Journal of Integrative Plant Biology最新文献

The burgeoning multi-omics data have provided deep insights into the regulatory mechanisms underlying plant growth and development. However, revealing the complete landscape of gene regulatory networks underpinning various developmental processes remains challenging. Here, a multi-omics integrative gene network of the pear fruit development process was constructed through integrating 3D genomic, transcriptomic, transcription factor (TF) binding, chromatin accessibility, protein structure, and proteomic data. This integrative network comprises over 45,678 elements interconnected by more than 3.15 million edges and exhibits great potential in predicting regulatory and interactive relationships involved in the formation of key fruit quality traits (e.g., sugar, stone cell). In particular, the integrative network was applied to predict interactors of PbrII5, an inhibitor of vacuolar sucrose hydrolysis, and the predicted interactors were further validated through molecular experiments. Moreover, the network showed good performance in automatically predicting fruit trait-related genes by leveraging machine learning models. Specifically, a set of sugar metabolism-related genes was newly predicted, and their functions were verified through overexpression in pear fruit. In addition, extensive regulatory network divergence was observed between duplicated genes, with neofunctionalization being the dominant evolutionary process reshaping network connections of duplicated genes. Lastly, a multi-omics network database, pearGRN (http://peargrn.njau.edu.cn), was developed to facilitate further research for resolving complex gene regulatory relationships. This study lays a strong foundation for revealing novel regulatory mechanisms underlying fruit development and quality formation.

Seed storability is critical for crop propagation, global grain preservation, and food security. However, knowledge of the molecular biology underlying seed storability remains elusive. Here, we identified the flavonoid 3' hydroxylase gene (F3'H) as a key gene governing seed storability in soybean through map-based cloning. Functional characterization revealed that GmF3'H not only modulates seed coat pigmentation but, more importantly, also reinforces the physical integrity of both seed coat and hilum, thereby preventing mechanical cracking. Furthermore, conserved F3'H function in soybean and Arabidopsis suggests its broad evolutionary relevance for seed storability. Our findings demonstrate that GmF3'H confers a dual-defense strategy combining structural reinforcement of seed protective layers with antioxidant enhancement for engineering seed longevity and storability. Based on these findings, we developed improved soybean germplasm with enhanced storability by selecting for favorable GmF3'H haplotypes, utilizing linked seed coat color as a visual marker. This study provides new insights for understanding plant seed longevity and offers a valuable avenue for broad-spectrum breeding applications on crop seed storability to sustain seed vigor and grain security.

Upon recognition of the microbial or endogenous pattern SERINE-RICH ENDOGENOUS PEPTIDE12 (SCOOP12), the kinase PBL32 is phosphorylated and transmits immune signals downstream of the MIK2 receptor complex. Heterologous expression of Arabidopsis PBL32 and MIK2 in other plants enhances their disease resistance, offering a promising strategy for improving crop disease resistance.

Genome size, the total amount of DNA content in the cell nucleus, varies greatly among flowering plants. One factor underlying this variation is the environment under which plants evolve. Given this premise, harsh environmental conditions in arid regions may profoundly influence genome evolution. However, the specific impact of aridification on genome size evolution, particularly for African lineages, remains largely unexplored. Here, we investigate linkages between genome size evolution and ecological adaptation using the genus Cyphostemma in the grape family (Vitaceae) as a model. Cyphostemma species exhibit genome size expansion and remarkable morphological traits in arid environments, including succulent stems or leaves and loss of tendrils. Our biogeographic reconstruction, based on substantial taxon sampling (112 of 200 species), reveals that Cyphostemma originated in continental Africa during the late Eocene to Oligocene and has undergone rapid radiation since the middle Miocene, coinciding with intensified aridification and geological activity in eastern Africa. Incorporating extensive data on traits, habitats, genome size, and chromosome numbers, we show that Cyphostemma species with the largest genomes are succulent polyploids restricted to nutrient-rich limestone outcrops. Broad-scale analyses across eudicots further confirm that larger genomes are significantly associated with both succulence and arid habitats. Our findings reveal a strong association between genome size expansion, polyploidy, and adaptive traits, indicating that genome size is a hitherto neglected trait associated with the radiation of succulent plants during the African aridification in the Cenozoic.

Phytosterols are a diverse class of isoprenoid-derived lipids that serve as essential structural components of plant membranes and regulators of growth and reproduction. Unlike animals and fungi, which predominantly utilize cholesterol and ergosterol, plants produce a complex array of over 250 sterol molecules. These include major forms such as β-sitosterol, stigmasterol, and campesterol as well as minor components like cholesterol and various sterol biosynthetic intermediates. This review provides a comprehensive overview of plant sterols, first addressing their structural diversity and distribution across species and tissues, and then exploring their biosynthesis, transport, and functions. A key focus is placed on their role as membrane modulators, influencing fluidity, permeability, and the formation of lipid rafts. Finally, we synthesize genetic and molecular evidence, demonstrating the critical functions of sterols and their derivatives in both reproductive and vegetative development. We conclude by highlighting persistent gaps in our knowledge and proposing future research directions to unravel the multifaceted roles of these essential molecules.

