordia by inhibiting CmWIP1 and CmACS-7 functions, respectively, making the UT1 plants hermaphrodite. The results of this study provide new insights into the molecular mechanisms of sex determination in melons and considerations for the application of femaleness in melon breeding.

Advance in sex differentiation in cucumber

Cucumber belongs to the family Cucurbitaceae (melon genus) and is an annual herbaceous vegetable crop. Cucumber is an important cash crop that is grown all over the world. From morphology to cytology, from canonical genetics to molecular biology, researchers have performed much research on sex differentiation and its regulatory mechanism in cucumber, mainly in terms of cucumber sex determination genes, environmental conditions, and the effects of plant hormones, revealing its genetic basis to improve the number of female flowers in cucumber, thus greatly improving the yield of cucumber. This paper reviews the research progress of sex differentiation in cucumber in recent years, mainly focusing on sex-determining genes, environmental conditions, and the influence of phytohormones in cucumber, and provides a theoretical basis and technical support for the realization of high and stable yield cultivation and molecular breeding of cucumber crop traits.

Evolution of sex in crops: recurrent scrap and rebuild

Sexuality is the main strategy for maintaining genetic diversity within a species. In flowering plants (angiosperms), sexuality is derived from ancestral hermaphroditism and multiple sexualities can be expressed in an individual. The mechanisms conferring chromosomal sex determination in plants (or dioecy) have been studied for over a century by both biologists and agricultural scientists, given the importance of this field for crop cultivation and breeding. Despite extensive research, the sex determining gene(s) in plants had not been identified until recently. In this review, we dissect plant sex evolution and determining systems, with a focus on crop species. We introduced classic studies with theoretical, genetic, and cytogenic approaches, as well as more recent research using advanced molecular and genomic techniques. Plants have undergone very frequent transitions into, and out of, dioecy. Although only a few sex determinants have been identified in plants, an integrative viewpoint on their evolutionary trends suggests that recurrent neofunctionalization events are potentially common, in a "scrap and (re)build" cycle. We also discuss the potential association between crop domestication and transitions in sexual systems. We focus on the contribution of duplication events, which are particularly frequent in plant taxa, as a trigger for the creation of new sexual systems.

Fine-mapping and candidate gene analysis of the Mcgy1 locus responsible for gynoecy in bitter gourd (Momordica spp.)

The Mcgy1 locus responsible for gynoecy was fine-mapped into a 296.94-kb region, in which four single-nucleotide variations and six genes adjacent to them might be associate with sex differentiation in bitter gourd. Gynoecy plays an important role in high-efficiency hybrid seed production, and gynoecious plants are excellent materials for dissecting sex differentiation in Cucurbitaceae crop species, including bitter gourd. However, the gene responsible for gynoecy in bitter gourd is unknown. Here, we first identified a gynoecy locus designated Mcgy1 using the F₂ population (n = 291) crossed from the gynoecious line S156G and the monoecious line K8-201 via bulked segregant analysis with whole-genome resequencing (BSA-seq) and molecular marker linkage analysis. Then, a large S156G × K8-201 F₂ population (n = 5,656) was used for fine-mapping to delimit the Mcgy1 locus into a 296.94-kb physical region on pseudochromosome MC01, where included 33 annotated genes different from any homologous gynoecy genes previously reported in Cucurbitaceae species. Within this region, four underlying single-nucleotide variations (SNVs) that might cause gynoecy were identified by multiple genomic sequence variation analysis, and their six neighbouring genes were considered as potential candidate genes for Mcgy1. Of these, only MC01g1681 showed a significant differential expression at two-leaf developmental stage between S156G and its monoecious near-isogenic line S156 based on RNA sequencing (RNA-seq) and qRT-PCR analyses. In addition, transcriptome analysis revealed 21 key differentially expressed genes (DEGs) and possible regulatory pathways of the formation of gynoecy in bitter gourd. Our findings provide a new clue for researching on gynoecious plants in Cucurbitaceae species and a theoretical basis for breeding gynoecious bitter gourd lines by the use of molecular markers-assisted selection.

