The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.

Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective

Abstract Potato ( Solanum tuberosum L.) is the world’s most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and production 1–4 . So far, relatively few studies have examined the genome evolution and diversity of wild and cultivated landrace potatoes, which limits the application of their diversity in potato breeding. Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota , the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum . Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution. We find that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the effect of tuber-based propagation strategies on the evolution of the potato genome. We discover a transcription factor that determines tuber identity and interacts with the mobile tuberization inductive signal SP6A. We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. This study will accelerate hybrid potato breeding and enrich our understanding of the evolution and biology of potato as a global staple food crop. 

https://www.nature.com/articles/s41586-022-04822-x.pdf

Genome evolution and diversity of wild and cultivated potatoes

Ethylene is a gaseous hormone which plays important roles in both plant growth and development and stress responses. Based on studies in the dicot model plant species Arabidopsis, a linear ethylene signaling pathway has been established, according to which ethylene is perceived by ethylene receptors and transduced through CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1) and ETHYLENE-INSENSITIVE 2 (EIN2) to activate transcriptional reprogramming. In addition to this canonical signaling pathway, an alternative ethylene receptor-mediated phosphor-relay pathway has also been proposed to participate in ethylene signaling. In contrast to Arabidopsis, rice, a monocot, grows in semiaquatic environments and has a distinct plant structure. Several novel regulators and/or mechanisms of the rice ethylene signaling pathway have recently been identified, indicating that the ethylene signaling pathway in rice has its own unique features. In this review, we summarize the latest progress and compare the conserved and divergent aspects of the ethylene signaling pathway between Arabidopsis and rice. The crosstalk between ethylene and other plant hormones is also reviewed. Finally, we discuss how ethylene regulates plant growth, stress responses and agronomic traits. These analyses should help expand our knowledge of the ethylene signaling mechanism and could further be applied for agricultural purposes.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/jipb.13028

Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms

Cucumber, Cucumis sativus L. (2n = 2x = 14), is an important vegetable crop worldwide. It was the first specialty crop with a publicly available draft genome. Its relatively small, diploid genome, short life cycle, and self-compatible mating system offers advantages for genetic studies. In recent years, significant progress has been made in molecular mapping, and identification of genes and QTL responsible for key phenotypic traits, but a systematic review of the work is lacking. Here, we conducted an extensive literature review on mutants, genes and QTL that have been molecularly mapped or characterized in cucumber. We documented 81 simply inherited trait genes or major-effect QTL that have been cloned or fine mapped. For each gene, detailed information was compiled including chromosome locations, allelic variants and associated polymorphisms, predicted functions, and diagnostic markers that could be used for marker-assisted selection in cucumber breeding. We also documented 322 QTL for 42 quantitative traits, including 109 for disease resistances against seven pathogens. By alignment of these QTL on the latest version of cucumber draft genomes, consensus QTL across multiple studies were inferred, which provided insights into heritable correlations among different traits. Through collaborative efforts among public and private cucumber researchers, we identified 130 quantitative traits and developed a set of recommendations for QTL nomenclature in cucumber. This is the first attempt to systematically summarize, analyze and inventory cucumber mutants, cloned or mapped genes and QTL, which should be a useful resource for the cucurbit research community.

