Gain-of-function of the 1-aminocyclopropane-1-carboxylate synthase gene ACS1G induces female flower development in cucumber gynoecy

Adaptation of the Invasive Plant Sphagneticola trilobata to Flooding Stress by Hybridization with Native Relatives

Hybridization is common between invasive and native species and may produce more adaptive hybrids. The hybrid (Sphagneticola × guangdongensis) of Sphagneticola trilobata (an invasive species) and S. calendulacea (a native species) was found in South China. In this study, S. trilobata, S. calendulacea, and Sphagneticola × guangdongensis were used as research materials to explore their adaptability to flooding stress. Under flooding stress, the ethylene content and the expression of key enzyme genes related to ethylene synthesis in Sphagneticola × guangdongensis and S. calendulacea were significantly higher than those in S. trilobata. A large number of adventitious roots and aerenchyma were generated in Sphagneticola × guangdongensis and S. calendulacea. The contents of reactive oxygen species and malondialdehyde in Sphagneticola × guangdongensis and S. calendulacea were lower than those in S. trilobata, and the leaves of S. trilobata were the most severely damaged under flooding stress. The results indicate that hybridization catalyzed the tolerance of Sphagneticola × guangdongensis to flooding stress, and the responses of Sphagneticola × guangdongensis to flooding stress were more similar to that of its native parent. This suggests that hybridization with native relatives is an important way for invasive species to overcome environmental pressure and achieve invasion.

Chromosome-level genome assembly and population genomics reveals crucial selection for subgynoecy development in chieh-qua

Chieh-qua is an important cucurbit crop and very popular in South China and Southeast Asia. Despite its significance, its genetic basis and domestication history are unclear. In this study, we have successfully generated a chromosome-level reference genome assembly for the chieh-qua 'A36' using a hybrid assembly strategy that combines PacBio long reads and Illumina short reads. The assembled genome of chieh-qua is approximately 953.3 Mb in size and is organized into 12 chromosomes, with contig N50 of 6.9 Mb and scaffold N50 of 68.2 Mb. Notably, the chieh-qua genome is comparable in size to the wax gourd genome. Through gene prediction analysis, we have identified a total of 24 593 protein-coding genes in the A36 genome. Additionally, approximately 56.6% (539.3 Mb) of the chieh-qua genome consists of repetitive sequences. Comparative genome analysis revealed that chieh-qua and wax gourd are closely related, indicating a close evolutionary relationship between the two species. Population genomic analysis, employing 129 chieh-qua accessions and 146 wax gourd accessions, demonstrated that chieh-qua exhibits greater genetic diversity compared to wax gourd. We also employed the GWAS method to identify related QTLs associated with subgynoecy, an interested and important trait in chieh-qua. The MYB59 (BhiCQ0880026447) exhibited relatively high expression levels in the shoot apex of four subgynoecious varieties compared with monoecious varieties. Overall, this research provides insights into the domestication history of chieh-qua and offers valuable genomic resources for further molecular research.

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.

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.

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.

Identifying Genes Associated with Female Flower Development of Phellodendron amurense Rupr. Using a Transcriptomics Approach

Phellodendron amurense Rupr., a species of Rutaceae, is a nationally protected and valuable medicinal plant. It is generally considered to be dioecious. With the discovery of monoecious P. amurense, the phenomenon that its sex development is regulated by epigenetics has been revealed, but the way epigenetics affects the sex differentiation of P. amurense is still unclear. In this study, we investigated the effect of DNA methylation on the sexual development of P. amurense. The young inflorescences of male plants were treated with the demethylation agent 5-azaC, and the induced female flowers were obtained. The induced female flowers’ morphological functions and transcriptome levels were close to those of normally developed plants. Genes associated with the development of female flowers were studied by comparing the differences in transcriptome levels between the male and female flowers. Referring to sex-related genes reported in other plants, 188 candidate genes related to the development of female flowers were obtained, including sex-regulating genes, genes related to the formation and development of sexual organs, genes related to biochemical pathways, and hormone-related genes. RPP0W, PAL3, MCM2, MCM6, SUP, PIN1, AINTEGUMENTA, AINTEGUMENTA-LIKE6, AGL11, SEUSS, SHI-RELATED SEQUENCE 5, and ESR2 were preliminarily considered the key genes for female flower development. This study has demonstrated that epigenetics was involved in the sex regulation of P. amurense, with DNA methylation as one of its regulatory modes. Moreover, some candidate genes related to the sexual differentiation of P. amurense were obtained with analysis. These results are of great significance for further exploring the mechanism of sex differentiation of P. amurense and studying of sex differentiation of plants.

