Plant Communications最新文献_第10页

OsNLP3 enhances grain weight and reduces grain chalkiness in rice. OsNLP3 可提高水稻的粒重并减少垩白粒。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-06-08 DOI: 10.1016/j.xplc.2024.100999

Liang-Qi Sun, Yu Bai, Jie Wu, Shi-Jun Fan, Si-Yan Chen, Zheng-Yi Zhang, Jin-Qiu Xia, Shi-Mei Wang, Yu-Ping Wang, Peng Qin, Shi-Gui Li, Ping Xu, Zhong Zhao, Cheng-Bin Xiang, Zi-Sheng Zhang

{"title":"OsNLP3 enhances grain weight and reduces grain chalkiness in rice.","authors":"Liang-Qi Sun, Yu Bai, Jie Wu, Shi-Jun Fan, Si-Yan Chen, Zheng-Yi Zhang, Jin-Qiu Xia, Shi-Mei Wang, Yu-Ping Wang, Peng Qin, Shi-Gui Li, Ping Xu, Zhong Zhao, Cheng-Bin Xiang, Zi-Sheng Zhang","doi":"10.1016/j.xplc.2024.100999","DOIUrl":"10.1016/j.xplc.2024.100999","url":null,"abstract":"Grain weight, a key determinant of yield in rice (Oryza sativa L.), is governed primarily by genetic factors, whereas grain chalkiness, a detriment to grain quality, is intertwined with environmental factors such as mineral nutrients. Nitrogen (N) is recognized for its effect on grain chalkiness, but the underlying molecular mechanisms remain to be clarified. This study revealed the pivotal role of rice NODULE INCEPTION-LIKE PROTEIN 3 (OsNLP3) in simultaneously regulating grain weight and grain chalkiness. Our investigation showed that loss of OsNLP3 leads to a reduction in both grain weight and dimension, in contrast to the enhancement observed with OsNLP3 overexpression. OsNLP3 directly suppresses the expression of OsCEP6.1 and OsNF-YA8, which were identified as negative regulators associated with grain weight. Consequently, two novel regulatory modules, OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8, were identified as key players in grain weight regulation. Notably, the OsNLP3-OsNF-YA8 module not only increases grain weight but also mitigates grain chalkiness in response to N. This research clarifies the molecular mechanisms that orchestrate grain weight through the OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8 modules, highlighting the pivotal role of the OsNLP3-OsNF-YA8 module in alleviating grain chalkiness. These findings reveal potential targets for simultaneous enhancement of rice yield and quality.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141297218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Streamlined whole-genome genotyping through NGS-enhanced thermal asymmetric interlaced (TAIL)-PCR. 通过 NGS 增强热不对称交错 (TAIL)-PCR 技术简化全基因组基因分型。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-06-05 DOI: 10.1016/j.xplc.2024.100983

Sheng Zhao, Yue Wang, Zhenghang Zhu, Peng Chen, Wuge Liu, Chongrong Wang, Hong Lu, Yong Xiang, Yuwen Liu, Qian Qian, Yuxiao Chang

{"title":"Streamlined whole-genome genotyping through NGS-enhanced thermal asymmetric interlaced (TAIL)-PCR.","authors":"Sheng Zhao, Yue Wang, Zhenghang Zhu, Peng Chen, Wuge Liu, Chongrong Wang, Hong Lu, Yong Xiang, Yuwen Liu, Qian Qian, Yuxiao Chang","doi":"10.1016/j.xplc.2024.100983","DOIUrl":"10.1016/j.xplc.2024.100983","url":null,"abstract":"Whole-genome genotyping (WGG) stands as a pivotal element in genomic-assisted plant breeding. Nevertheless, sequencing-based approaches for WGG continue to be costly, primarily owing to the high expenses associated with library preparation and the laborious protocol. During prior development of foreground and background integrated genotyping by sequencing (FBI-seq), we discovered that any sequence-specific primer (SP) inherently possesses the capability to amplify a massive array of stable and reproducible non-specific PCR products across the genome. Here, we further improved FBI-seq by replacing the adapter ligated by Tn5 transposase with an arbitrary degenerate (AD) primer. The protocol for the enhanced FBI-seq unexpectedly mirrors a simplified thermal asymmetric interlaced (TAIL)-PCR, a technique that is widely used for isolation of flanking sequences. However, the improved TAIL-PCR maximizes the primer-template mismatched annealing capabilities of both SP and AD primers. In addition, leveraging of next-generation sequencing enhances the ability of this technique to assay tens of thousands of genome-wide loci for any species. This cost-effective, user-friendly, and powerful WGG tool, which we have named TAIL-PCR by sequencing (TAIL-peq), holds great potential for widespread application in breeding programs, thereby facilitating genome-assisted crop improvement.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141285316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Brassinosteroid biosynthesis and signaling: Conserved and diversified functions of core genes across multiple plant species. 芸苔素类固醇的生物合成和信号传导：多个植物物种核心基因的保守和多样化功能。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-05-29 DOI: 10.1016/j.xplc.2024.100982