During meiosis, crossovers between homologous chromosomes generate genetic diversity but are limited in number, widely spaced by interference, and biased toward gene-rich euchromatin while suppressed in pericentromeric heterochromatin. This constrained crossover patterning restricts the genetic variation available for plant breeding. Recent studies have identified key crossover regulators-including the anti-crossover helicases FANCM and RECQ4, the pro-crossover factor HEI10, and heterochromatin-organizing proteins-that can modulate crossover frequency and positioning, although the effects on fertility are species- and context-dependent. Manipulating these pathways offers a strategy to increase crossovers along chromosomes, including recombination-suppressed regions, thereby unlocking hidden genetic variation. Genetic and epigenetic control of crossover formation is emerging as a powerful tool to accelerate crop improvement and enhance genetic gain.

Plants must coordinate chloroplast biogenesis with environmental conditions during seedling establishment, as failure to do so results in impaired phototrophic growth. Despite the biological importance of this early developmental stage, the influence of environmental factors on chloroplast biogenesis remains poorly understood. Here, we reveal a crucial role for GENOMES UNCOUPLED1 (GUN1)-mediated biogenic retrograde signaling in safeguarding chloroplast development and supporting seedling growth under heat stress. Loss of GUN1 causes severe bleaching and impaired photomorphogenesis at elevated temperatures. Genetic interaction analyses show that EXECUTER1 (EX1) and EXECUTER2 (EX2), key components of chloroplast ROS-associated operational retrograde signaling, modulate the heat-sensitive phenotype of gun1 mutants, indicating crosstalk between biogenic and operational retrograde pathways. We further demonstrate that the de-repressed expression of photosynthesis-associated nuclear genes, that is, genomes uncoupled expression, is a major contributor to the heat sensitivity and failed chloroplast biogenesis in gun1 seedlings under heat stress. These findings extend the current understanding of GUN1 function by showing its contribution to chloroplast development and thermotolerance through biogenic retrograde signaling during early seedling growth.

Parent-of-origin effects are usually caused by selective expression of maternal or paternal alleles. Although genome-wide studies suggest that imprinted gene expression occurs primarily in the endosperm in plants, detailed studies of allele-specific gene expression and its associations with parent-of-origin phenotypes are scarce. NAC20 and NAC26 (NAC20/26 hereafter), a pair of tightly linked NAC-family transcription factors, redundantly regulate grain filling and albumin accumulation in rice endosperm. Here, we show that NAC20/26 exhibited allele-specific maternal expression, and the floury endosperm phenotype of the nac20/26 double mutant was inherited with a maternal effect. Further studies showed that the imprinted NAC20/26 expression and floury endosperm phenotype with a maternal effect are associated with insertions of two TEs in NAC20/26 of two Japonica rice varieties, but not in two Indica ones examined. The maternal NAC20/26 expression was associated with elevated DNA methylation in their paternal DMRs, and deletions of those TEs by gene editing led to decreased methylation in these DMRs, and biallelic NAC20/26 expression. Geographical analyses showed that Japonica varieties with high-latitude origins examined carried these TEs. These results establish that TE-mediated DNA methylation lead to grain filling with a maternal effect in high-latitude Japonica rice varieties, which may associate with northward expansion of rice during domestication.

The domestication of crops originates from their wild ancestors and typically begins with the selection of phenotypes carrying specific alleles within wild populations. Subsequently, artificial hybridization and the retention of novel mutations introduce new alleles, leading to the continual creation of new phenotypes. The modern maize (Zea mays L.), as one of the most important food crops worldwide, has long attracted significant attention from researchers regarding its domestication and origin. In this review, we have summarized the related advances in clarifying hybrid origin and identifying related genes and allelic origins in maize. Modern maize was initially domesticated from Zea mays ssp. parviglumis approximately 9,000 years ago, followed by hybridization with Z. mays ssp. mexicana around 6,000 years ago, which gave rise to the modern maize lineage. Modern maize, as a hybrid lineage, possesses extensive genetic admixture that serves as the foundation for its phenotypic diversity and wide adaptability to various cultivation environments. Compared to ssp. parviglumis and mexicana, the unique phenotypes of maize were shaped through the selection of allelic combinations from both ancestors and/or the accumulation of novel mutations. Elite alleles from both ancestors hold significant value for biotic and abiotic stress resistance. Identifying these alleles and the underlying molecular mechanisms and incorporating them into modern breeding programs could facilitate the development of new maize germplasm with enhanced adaptability to today's changing environments and improved agricultural productivity.

This Commentary examines research by Wu et al. showing that β-1,3-glucan synthase-like 5 (GSL5) functions as a key gene for susceptibility to clubroot in Brassica family members by suppressing immunity regulated by jasmonic acid. Inaction of GSL5 through genome editing provides broad-spectrum resistance to clubroot.