Journal of Integrative Plant Biology最新文献

A single recessive gene, Multi-Grain Spikelet 1 (MGS1), governs the multiple-grain spikelet trait in sorghum. The natural variants mgs1^9E and mgs1^BA45 trigger adjacent double-pistil primordia, significantly boosting grain numbers per panicle, suggesting potential strategies for breeding high-yield sorghum.

Plants have co-evolved with a wide range of microbial communities over hundreds of millions of years, this has drastically influenced their adaptation to biotic and abiotic stress. The rapid development of multi-omics approaches has greatly improved our understanding of the diversity, composition, and functions of plant microbiomes, but how global climate change affects the assembly of plant microbiomes and their roles in regulating host plant adaptation to changing environmental conditions is not fully known. In this review, we summarize recent advancements in the community assembly of plant microbiomes, and their responses to climate change factors such as elevated CO₂ levels, warming, and drought. We further delineate the research trends and hotspots in plant–microbiome interactions in the context of climate change, and summarize the key mechanisms by which plant microbiomes influence plant adaptation to the changing climate. We propose that future research is urgently needed to unravel the impact of key plant genes and signal molecules modulated by climate change on microbial communities, to elucidate the evolutionary response of plant–microbe interactions at the community level, and to engineer synthetic microbial communities to mitigate the effects of climate change on plant fitness.

Sex chromosomes have evolved independently in numerous lineages across the Tree of Life, in both diploid-dominant species, including many animals and plants, and the less studied haploid-dominant plants and algae. Strict genetic sex determination ensures that individuals reproduce by outcrossing. However, species with separate sexes (termed dioecy in diploid plants, and dioicy in haploid plants) may sometimes evolve different sex systems, and become monoicous, with the ability to self-fertilize. Here, we studied dioicy-monoicy transitions in the ancient liverwort haploid-dominant plant lineage, using three telomere-to-telomere gapless chromosome-scale reference genome assemblies from the Ricciaceae group of Marchantiales. Ancestral liverworts are believed to have been dioicous, with U and V chromosomes (chromosome 9) determining femaleness and maleness, respectively. We confirm the finding that monoicy in Ricciocarpos natans evolved from a dioicous ancestor, and most ancestrally U chromosomal genes have been retained on autosomes in this species. We also describe evidence suggesting the possible re-evolution of dioicy in the genus Riccia, with probable de novo establishment of a sex chromosome from an autosome (chromosome 5), and further translocations of genes from the new sex chromosome to autosomes. Our results also indicated that micro-chromosomes are consistent genomic features, and may have evolved independently from sex chromosomes in Ricciocarpos and Riccia lineages.

Seedlessness is a most valuable trait in fruit crops for fresh consumption and processing. The mutations in essential meiosis genes are known to confer sterility and seed abortion in plants. However, defects in meiosis have rarely been reported in fruit crops. Here, we found meiosis defects caused sterility in a seedless citrus bud sport cultivar, with massive unpaired univalents during diakinesis, indicating a disruption in crossover formation. A non-functional CrMER3A^{-103 bp} allele with a 103-bp deletion in the gene body, together with the other non-functional CrMER3a allele with a T deletion in exon, were identified in the seedless cultivar. The CrMER3 protein was undetectable at meiotic prophase I in the seedless cultivar, and knock out of CrMER3 resulted in sterility in precocious Mini-citrus. Therefore, the natural variation in CrMER3 is responsible for sterility and seedlessness in this bud sport cultivar. The CrMER3a allele originated from the primitive wild mandarin and was passed to cultivated mandarins. A Kompetitive Allele-Specific PCR (KASP) marker was developed to identify citrus germplasm with CrMER3a allele and to screen potential sterile and seedless hybrids in citrus cross breeding. Uncovering the natural mutations responsible for meiosis defects in citrus enhances our understanding of mechanisms controlling seedlessness in fruit crops and facilitates breeding of seedless varieties.

NONEXPRESSER OF PATHOGENESIS-RELATED GENES 1 (NPR1), the receptor for salicylic acid (SA), plays a central role in the SA-mediated basal antiviral responses. Recent studies have shown that two different plant RNA viruses encode proteins that suppress such antiviral responses by inhibiting its SUMOylation and inducing its degradation, respectively. However, it is unclear whether targeting NPR1 is a general phenomenon in viruses and whether viruses have novel strategies to inhibit NPR1. In the present study, we report that two different positive-sense single-stranded RNA (+ssRNA) viruses, namely, alfalfa mosaic virus (AMV) and potato virus X (PVX); one negative-sense single-stranded RNA (-ssRNA) virus (calla lily chlorotic spot virus, CCSV); and one single-stranded DNA virus (beet severe curly-top virus, BSCTV) that also encode one or more proteins that interact with NPR1. In addition, we found that the AMV-encoded coat protein (CP) can induce NPR1 degradation by recruiting S-phase kinase-associated protein 1 (Skp1), a key component of the Skp1/cullin1/F-box (SCF) E3 ligase. In contrast, the BSCTV-encoded V2 protein inhibits NPR1 function, probably by affecting its nucleocytoplasmic distribution via the nuclear export factor ALY. Taken together, these data suggest that NPR1 is one of the central hubs in the molecular arms race between plants and viruses and that different viruses have independently evolved different strategies to target NPR1 and disrupt its function.

