The Plant Journal最新文献

Tillering contributes greatly to grain yield in rice (Oryza sativa). At present, many genes involved in rice tillering regulation have been cloned and characterized. However, the identification of more novel genes is still necessary to fully understand the molecular mechanisms regulating rice tillering. In this study, we isolated a low-tillering and dwarf 1 (ltd1) mutant in indica rice. Map-based cloning and MutMap analysis showed that the candidate gene LTD1 (LOC_Os01g19760) encodes a putative FAM91A1 protein with an unknown function in plants. LTD1-complementation and -RNAi confirmed that LTD1 is responsible for the mutant phenotype of ltd1. The LTD1 protein is localized to the plasma membrane, endoplasmic reticulum, and multi-vesicular bodies. Furthermore, protein interaction and colocalization assays showed that LTD1 interacts with both the TFB2 subunit of the core subcomplex and the CycH1;1 subunit of the cyclin-dependent kinase-activating kinase (CAK) subcomplex of the TFIIH complex, and TFB2 also interacts with CycH1;1. qRT-PCR demonstrated that the expression levels of most genes related to the cell cycle are changed significantly in the ltd1 tiller buds, and flow cytometry assays revealed that there are more polyploid nuclei in the ltd1 leaves and roots, suggesting that LTD1 could be involved in cell cycle regulation. Taken together, our findings indicated that LTD1 plays a key role in rice tillering regulation by involvement in the cell cycle through cooperation with CycH1;1 and TFB2 subunits of TFIIH. This work also sheds light on the biological function of FAM91A1 in regulating important agronomic traits of rice.

Variegation, a common phenomenon in plants, can be the result of several genetic, developmental, and physiological factors. Leaves of some lettuce cultivars exhibit dramatic red variegation; however, the genetic mechanisms underlying this variegation remain unknown. In this study, we cloned the causal gene for variegation on lettuce leaves and elucidated the underlying molecular mechanisms. Genetic analysis revealed that the polymorphism of variegated versus uniformly red leaves is caused by an “AT” repeat in the promoter of the RLL2A gene encoding a MYB transcription factor. Complementation tests demonstrated that the RLL2A allele (RLL2A^V) with (AT)_n repeat numbers other than five led to variegated leaves. RLL2A^V was expressed in the red spots but not in neighboring green regions. This expression pattern was in concert with a relatively low level of methylation in a retrotransposon inserted in −761 bp of the gene in the red spots compared to high methylation of the retrotransposon in the green region. The presence of (AT)₅ in the promoter region, however, stabilized the expression of RLL2A, resulting in uniformly red leaves. In summary, we identified a novel promoter mechanism controlling variegation through inconsistent levels of methylation and showed that the presence of a simple sequence repeat of specific size could stabilize gene expression.

Alfalfa (Medicago sativa L.) is a high-quality forage crop and an essential resource for livestock. Understanding the molecular mechanisms underlying male sterility in alfalfa is pivotal for the development of superior forage varieties. Despite the critical role of anther development in plant reproduction, its molecular regulation—particularly the involvement of transcription factors in M. sativa—remains insufficiently explored. This study bridges this gap by isolating and characterizing an R2R3-MYB transcription factor, MsMYB35, and unveiling its regulatory role in anther development. Quantitative RT-PCR (qRT-PCR) revealed that MsMYB35 is predominantly expressed during early anther development and is homologous to AtMYB35. MsMYB35 was found to localize in both the cytoplasm and nucleus. DNA affinity purification sequencing (DAP-seq) identified 3647 target genes of MsMYB35, with enrichment analysis uncovering three recognition motifs. Integrated DAP-seq and RNA-seq analyses revealed that MsMYB35 directly regulates two key anther development-related genes. Functional analyses showed that overexpression of MsMYB35 promotes anther development, while silencing MsMYB35 leads to defective anther sacs and wrinkled pollen grains. Proper MsMYB35 expression ensures the formation of viable and fertile pollen grains, solidifying its role as a critical regulator of anther development. These findings provide a novel perspective on the molecular mechanisms regulating anther development in M. sativa and offer valuable insights for improving molecular breeding and hybrid seed production strategies. By advancing the fundamental understanding of transcriptional regulation in anther development, this study sets the stage for innovative approaches to alfalfa crop improvement.