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.

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.

Reference genes identification for qRT-PCR normalization of gene expression analysis in Cucumis sativus under Meloidogyne incognita infection and Pseudomonas treatment

qRT-PCR is a common and key technical means to study gene expression in biological research. However, reliability and accuracy of quantification by qRT-PCR is entirely dependent on the identification of appropriate reference genes. Cucumber as an economical vegetable is widely cultivated worldwide and is subject to serious nematode infection, especially from M. incognita. Plant could employ beneficial soil bacteria in the rhizosphere to enhance plant adaptability to various stresses. In this study, the optimal reference genes in cucumber under M. incognita stress and Pseudomonas treatment were calculated and confirmed. A total of thirteen candidate reference genes were identified across three different treatments. Of these, geNorm, NormFinder and BestKeeper programs combined RefFinder software identified EF1 and UBI are the most suitable reference gene in the root knot and whole root of cucumber infected M. incognita, respectively, and CACS is the most suitable reference gene in the whole root of cucumber treated by Pseudomonas. The work first validated the most suitable reference genes for the normalization gene expression in cucumber by nematode infected or Pseudomonas inoculated, and these results would facilitate the further research on M. incognita or Pseudomonas soil rhizosphere microbe interaction with cucumber.

The transcription factors DcHB30 and DcWRKY75 antagonistically regulate ethylene-induced petal senescence in carnation (Dianthus caryophyllus)

Although numerous transcription factors with antagonistic activities have been shown to contribute to growth and development, whether and how they regulate senescence in plants is largely unknown. In this study, we investigated the role of antagonistic transcription factors in petal senescence in carnation (Dianthus caryophyllus), one of the most common types of ethylene-sensitive cut flowers produced worldwide. We identified DcHB30 that encodes a ZF-HD transcription factor that is down-regulated in ethylene-treated petal transcriptomes. We found that silencing DcHB30 accelerated ethylene-induced petal senescence and that DcHB30 physically interacts with DcWRKY75, a positive regulator of ethylene-induced petal senescence. Phenotypic characterization and molecular evidence indicated that DcHB30 and DcWRKY75 competitively regulate the expression of their co-targeted genes DcACS1, DcACO1, DcSAG12, and DcSAG29 by reciprocally inhibiting the DNA-binding activity of each other on the gene promoters. This transcriptional regulation mechanism demonstrates that these transcription factors serve as positive and negative regulators in ethylene-induced petal senescence in carnation. Thus, our study provides insights into how antagonizing transcription factors regulate plant senescence.

Genic male and female sterility in vegetable crops

Vegetable crops are greatly appreciated for their beneficial nutritional and health components. Hybrid seeds are widely used in vegetable crops for advantages such as high yield and improved resistance, which require the participation of male (stamen) and female (pistil) reproductive organs. Male- or female-sterile plants are commonly used for production of hybrid seeds or seedless fruits in vegetables. In this review we will focus on the types of genic male sterility and factors affecting female fertility, summarize typical gene function and research progress related to reproductive organ identity and sporophyte and gametophyte development in vegetable crops [mainly tomato (Solanum lycopersicum) and cucumber (Cucumis sativus)], and discuss the research trends and application perspectives of the sterile trait in vegetable breeding and hybrid production, in order to provide a reference for fertility-related germplasm innovation.

Identification of suitable reference genes for quantitative reverse transcription PCR in Luffa (Luffa cylindrica)

Reverse transcription real-time quantitative PCR is widely used to quantify gene expression. Reference genes are usually used as internal controls to measure the target gene expression level. To date, there is no consensus on the use of systematically validated reference genes in different tissues of Luffa. This study evaluated the expression stability of 11 candidate reference genes in different tissues using five algorithms (BestKeeper, comparative delta-Ct method, GeNorm, NormFinder, and RefFinder). Protein phosphatase 2A was the most stable gene, while alpha Tubulin was the least stable. The relative expression of ethylene-related genes in different tissues was also analyzed to reveal their role in sex determination. This study provides the basis for using suitable reference genes to evaluate targeted gene expression.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01182-8.

