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.

Histone deacetylase (HDAC) proteins participate in diverse and tissue-specific developmental processes by forming various corepressor complexes with different regulatory subunits. An important HDAC machinery hub, the Histone Deacetylase Complex1 (HDC1) protein, participates in multiple protein–protein interactions and regulates organ size in plants. However, the mechanistic basis for this regulation remains unclear. Here, we identified a cucumber (Cucumis sativus) short-fruit mutant (sf2) with a phenotype that includes repressed cell proliferation. SF2 encodes an HDC1 homolog, and its expression is enriched in meristematic tissues, consistent with a role in regulating cell proliferation through the HDAC complex. A weak sf2 allele impairs HDAC targeting to chromatin, resulting in elevated levels of histone acetylation. Genome-wide mapping revealed that SF2 directly targets and promotes histone deacetylation associated with key genes involved in multiple phytohormone pathways and cell cycle regulation, by either directly repressing or activating their expression. We further show that SF2 controls fruit cell proliferation through targeting the biosynthesis and metabolism of cytokinin and polyamines. Our findings reveal a complex regulatory network of fruit cell proliferation mediated by HDC1 and elucidate patterns of HDC1-mediated regulation of gene expression.

Summary: Drought, especially terminal drought, severely limits wheat growth and yield. Understanding the complex mechanisms behind the drought response in wheat is essential for developing drought‐resistant varieties. This study aimed to dissect the genetic architecture and high‐yielding wheat ideotypes under terminal drought. An automated high‐throughput phenotyping platform was used to examine 28 392 image‐based digital traits (i‐traits) under different drought conditions during the flowering stage of a natural wheat population. Of the i‐traits examined, 17 073 were identified as drought‐related. A genome‐wide association study (GWAS) identified 5320 drought‐related significant single‐nucleotide polymorphisms (SNPs) and 27 SNP clusters. A notable hotspot region controlling wheat drought tolerance was discovered, in which TaPP2C6 was shown to be an important negative regulator of the drought response. The tapp2c6 knockout lines exhibited enhanced drought resistance without a yield penalty. A haplotype analysis revealed a favored allele of TaPP2C6 that was significantly correlated with drought resistance, affirming its potential value in wheat breeding programs. We developed an advanced prediction model for wheat yield and drought resistance using 24 i‐traits analyzed by machine learning. In summary, this study provides comprehensive insights into the high‐yielding ideotype and an approach for the rapid breeding of drought‐resistant wheat.

Mulberry (Morus alba L.) leaf, a “source of both medicine and food”, contains antioxidant ingredients such as flavonoids, alkaloids and polyphenols. The effects of 6-benzylaminopurine (6-BA) treatment on plant growth and flavonoid contents in mulberry leaves were investigated in this study. The expression of rutin (Rut), chlorogenic acid (ChA), isoquercitrin (IQ) and astragaloside IV (Ast) related genes in the flavonoid synthesis pathways was investigated in mulberry leaves. The results showed that 6-BA treatment significantly promoted mulberry differentiation and growth as well as, increased the numbers of new shoots and buds compared to the control. In addition, 30 mg/L 6-BA significantly increased the contents of Rut, IQ and Ast, and it strongly induced the expression of flavonoid biosynthesis-related genes, including flavonoid 3-O-glucosyltransferase (F3GT), 4-xoumarate-CoA ligase (4CL), phenylalanine (PAL) and chalcone synthase (CHS). The dietary risk assessment of mulberry leaves was based on hormone residues 5 days after treatment with 30 mg /L 6-BA, and the results showed that the dietary exposure risk of 6-BA was extremely low without causing any health concern. Thus, treatment with 30 mg/L 6-BA is a new method to improve the medicinal quality and development of high-value mulberry leaf foods without any potential risk.

Manipulation of gene expression is central to understanding gene function, engineering cell behavior, and altering biological traits according to production demands. Nuclease-dead Cas9 (dCas9), a variant of active Cas9, offers a versatile platform for the precise control of genome function without DNA cleavage. Notably, however, an effective and universal dCas9-based transcriptional repression system remains unavailable in plants. The non-canonical histone acetyltransferase TENDRIL-LESS (CsTEN) is responsible for chromatin loosening and histone modification in cucumber (Cucumis sativus). In this study, we engineered a gene regulation tool by fusing TEN and its truncated proteins with dCas9. The full-length dCas9-TEN protein substantially repressed gene expression, with the N-terminal domain identified as the core repression domain. We subsequently validated the specificity and efficacy of this system through both transient infection and genetic transformation in cucumber and Arabidopsis (Arabidopsis thaliana). Electrophoretic mobility shift assay (EMSA) revealed the ability of the N-terminal domain of TEN to bind to chromatin, which may promote target binding of the dCas9 complex and enhance the transcriptional repression effect. Our tool enriches the arsenal of genetic regulation tools available for precision breeding in crops.

The root system architecture (RSA) determines plant growth and yield. The characterization of optimal RSA and discovery of genetic loci or candidate genes that control root traits are therefore important research goals. However, the hidden nature of the root system makes it difficult to perform nondestructive, rapid analyses of RSA. In this study, we developed an automated, nondestructive, high-throughput root phenotyping platform (Root-HTP) and a corresponding data processing pipeline for efficient, large-scale characterization of wheat (Triticum aestivum L.) RSA. This system is capable of tracking root growth dynamics and RSA variation across all wheat developmental stages. In situ phenotyping using Root-HTP extracted 47 RSA traits, including 33 novel traits in wheat and 23 novel traits in other crops. We used root trait data from the phenotyping system and yield trait data to conduct a genome-wide association study (GWAS) of 155 wheat accessions, which identified 2,650 SNPs and 233 quantitative trait loci (QTLs) associated with aspects of root architecture. The candidate gene TaMYB93 was detected in a QTL for root tortuosity, and EMS mutants confirmed its effect on RSA in wheat. We explored the relationship between root- and yield-related traits and identified 20 root-related QTLs that were also associated with yield traits. Furthermore, we have built a predictive model for wheat yield based on 18 RSA traits and propose a parsimonious RSA ideotype associated with high yields. The data generated from this study provide insight into the genetic architecture of wheat RSA and support for RSA ideotype-based wheat breeding and yield prediction.