The Plant Journal最新文献

BES1/BZR1, a kind of plant-specific transcription factor (TF), has been reported to regulate growth, development, and stress response. However, the maize BES1/BZR1 members are still largely unknown. In this study, we investigated the function and regulatory mechanism of maize ZmBES1/BZR1-4 in regulating drought response and seed development. The ZmBES1/BZR1-4 was localized in the nucleus depending on its bHLH domain and showed no self-transactivation activity. The transcription level of ZmBES1/BZR1-4 was induced by drought stress and was predominantly higher in seeds 25 days after pollination. Overexpression of ZmBES1/BZR1-4 reduced drought tolerance but produced bigger seeds with higher seed weight in transgenic Arabidopsis, rice, and maize. Inversely, the ZmBES1/BZR1-4 mutant Mu4-1 and Mu4-2 showed enhancement of drought tolerance and decreased seed size and weight. The ZmBES1/BZR1-4 could directly bind to E-box elements in the ZmMBP1 and ZmPum6 promoters to activate their transcription. Furthermore, the interaction between ZmBES1/BZR1-4 and ZmTLP5 enhanced the ZmMBP1 and ZmPum6 transcription. Moreover, ZmMBP1 and ZmPum6 positively regulated seed size and weight, but ZmPum6 negatively regulated drought tolerance. Therefore, our findings reveal that ZmBES1/BZR1-4 recruits ZmTLP5 to regulate drought tolerance and seed development by regulating ZmMBP1 and ZmPum6, which contributes to uncovering the function of BES1/BZR1s regulating growth, development, and stress response in crops.

The pan-genome represents the complete genomic diversity of specific species, serving as a valuable resource for studying species evolution, crop domestication, and guiding crop breeding and improvement. While there are several single-species-specific plant pan-genome databases, the availability of multi-species pan-genome databases is limited. Additionally, variations in methods and data types used for plant pan-genome analysis across different databases hinder the comparison and integration of pan-genome information from various projects at multi-species or single-species levels. To tackle this challenge, we introduce PlantPan, a comprehensive database housing the results of pan-genome analysis for 195 genomes from 11 plant species. PlantPan aims to provide extensive information, including gene-centric and sequence-centric pan-genome information, graph-based pan-genome, pan-genome openness profiles, gene functions and its variation characteristics, homologous genes, and gene clusters across different species. Statistically, PlantPan incorporates 9 163 011 genes, 694 191 gene clusters, 526 973 370 genome variations, and 1 616 089 non-redundant genome variation groups at the species level, 33 455,098 genome synteny, and 177 827 non-redundant genome synteny groups at the species level. Regarding functional genes, PlantPan contains 5 222 720 genes related to transcription factors, 395 247 literature-reported resistance genes, 455 748 predicted microbial/disease resistance genes, and 1 612 112 genes related to molecular pathways. In summary, PlantPan is a vital platform for advancing the application of pan-genomes in molecular breeding for crops and evolutionary research for plants.

Plant height and flag leaf morphology critically affect plant yield because they determine above-ground plant biomass and photosynthate production. However, few genetic basis analyses and gene mining studies on plant height, flag leaf length, and flag leaf width have been performed, and there is little available information about the evolution and utilization of the underlying natural alleles. This study conducted a genome-wide association study (GWAS) using 689 rice accessions collected from diverse regions across the globe. The GWAS identified 73, 159, and 158 significant loci associated with plant height, flag leaf length, and flag leaf width, respectively. SD1^HAP1 and NAL1^A were also identified as superior alleles that could be used to improve plant architecture by reducing plant height and increasing flag leaf width, respectively. LEAF1 and its elite allele LEAF1^G, which simultaneously modulated plant height and flag leaf morphology, were isolated, and the LEAF1 knockout lines showed reduced flag leaf length and plant height, whereas LEAF1^G-complementary lines in the LEAF1^A background had the opposite phenotypes. The results also showed that LEAF1^G and SD1^HAP1 evolved directly from wild rice and were mainly found in the Xian subgroup, whereas NAL1^A might have originated from de novo mutation during domestication and was mainly found in the Geng subgroup. A joint haplotype analysis revealed that pyramiding SD1^HAP1, NAL1^A, and LEAF1^G in Type I accessions optimized plant architecture, reduced plant height, and enlarged the flag leaves. In addition, genomic regions and genes that had been convergently selected for these traits were identified by combining a population genetics analysis with a GWAS. These findings provide valuable genetic targets for molecular breeding that will improve plant height and flag leaf morphology in rice.

The grains of rice (Oryza sativa) are enclosed by a spikelet hull comprising the lemma and palea. Development of the spikelet hull determines the storage capacity of the grain, thus affecting grain yield and quality. Although multiple signaling pathways controlling grain size have been identified, the transcriptional regulatory mechanisms underlying grain development remain limited. Here, we used RNA-seq and ATAC-seq to characterize the transcription and chromatin accessibility dynamics during the development of spikelet hulls. A time-course analysis showed that more than half of the genes were sequentially expressed during hull development and that the accessibility of most open chromatin regions (OCRs) changed moderately, although some regions positively or negatively affected the expression of their closest genes. We revealed a crucial role of GROWTH-REGULATING FACTORs in shaping grain size by influencing multiple metabolic and signaling pathways, and a coordinated transcriptional regulation in response to auxin and cytokinin signaling. We also demonstrated the function of SCL6-IIb, a member of the GRAS family transcription factors, in regulating grain size, with SCL6-IIb expression being activated by SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 18 (OsSPL18). When we edited the DNA sequences within OCRs upstream of the start codon of BRASSINAZOLE-RESISTANT 1 (BZR1) and SCL6-IIb, we generated multiple mutant lines with longer grains. These findings offer a comprehensive overview of the cis-regulatory landscape involved in forming grain capacity and a valuable resource for exploring the regulatory network behind grain development.

Taxol, a chemotherapeutic agent widely used for treating various cancers, is extracted from the stems of Taxus mairei. However, current knowledge regarding the effects of stem tissue and age on Taxol accumulation is limited. We employed matrix-assisted laser desorption/ionization mass spectrometry to visualize taxoids in stem section sections of varying ages from T. mairei. Laser capture microdissection integrated with data-dependent acquisition–MS/MS analysis identified that several Taxol biosynthesis pathway-related enzymes were predominantly produced in the endodermis, elucidating the molecular mechanisms underlying endodermis-specific Taxol accumulation. We identified an endodermis-specific MYB1-like (MYB1L) protein and proposed a potential function for the miR858-MYB1L module in regulating secondary metabolic pathways. DNA affinity purification sequencing analysis produced 92 506 target peaks for MYB1L. Motif enrichment analysis identified several de novo motifs, providing new insights into MYB recognition sites. Four target peaks of MYB1L were identified within the promoter sequences of Taxol synthesis genes, including TBT, DBTNBT, T13OH, and BAPT, and were confirmed using electrophoretic mobility shift assays. Dual-luciferase assays showed that MYB1L significantly activated the expression of TBT and BAPT. Our data indicate that the miR858b-MYB1L module plays a crucial role in the transcriptional regulation of Taxol biosynthesis by up-regulating the expression of TBT and BAPT genes in the endodermis.