NS encodes an auxin transporter that regulates the 'numerous spines' trait in cucumber (Cucumis sativus) fruit

Fruit spine is an important agronomic trait in cucumber and the "numerous spines (ns)" cucumber varieties are popular in Europe and West Asia. Although the classical genetic locus of ns was reported more than two decades ago, the NS gene has not been cloned yet. In this study, nine genetic loci for the different densities of fruit spines were identified by a genome-wide association study. Among the nine loci, fsdG2.1 was closely associated with the classical genetic locus ns, which harbors a candidate gene Csa2G264590. Overexpression of Csa2G264590 resulted in lower fruit spine density, and the knockout mutant generated by CRISPR/Cas9 displayed an increased spine density, demonstrating that the Csa2G264590 gene is NS. NS is specifically expressed in the fruit peel and spine. Genetic analysis showed that NS regulates fruit spine development independently of the tuberculate gene, Tu, which regulates spine development on tubercules; the cucumber glabrous mutants csgl1 and csgl3 are epistatic to ns. Furthermore, we found that auxin levels in the fruit peel and spine were significantly lower in the knockout mutant ns-cr. Moreover, RNA-sequencing showed that the plant hormone signal transduction pathway was enriched. Notably, most of the auxin responsive Aux/IAA family genes were downregulated in ns-cr. Haplotype analysis showed that the non-functional haplotype of NS exists exclusively in the Eurasian cucumber backgrounds. Taken together, the cloning of NS gene provides new insights into the regulatory network of fruit spine development.

Comparative Transcriptome Analysis Reveals Sex-Biased Expression of Hormone-Related Genes at an Early Stage of Sex Differentiation in Red Bayberry (Morella rubra)

The molecular mechanism of sex development and differentiation in the economically important dioecious fruit tree, red bayberry (Morella rubra), was revealed using next-generation transcriptome sequencing (NGS), and comparative analyses were used to identify differentially expressed genes (DEGs) in female and male flower buds. A total of 7,029 of these DEGs were identified at two early development stages. KEGG pathway enrichment analysis revealed that plant hormone signal transduction was significantly overrepresented, and 91 genes related to hormones were identified. An analysis of 7,029 DEGs revealed 161 hormone-related genes, with the 42 related to auxin and 26 related to ethylene being the most highly represented. A total of 62 genes were significantly up-regulated in females and 29 were in males, with 18 of them specifically expressed in females and 10 in males. A total of 415 transcription factors were identified, with 129 genes up-regulated in females and 53 in males. Moreover, 38 had female-specific expression and 18 had male-specific expression. Using weighted gene co-expression network analysis (WGCNA), two modules were found to be associated with sexual type. In the module coded light-green, there were five genes related to hormones, one to flower development and ten transcription factors with four genes specifically expressed in the males and four in females. The hub gene in the light-green module is MR0TCONS_00017483.1 (ACO), which is involved in ethylene biosynthesis and had male-specific expression. Among the transcription factors, three of the four male-specific expressed genes involved in flavonoid biosynthesis, including the MYB gene MR1TCONS_00020658.1 and two BHLH genes, MR6G001563.1 and MR8G020751.1, played important roles in male floral differentiation. In the dark-cyan module, six hormone-related genes, five transcription factors and three flower development genes were identified with the hub gene MR1G019545.1 (ETR1), which participates in the ethylene signaling pathway, and MR4G023618.1, which encodes the C3H zinc finger transcription factor. These results indicate that ethylene is the key hormone that interacts with other hormones and transcription factors to regulate sex differentiation in the red bayberry, which also provides new insights into the mechanism of sex determination and differentiation in the red bayberry.

Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber

Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and characterization in cucumber (Cucumis sativus L.) have been hindered by the lack of a high-quality pan-genome. Here, we report a graph-based cucumber pan-genome by analyzing twelve chromosome-scale genome assemblies. Genotyping of seven large chromosomal rearrangements based on the pan-genome provides useful information for use of wild accessions in breeding and genetic studies. A total of ~4.3 million genetic variants including 56,214 SVs are identified leveraging the chromosome-level assemblies. The pan-genome graph integrating both variant information and reference genome sequences aids the identification of SVs associated with agronomic traits, including warty fruits, flowering times and root growth, and enhances the understanding of cucumber trait evolution. The graph-based cucumber pan-genome and the identified genetic variants provide rich resources for future biological research and genomics-assisted breeding.

Increasing studies have suggested that single reference genome is insufficient to capture all variations in the genome. Here, the authors report a graph-based cucumber pan-genome by analyzing 12 chromosome-scale assemblies and reveal variations associated with agronomic traits and domestication.