/pdf/molecularly-tagged-genes-and-quantitative-trait-loci-in-45njzidd75.pdf

Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature

Complex biological processes such as plant growth and development are often under the control of transcription factors that regulate the expression of large sets of genes and activate subordinate transcription factors in a cascade-like fashion. Here, by screening candidate photosynthesis-related transcription factors in rice, we identified a DREB (Dehydration Responsive Element Binding) family member, OsDREB1C, in which expression is induced by both light and low nitrogen status. We show that OsDREB1C drives functionally diverse transcriptional programs determining photosynthetic capacity, nitrogen utilization, and flowering time. Field trials with OsDREB1C-overexpressing rice revealed yield increases of 41.3 to 68.3% and, in addition, shortened growth duration, improved nitrogen use efficiency, and promoted efficient resource allocation, thus providing a strategy toward achieving much-needed increases in agricultural productivity. Description Genetic improvement drives rice yield Improvements in agricultural productivity could lessen the impact of agriculture on the environment and perhaps supply more food from less land. Working in rice, Wei et al. identified a transcription factor that, when overexpressed, has a variety of useful effects (see the Perspective by Kelly). The gene’s expression is induced by both light and low-nitrogen status, and it regulates photosynthetic capacity, nitrogen utilization, and flowering time. In field trials, plants overexpressing this gene delivered greater yield, shortened growth duration, and improved nitrogen use efficiency. —PJH Overexpression of a single transcription factor improves the agricultural productivity of rice. INTRODUCTION Rapid population growth, rising meat consumption, and the expanding use of crops for nonfood and nonfeed purposes increase the pressure on global food production. At the same time, the excessive use of nitrogen fertilizer to enhance agricultural production poses serious threats to both human health and the environment. To achieve the required yield increases and make agriculture more sustainable, intensified breeding and genetic engineering efforts are needed to obtain new crop varieties with higher photosynthetic capacity and improved nitrogen use efficiency (NUE). However, progress has been slow, largely due to the limited knowledge about regulator genes that potentially can coordinately optimize carbon assimilation and nitrogen utilization. RATIONALE Transcription factors control diverse biological processes by binding to the promoters (or intragenic regions) of target genes, and a number of transcription factors have been identified that control carbon fixation and nitrogen assimilation. A previous comparative analysis of maize and rice leaf transcriptomes and metabolomes revealed a set of 118 candidate transcription factors that may act as regulators of C4 photosynthesis. We screened these transcription factors for their responsiveness to light and nitrogen supply in rice, and found that the gene Dehydration-Responsive Element-Binding Protein 1C (OsDREB1C), a member of the APETALA2/ethylene-responsive element binding factor (AP2/ERF) family, exhibits properties expected of a regulator that can simultaneously modulate photosynthesis and nitrogen utilization. RESULTS OsDREB1C expression is induced in rice by both light and low-nitrogen status. We generated overexpression lines (OsDREB1C-OE) and knockout mutants (OsDREB1C-KO) in rice, and conducted field trials in northern, southeastern, and southern China from 2018 to 2021. OsDREB1C-OE plants exhibited 41.3 to 68.3% higher yield than wild-type (WT) plants due to increased grain number per panicle, elevated grain weight, and enhanced harvest index. We observed that light-induced growth promotion of OsDREB1C-OE plants was accompanied by enhanced photosynthetic capacity and concomitant increases in photosynthetic assimilates. In addition, 15N feeding experiments and field studies with different nitrogen fertilization regimes revealed that NUE was improved in OsDREB1C-OE plants due to elevated nitrogen uptake and transport activity. Moreover, OsDREB1C overexpression led to more efficient carbon and nitrogen allocation from source to sink, thus boosting grain yield, particularly under low-nitrogen conditions. Additionally, the OsDREB1C-OE plants flowered 13 to 19 days earlier and accumulated higher biomass at the heading stage than WT plants under long-day conditions. OsDREB1C is localized in the nucleus and the cytosol and functions as a transcriptional activator that directly binds to cis elements in the DNA, including dehydration-responsive element (DRE)/C repeat (CRT), GCC, and G boxes. Chromatin immunoprecipitation sequencing (ChIP-seq) and transcriptomic analyses identified a total of 9735 putative OsDREB1C-binding sites at the genome-wide level. We discovered that five genes targeted by OsDREB1C [ribulose-l,5-bisphosphate carboxylase/oxygenase small subunit 3 (OsRBCS3), nitrate reductase 2 (OsNR2), nitrate transporter 2.4 (OsNRT2.4), nitrate transporter 1.1B (OsNRT1.1B), and flowering locus T-like 1 (OsFTL1)] are closely associated with photosynthesis, nitrogen utilization, and flowering, the key traits altered by OsDREB1C overexpression. ChIP-quantitative polymerase chain reaction (ChIP-qPCR) and DNA affinity purification sequencing (DAP-seq) assays confirmed that OsDREB1C activates the transcription of these genes by binding to the promoter of OsRBCS3 and to exons of OsNR2, OsNRT2.4, OsNRT1.1B, and OsFTL1. By showing that biomass and yield increases can also be achieved by OsDREB1C overexpression in wheat and Arabidopsis, we have demonstrated that the mode of action and the biological function of the transcription factor are evolutionarily conserved. CONCLUSION Overexpression of OsDREB1C not only boosts grain yields but also confers higher NUE and early flowering. Our work demonstrates that by genetically modulating the expression of a single transcriptional regulator gene, substantial yield increases can be achieved while the growth duration of the crop is shortened. The existing natural allelic variation in OsDREB1C, the highly conserved function of the transcription factor in seed plants, and the ease with which its expression can be altered by genetic engineering suggest that this gene could be the target of future crop improvement strategies toward more efficient and more sustainable food production. OsDREB1C coordinates yield and growth duration. OsDREB1C was identified by its responsiveness to light and low nitrogen in a screen of 118 transcription factors related to C4 photosynthesis. Transcriptional activation of multiple downstream target genes by OsDREB1C confers enhanced photosynthesis, improved nitrogen utilization, and early flowering. Together, the activated genes cause substantial yield increases in rice and wheat.