Molecular mapping of genomic regions and identification of possible candidate genes associated with gynoecious sex expression in bitter gourd

Bitter gourd is an important vegetable crop grown throughout the tropics mainly because of its high nutritional value. Sex expression and identification of gynoecious trait in cucurbitaceous vegetable crops has facilitated the hybrid breeding programme in a great way to improve productivity. In bitter gourd, gynoecious sex expression is poorly reported and detailed molecular pathways involve yet to be studied. The present experiment was conducted to study the inheritance, identify the genomic regions associated with gynoecious sex expression and to reveal possible candidate genes through QTL-seq. Segregation for the gynoecious and monoecious sex forms in the F₂ progenies indicated single recessive gene controlling gynoecious sex expression in the genotype, PVGy-201. Gynoecious parent, PVGy-201, Monoecious parent, Pusa Do Mausami (PDM), and two contrasting bulks were constituted for deep-sequencing. A total of 10.56, 23.11, 15.07, and 19.38 Gb of clean reads from PVGy-201, PDM, gynoecious bulk and monoecious bulks were generated. Based on the ΔSNP index, 1.31 Mb regions on the chromosome 1 was identified to be associated with gynoecious sex expression in bitter gourd. In the QTL region 293,467 PVGy-201 unique variants, including SNPs and indels, were identified. In the identified QTL region, a total of 1019 homozygous variants were identified between PVGy1 and PDM genomes and 71 among them were non-synonymous variants (SNPS and INDELs), out of which 11 variants (7 INDELs, 4 SNPs) were classified as high impact variants with frame shift/stop gain effect. In total twelve genes associated with male and female gametophyte development were identified in the QTL-region. Ethylene-responsive transcription factor 12, Auxin response factor 6, Copper-transporting ATPase RAN1, CBL-interacting serine/threonine-protein kinase 23, ABC transporter C family member 2, DEAD-box ATP-dependent RNA helicase 1 isoform X2, Polygalacturonase QRT3-like isoform X2, Protein CHROMATIN REMODELING 4 were identified with possible role in gynoecious sex expression. Promoter region variation in 8 among the 12 genes indicated their role in determining gynoecious sex expression in bitter gourd genotype, DBGy-1. The findings in the study provides insight about sex expression in bitter gourd and will facilitate fine mapping and more precise identification of candidate genes through their functional validation.

Expression patterns of ABCE model genes during flower development of melon (Cucumis melo L.)

In production, most cultivars of melon are andromonoecious and characterized by carrying both male and bisexual flowers on the same plant. In this study, four A-class genes (CmAP1a, CmAP1b, CmAP2a and CmAP2b), two B-class genes (CmAP3 and CmPI), two C-class genes (CmAGa and CmAGb) and four E-class genes (CmSEP1,2,3,4) were identified in melon. However, no D-class gene of melon was identified. The conserved domains of ABCE function proteins showed relatively high similarity between Arabidopsis and melon. The expression patterns of ABCE homeotic genes in different flower buds of melon suggested that transcripts of CmAP1a, CmPI and CmSEP1 in bisexual buds were significantly lower than that in male flower buds, while the expression levels of CmAGa, CmAGb and CmSEP4 in bisexual flower buds were significantly higher than that in male flower buds. There was no significant difference in expression levels of other ABCE model genes between male buds and bisexual buds. Subsequently, qRT-PCR was performed in different floral organs of bisexual flowers in melon. For A class genes, CmAP1a and CmAP1b showed the highest accumulation in sepals than petals, stamens and pistil, while CmAP2a and CmAP2b revealed the highest expression in pistil than other three floral organs. For B class genes, CmAP3 and CmPI were highly accumulated in petals and stamens though CmAP3 also showed abundant accumulation in pistil. For C class genes, the expression levels of CmAGa and CmAGb were higher in stamens and pistil than that in sepals and petals. For E class genes, CmSEP1 showed higher expression level in sepals and petals than stamens and pistil. CmSEP2, CmSEP3 and CmSEP4 showed the highest accumulation in pistil than other floral organs. These results provided a theoretical basis for studying the function of ABCE homeotic genes in floral organs development of melon.

Vegetable biology and breeding in the genomics era

Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.