Exogenous auxin-induced ENHANCER OF SHOOT REGENERATION 2 (ESR2) enhances femaleness of cucumber via activating CsACS2 gene

Cucumber (Cucumis sativus L.) is a model for the study of sex differentiation in the last two decades. In cucumber, sex differentiation is mainly controlled by genetic material, but plant growth regulators can also influence or even change it. However, the effect of exogenous auxin application on cucumber sex differentiation is mostly limited in physiological level. In this study, we explored the effects of different exogenous auxin concentrations on the varieties with different mutant sex-controlling genotypes and found that there was a dosage effect of exogenous indole-3-acetic acid (IAA) on the enhancement of cucumber femaleness. Several ACC synthetase (ACS) family members could directly respond to the induction of exogenous IAA to improve endogenous ethylene synthesis, and this process can be independent on the previously identified sex-related ACC oxidase CsACO2. We further demonstrated that ENHANCER OF SHOOT REGENERATION 2 (ESR2), responding to the induction of exogenous auxin, could directly activate CsACS2 expression by combining the ERE cis-acting element regions in the promoter, and then increase endogenous ethylene content, which may induce femaleness. These findings reveal that exogenous auxin improves cucumber femaleness via inducing sex-controlling gene and promoting ethylene synthesis.

Cucurbitaceae genome evolution, gene function and molecular breeding

The Cucurbitaceae is one of the most genetically diverse plant families in the world. Many of them are important vegetables or medicinal plants and are widely distributed worldwide. The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species. This has greatly facilitated research on gene identification, genome evolution, genetic variation and molecular breeding of cucurbit crops. So far, genome sequences of 18 different cucurbit species belonging to tribes Benincaseae, Cucurbiteae, Sicyoeae, Momordiceae and Siraitieae have been deciphered. This review summarizes the genome sequence information, evolutionary relationship, and functional genes associated with important agronomic traits (e.g., fruit quality). The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed.

A donor-DNA-free CRISPR/Cas-based approach to gene knock-up in rice

Structural variations (SVs), such as inversion and duplication, contribute to important agronomic traits in crops¹. Pan-genome studies revealed that SVs were a crucial and ubiquitous force driving genetic diversification^2-4. Although genome editing can effectively create SVs in plants and animals^5-8, the potential of designed SVs in breeding has been overlooked. Here, we show that new genes and traits can be created in rice by designed large-scale genomic inversion or duplication using CRISPR/Cas9. A 911 kb inversion on chromosome 1 resulted in a designed promoter swap between CP12 and PPO1, and a 338 kb duplication between HPPD and Ubiquitin2 on chromosome 2 created a novel gene cassette at the joint, promoter_Ubiquitin2::HPPD. Since the original CP12 and Ubiquitin2 genes were highly expressed in leaves, the expression of PPO1 and HPPD in edited plants with homozygous SV alleles was increased by tens of folds and conferred sufficient herbicide resistance in field trials without adverse effects on other important agronomic traits. CRISPR/Cas-based genome editing for gene knock-ups has been generally considered very difficult without inserting donor DNA as regulatory elements. Our study challenges this notion by providing a donor-DNA-free strategy, thus greatly expanding the utility of CRISPR/Cas in plant and animal improvements.

OBV (obscure vein), a C2H2 zinc finger transcription factor, positively regulates chloroplast development and bundle sheath extension formation in tomato (Solanum lycopersicum) leaf veins

Leaf veins play an important role in plant growth and development, and the bundle sheath (BS) is believed to greatly improve the photosynthetic efficiency of C₄ plants. The OBV mutation in tomato (Solanum lycopersicum) results in dark veins and has been used widely in processing tomato varieties. However, physiological performance has difficulty explaining fitness in production. In this study, we confirmed that this mutation was caused by both the increased chlorophyll content and the absence of bundle sheath extension (BSE) in the veins. Using genome-wide association analysis and map-based cloning, we revealed that OBV encoded a C₂H₂L domain class transcription factor. It was localized in the nucleus and presented cell type-specific gene expression in the leaf veins. Furthermore, we verified the gene function by generating CRISPR/Cas9 knockout and overexpression mutants of the tomato gene. RNA sequencing analysis revealed that OBV was involved in regulating chloroplast development and photosynthesis, which greatly supported the change in chlorophyll content by mutation. Taken together, these findings demonstrated that OBV affected the growth and development of tomato by regulating chloroplast development in leaf veins. This study also provides a solid foundation to further decipher the mechanism of BSEs and to understand the evolution of photosynthesis in land plants.