A transcriptional regulator that boosts grain yields and shortens the growth duration of rice

Plant organ growth and development are determined by a subtle balance between growth stimulation and inhibition. Fruit size and shape are important quality traits influencing yield and market value; however, the underlying mechanism regulating the balance of fruit growth to achieve final size and shape is not well understood. Here, we report a mechanistic model that governs cucumber (Cucumis sativus) fruit elongation through fine-tuning of ethylene homeostasis. We identified a cucumber mutant that bears short fruits owing to repressed cell division. SF1 (Short Fruit 1) encodes a cucurbit-specific RING-type E3 ligase, and the mutation resulted in its enhanced self-ubiquitination and degradation, but accumulation of ACS2 (1-aminocyclopropane-1-carboxylate synthase 2), a rate-limiting enzyme for ethylene biosynthesis. The overproduction of ethylene contributes to the short-fruit phenotype of sf1. Dysfunction of ACS2 resulted in reduced ethylene production, but still repressed cell division and shorter fruit, suggesting that ethylene is still required for basal fruit elongation. SF1 ubiquitinates and degrades both itself and ACS2 to control ethylene synthesis for dose-dependent effect on cell division and fruit elongation. Our findings reveal the mechanism by which ethylene dosage is regulated for the control of cell division in developing fruit.

/pdf/genetic-regulation-of-ethylene-dosage-for-cucumber-fruit-1o4yp9dtn0.pdf

Genetic Regulation of Ethylene Dosage for Cucumber Fruit Elongation

Axillary meristem development determines both plant architecture and crop yield; this critical process is regulated by the PROLIFERATING CELL FACTORS (TCP) family of transcription factors. Although TCP proteins bind primarily to promoter regions, some also target gene bodies for expression activation. However, the underlying regulatory mechanism remains unknown. Here we show that TEN, a TCP from cucumber (Cucumis sativus L.), controls the identity and mobility of tendrils. Through its C terminus, TEN binds at intragenic enhancers of target genes; its N-terminal domain functions as a non-canonical histone acetyltransferase (HAT) to preferentially act on lysine 56 and 122 of the histone H3 globular domain. This HAT activity is responsible for chromatin loosening and host-gene activation. The N termini of all tested CYCLOIDEA and TEOSINTE BRANCHED 1-like TCP proteins contain an intrinsically disordered region; despite their sequence divergence, they have conserved HAT activity. This study identifies a non-canonical class of HATs and provides a mechanism by which modification at the H3 globular domain is integrated with the transcription process.

Regulation of plant architecture by a new histone acetyltransferase targeting gene bodies.

Abstract Fruits and vegetables in the Cucurbitaceae family, such as cucumber, melon, watermelon, and squash, contribute greatly to the human diet. The widespread use of genome editing technologies has greatly accelerated gene functional characterization and crop improvement. However, most economically important cucurbit plants, including melon and squash, remain recalcitrant to standard Agrobacterium tumefaciens-mediated transformation, limiting the effective use of genome editing technology. In this study, we used an “optimal infiltration intensity” strategy to establish an efficient genetic transformation system for melon and squash. We harnessed the power of this method to target homologs of the ERECTA family of receptor kinase genes and created alleles that resulted in a compact plant architecture with shorter internodes in melon, squash, and cucumber. The optimized transformation method presented here enables stable CRISPR/Cas9-mediated mutagenesis and provides a solid foundation for functional gene manipulation in cucurbit crops.

/pdf/targeted-creation-of-new-mutants-with-compact-plant-14x1efyv.pdf

Targeted creation of new mutants with compact plant architecture using CRISPR/Cas9 genome editing by an optimized genetic transformation procedure in cucurbit plants

Fruit spine is an important agronomic trait in cucumber and the "numerous spines" cucumber varieties are popular in Europe and West Asia. Although the classical genetic locus of numerous spines (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 (GWAS). Among the nine loci, fsdG2.1 was closely associated with the classical genetic locus ns, in 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-seq showed that the plant hormone signal transduction pathway was enriched. Notably, most of the auxin responsive Aux/IAA family genes were down-regulated in ns-cr. Haplotype analysis showed that the nonfunctional 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.

Tongxu Xin

Papers

Genetic Regulation of Ethylene Dosage for Cucumber Fruit Elongation

Regulation of plant architecture by a new histone acetyltransferase targeting gene bodies.

Targeted creation of new mutants with compact plant architecture using CRISPR/Cas9 genome editing by an optimized genetic transformation procedure in cucurbit plants

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

Architecture design of cucurbit crops for enhanced productivity by a natural allele