Evolution of plant sex and molecular mechanisms underlying plants sex separation

Unlike animals, plants exhibit more complexity of sexual morphs. The genetic mechanism underlying plant sex is a hot research topic in plant biology. In recent decades, advanced theories have been put forth on plant sex determination, but experimental proof is scarce. In recent years, vast achievements have been made to reveal the genetic mechanisms underlying sex separation of plants at the molecular level. Although the sex determination mechanisms have been clarified only in a limited number of plant species thus far, the discoveries offer us an opportunity to understand the genetic mechanisms triggering the separation of plant sexes. This paper reviewed the different aspects of the advanced studies on plant sex evolution and the molecular mechanisms underlying plant sex separation.

Fine mapping and candidate gene analysis of gynoecy trait in chieh-qua (Benincasa hispida Cogn. var. chieh-qua How)

Gynoecy demonstrates an earlier production of hybrids and a higher yield and improves the efficiency of hybrid seed production. Therefore, the utilization of gynoecy is beneficial for the genetic breeding of chieh-qua. However, little knowledge of gynoecious-related genes in chieh-qua has been reported until now. Here, we used an F₂ population from the cross between the gynoecious line 'A36' and the monoecious line 'SX' for genetic mapping and revealed that chieh-qua gynoecy was regulated by a single recessive gene. We fine-mapped it into a 530-kb region flanked by the markers Indel-3 and KASP145 on Chr.8, which harbors eight candidate genes. One of the candidate genes, Bhi08G000345, encoding networked protein 4 (CqNET4), contained a non-synonymous SNP resulting in the amino acid substitution of isoleucine (ATA; I) to methionine (ATG; M). CqNET4 was prominently expressed in the female flower, and only three genes related to ethylene synthesis were significantly expressed between 'A36' and 'SX.' The results presented here provide support for the CqNET4 as the most likely candidate gene for chieh-qua gynoecy, which differed from the reported gynoecious genes.

Novel Bisexual Flower Control Gene Regulates Sex Differentiation in Melon (Cucumis melo L.)

The sex-control system involves several mechanisms in melon. The present study identified a novel bisexual flower control gene from the hermaphroditic melon germplasm, different from the previously recognized one. Genetic analysis showed that a single recessive gene in the newly identified locus b controlled the bisexual flower phenotype in melons. We generated 1431 F₂ segregating individuals for genetic mapping of locus b, which was delimited to a 47.94 kb region. Six candidate genes were identified in the delimited interval, and candidate No. 4 encoding melon CPR5 protein was selected as the suitable one for locus b and was denoted CmCPR5. CPR5 reportedly interacted with ethylene receptor ETR1 to regulate ethylene signal transduction. Moreover, the ethephon assays showed that the parental lines (unisexual line and bisexual line) had contrasting expression patterns of CmCPR5. The BiFC and LCI assays also confirmed that CmCPR5 interacted with CmETR1 in 0426 but not in Y101. However, crossover tests showed that CmETR1 functioned normally in both parental lines, suggesting CPR5 malfunction in Y101. This study proposed a corollary mechanism of bisexual flower regulation during stamen primordium development in which the inhibition of stamen primordia development was prevented by the malfunctioning CmCPR5, resulting in bisexual flowers.

The genome of Areca catechu provides insights into sex determination of monoecious plants

The areca palm (Areca catechu) has a monoecious spadix, with male flowers on the apical side and females on the basal side. Here, we applied multiomics analysis to investigate sex determination and floral organ development in areca palms. We generated a chromosome-level reference genome of A. catechu with 16 pseudochromosomes, composed of 2.73 Gb and encoding 31 406 genes. Data from RNA-seq and ATAC-seq (assay for transposase accessible chromatin sequencing) suggested that jasmonic acid (JA) synthesis and signal transduction-related genes were differentially expressed between female and male flowers via epigenetic modifications. JA concentration in female flowers was c. 10 times than that in males on the same inflorescence, while JA concentration in hermaphroditic flowers of abnormal inflorescences was about twice that in male flowers of normal inflorescences. JA promotes the development of female flower organs by decreasing the expression of B-function genes, including AGL16, AP3, PIb and PIc. There is also a region on pseudochromosome 15 harboring sex-related genes, including CYP703, LOG, GPAT, AMS and BiP. Among them, CYP703, AMS and BiP were specifically expressed in male flowers.