Nicotiana benthamiana requires the coiled-coil nucleotide-binding leucine-rich repeat receptor protein NbZAR1 to recognize the type III effector RipP1 from Ralstonia solanacearum. Moreover, RipP1-induced cell death and immunity relies on EDS1 and NRG1, two core components of the Toll-interleukin 1-like receptor nucleotide-binding leucine-rich repeat receptor signaling pathway.

Incorporating genotype-by-environment (GE) interaction effects into genomic prediction (GP) models with multi-environment climate data can improve selection accuracy to accelerate crop breeding but has received little research attention. Here, we conducted a cross-region GP study of grain moisture content (GMC) and grain yield (GY) in maize hybrids in two major Chinese growing regions using data for 19 climatic factors across 34 environments in 2020 and 2021. Predictions were conducted in 2,126 hybrids generated from 475 maize inbred lines, using 9,355 single nucleotide polymorphism markers for genotyping. Models based on genomic best linear unbiased prediction (GBLUP) incorporating GE interaction effects of 19 climatic factors associated with day length, transpiration, temperature, and radiation (GBLUP-GE_19CF) trained on whole data set outperformed the traditional GBLUP or BayesB models in predicting GMC or GY by 10-fold cross-validation, achieving prediction accuracies of 0.731 and 0.331, respectively. To refine the climate data, we examined 84 statistical features associated with these climatic factors and identified nine factors most correlated with GMC or GY. Principal component analysis of climate data yielded nine principal components responsible for 97% of the variability in the data. Incorporating these nine factors or principal components into the GBLUP-GE framework with a similarity matrix of environments (GBLUP-GE_9CF and GBLUP-GE_PCA) provided similar prediction accuracies but could reduce the computational burden. In addition, increasing the number of test set environments in the training set from 8 to 14 increased the prediction accuracy of GBLUP-GE_19CF trained with monthly average climate data for 2020-2021. Examining prediction accuracy based on concordance, the proportion of overlapping hybrids between the top 50% of predicted and observed values for GMC and GY, indicated that concordance exceeded 50% for the GBLUP-GE_19CF model, confirming the reliability of our predictions. This study can provide practical guidance for optimizing GPs for maize breeding programs in multi-environment selection.

Flowering time is a critical agronomic trait in rice, directly influencing grain yield and adaptability to specific planting regions and seasons. Florigens, including FLOWERING LOCUS T (FT) proteins Hd3a (OsFTL2) and RFT1 (OsFTL3), play central roles in transmitting flowering signals through rice's photoperiod regulatory network. While Hd3a and RFT1 have been extensively studied, the functions and interactions of other FT-like proteins remain unclear, limiting advancements in breeding strategies for early-maturing rice varieties. Here, we demonstrate that the florigen-like protein OsFTL1 forms a florigen activation complex (FAC) and promotes flowering under both short-day and long-day conditions. OsFTL1 localizes to the nucleus and cytoplasm, with predominant expression in the shoot base, facilitating its mobilization to the shoot apical meristem (SAM) to initiate flowering. Overexpression of OsFTL1 (OsFTL1-OE) in leaves or shoot bases significantly accelerates flowering and alters plant architecture. In the nucleus, OsFTL1 interacts with GF14c and OsFD1 to form an FAC, activating OsMADS14 and OsMADS15 expression to drive flowering. Markedly, OsFTL1-OE plants deficient in Hd3a and RFT1 exhibited earlier flowering compared with wild-type plants, indicating that OsFTL1 can independently promote flowering. Furthermore, haplotype analysis identified OsFTL1-Hap3, a beneficial variant associated with early flowering and comparable grain yields. These findings revealed that OsFTL1 can substitute for Hd3a and RFT1 in FAC formation, promoting flowering across photoperiods, and highlighting its potential application in breeding early-maturing, high-yield rice varieties suitable for diverse environments.

NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) are a family of plant-specific TFs that play crucial roles in various aspects of plant development and stress responses. Here, we provide an in-depth review of the structural characteristics, regulatory mechanisms, and functional roles of NACs in different plant species. One of the key features of NACs is their ability to regulate gene expression through a variety of mechanisms, including binding to DNA sequences in the promoter regions of target genes, interacting with other TFs, and modulating chromatin structure. We discuss these mechanisms in detail, providing insights into the complex regulatory networks that govern the activity of NACs. We explore the diverse functions of these TFs in plant growth and development processes, including embryogenesis, seed development, root and shoot development, floral development and fruit ripening, secondary cell wall formation, and senescence. We also discuss the diverse regulatory roles of NACs in response to various stresses, including drought, flooding, heat, cold, salinity, nutrient deficit, and diseases. Lastly, we emphasize the crosstalk role of NACs between developmental processes and stress responses. This integrated perspective highlights how NACs orchestrate plant growth and resilience. Overall, this review provides a comprehensive overview of the pivotal roles of NACs in plant development and stress responses, emphasizing their potential for engineering stress-resistant crops and enhancing agricultural productivity.

Targeted knockout of the betaine aldehyde dehydrogenase genes AhBADH1 and AhBADH2 using CRISPR/Cas9 produced peanut mutant lines with significantly elevated 2-acetyl-1-pyrroline levels and a strong aroma, marking the first creation of fragrant peanut lines.