Persian walnut (Juglans regia) is an economically important nut oil tree; the fruit has a hard endocarp/shell to protect seeds, thus playing a key role in its evolution, and the shell thickness is an important trait for walnut breeding. However, the genomic landscape and the gene regulatory networks associated with walnut shell development remain to be systematically elucidated. Here, we report a high-quality genome assembly of the walnut cultivar ‘Xiangling’ and construct a graphic structure pan-genome of eight Juglans species to reveal the genetic variations at the genome level. We re-sequence 285 accessions to characterize the genomic variation landscape. Through genome-wide association studies (GWAS), we identified 19 loci associated with more than 268 loci that underwent selection during walnut domestication and improvement. Multi-omics analyses, including transcriptomics, metabolomics, DNA methylation, and spatial transcriptomics across eleven developmental stages, revealed several candidate genes related to secondary cell biosynthesis and lignin accumulation. This integrated multi-omics approach revealed several candidate genes associated with secondary cell biosynthesis and lignin accumulation, such as UGP, MYB308, MYB83, NAC043, NAC073, CCoAOMT1, CCoAOMT7, CHS2, CESA7, LAC7, COBL4, and IRX12. Overexpression of JrUGP and JrMYB308 in Arabidopsis thaliana confirmed their roles in lignin biosynthesis and cell wall thickening. Consequently, our comprehensive multi-omics findings offer novel insights into walnut genetic variation and network regulation of endocarp development and shell thickness, which enable further genome-informed breeding strategies for walnut cultivar improvement.

Autophagy is an evolutionarily conserved process in eukaryotes that regulates metabolic reprogramming and organelle recycling in response to various environmental signals and developmental cues. However, little is known about its regulatory mechanism during fruit colouration and ripening, which also undergo dramatic metabolic and cellular alterations. Here, we demonstrate that the autophagy pathway is activated during citrus fruit colouration, and the colour transition of citrus fruit is significantly delayed when autophagy is blocked. Furthermore, we revealed that ethylene, a plant hormone crucial for citrus fruit colouration, activates the autophagy pathway through the ethylene-responsive factor, CsERF061. Further analysis revealed that CsERF061 directly binds to the promoter of CsATG8h and activates its expression, thereby promoting autophagy and fruit colouration, suggesting autophagy is a key determinant of citrus fruit colouration in response to ethylene. These findings enhance our understanding of fruit colouration and offer a potential method to improve citrus fruit colour and quality for future applications.

The microbial community residing on the phyllosphere is influenced by many factors, including the host plant's genotype as well as its secondary metabolites. Anthocyanins are a group of flavonoids renowned for their antioxidative properties and are widely distributed across plant tissues. However, the potential impact of anthocyanins on plant-associated microbial communities remains unknown. In the model legume Medicago truncatula, we isolated a mutant named purple leaves (pl) that produces purple leaves at a young stage due to over-accumulated anthocyanins. Through sequencing 16S rRNA amplicons of phyllosphere microbes in the pl mutant, we show that anthocyanins significantly enhance the abundance of endophytic lactic acid bacteria within plant leaves. Further in vitro study revealed that anthocyanins derived from pl can significantly promote the growth of lactic acid bacteria under anaerobic conditions. The accumulated anthocyanins in pl leaves reduced reactive oxygen species (ROS), thereby creating a favorable environment for the growth of facultative anaerobic lactic acid bacteria and resultantly increasing the abundance of phyllosphere lactic acid bacteria. Our findings elucidate the role of anthocyanins in modulating the community structure of phyllosphere microbiota in M. truncatula and provide new insights into the relationship between plant secondary metabolites and phyllosphere microbiota.

Environmental stimuli can induce the transfer of chloroplast DNA to the nuclear genome, resulting in nuclear-integrated plastid DNAs (NUPTs). However, their role in plant adaptability remains unclear. Species within the Caryophyllales order, known for their adaptation to extreme environments, provide an ideal model for studying the evolutionary dynamics and functions of NUPTs. In this study, we analyzed NUPTs in 24 Caryophyllales species to investigate their evolution and regulatory roles in gene expression, particularly in response to environmental stimuli. We found significant interspecies variation in NUPT abundance, ranging from 566 insertions in Amaranthus cruentus to 3585 in Beta vulgaris, with sizes spanning from 100 bp to over 100 kb. Approximately 62% of NUPTs were inserted within the last 20 million years, while some species exhibit insertion peaks dating back 49 million years. NUPT presence/absence polymorphisms in six related species suggest that NUPT insertions and deletions are dynamic processes influenced by phylogeny. NUPTs predominantly integrate into intergenic regions but also insert into genes and promoters, with certain regions acting as hotspots. Notably, NUPTs introduce numerous environmental-responsive cis-acting elements in promoter regions. Genes with NUPT insertions in their promoters are significantly enriched for functions related to environmental response. Further luciferase assays in Spinacia oleracea demonstrated that NUPT insertions can regulate the expression of genes related to environmental responses, indicating their potential role in adaptive evolution. Overall, our study provides insights into NUPT evolution and their influence on gene function and plant adaptability to environmental stimuli.