Brian Zebosi, Erik Vollbrecht, Norman B Best

{"title":"Brassinosteroid biosynthesis and signaling: Conserved and diversified functions of core genes across multiple plant species.","authors":"Brian Zebosi, Erik Vollbrecht, Norman B Best","doi":"10.1016/j.xplc.2024.100982","DOIUrl":"10.1016/j.xplc.2024.100982","url":null,"abstract":"Brassinosteroids (BRs) are important regulators that control myriad aspects of plant growth and development, including biotic and abiotic stress responses, such that modulating BR homeostasis and signaling presents abundant opportunities for plant breeding and crop improvement. Enzymes and other proteins involved in the biosynthesis and signaling of BRs are well understood from molecular genetics and phenotypic analysis in Arabidopsis thaliana; however, knowledge of the molecular functions of these genes in other plant species, especially cereal crop plants, is minimal. In this manuscript, we comprehensively review functional studies of BR genes in Arabidopsis, maize, rice, Setaria, Brachypodium, and soybean to identify conserved and diversified functions across plant species and to highlight cases for which additional research is in order. We performed phylogenetic analysis of gene families involved in the biosynthesis and signaling of BRs and re-analyzed publicly available transcriptomic data. Gene trees coupled with expression data provide a valuable guide to supplement future research on BRs in these important crop species, enabling researchers to identify gene-editing targets for BR-related functional studies.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141181828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The PRR-EC complex and SWR1 chromatin remodeling complex function cooperatively to repress nighttime hypocotyl elongation by modulating PIF4 expression in Arabidopsis. 拟南芥中的 PRR-EC 复合物和 SWR1 染色质重塑复合物通过调节 PIF4 的表达协同抑制夜间下胚轴伸长。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-05-29 DOI: 10.1016/j.xplc.2024.100981

Jin Hoon Won, Jeonghyang Park, Hong Gil Lee, Sangrae Shim, Hongwoo Lee, Eunkyoo Oh, Pil Joon Seo

{"title":"The PRR-EC complex and SWR1 chromatin remodeling complex function cooperatively to repress nighttime hypocotyl elongation by modulating PIF4 expression in Arabidopsis.","authors":"Jin Hoon Won, Jeonghyang Park, Hong Gil Lee, Sangrae Shim, Hongwoo Lee, Eunkyoo Oh, Pil Joon Seo","doi":"10.1016/j.xplc.2024.100981","DOIUrl":"10.1016/j.xplc.2024.100981","url":null,"abstract":"The circadian clock entrained by environmental light-dark cycles enables plants to fine-tune diurnal growth and developmental responses. Here, we show that physical interactions among evening clock components, including PSEUDO-RESPONSE REGULATOR 5 (PRR5), TIMING OF CAB EXPRESSION 1 (TOC1), and the Evening Complex (EC) component EARLY FLOWERING 3 (ELF3), define a diurnal repressive chromatin structure specifically at the PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) locus in Arabidopsis. These three clock components act interdependently as well as independently to repress nighttime hypocotyl elongation, as hypocotyl elongation rate dramatically increased specifically at nighttime in the prr5-1 toc1-21 elf3-1 mutant, concomitantly with a substantial increase in PIF4 expression. Transcriptional repression of PIF4 by ELF3, PRR5, and TOC1 is mediated by the SWI2/SNF2-RELATED (SWR1) chromatin remodeling complex, which incorporates histone H2A.Z at the PIF4 locus, facilitating robust epigenetic suppression of PIF4 during the evening. Overall, these findings demonstrate that the PRR-EC-SWR1 complex represses hypocotyl elongation at night through a distinctive chromatin domain covering PIF4 chromatin.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141180632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The haplotype-resolved T2T genome assembly of the wild potato species Solanum commersonii provides molecular insights into its freezing tolerance. 野生马铃薯物种Solanum commersonii的单倍型解析T2T基因组组装提供了有关其耐寒性的分子见解。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-05-27 DOI: 10.1016/j.xplc.2024.100980

Yang Feng, Jie Zhou, Dianjue Li, Zhen Wang, Cheng Peng, Guangtao Zhu

引用次数: 0

A faster killing effect of plastid-mediated RNA interference on a leaf beetle through induced dysbiosis of the gut bacteria. 通过诱导肠道菌群失调，质粒介导的 RNA 干扰对叶甲虫产生了更快的杀伤效果。

IF 10.5 1区生物学

Plant Communications Pub Date : 2024-05-14 DOI: 10.1016/j.xplc.2024.100974

Yiqiu Zhang, Zebin Ke, Letian Xu, Yang Yang, Ling Chang, Jiang Zhang

{"title":"A faster killing effect of plastid-mediated RNA interference on a leaf beetle through induced dysbiosis of the gut bacteria.","authors":"Yiqiu Zhang, Zebin Ke, Letian Xu, Yang Yang, Ling Chang, Jiang Zhang","doi":"10.1016/j.xplc.2024.100974","DOIUrl":"10.1016/j.xplc.2024.100974","url":null,"abstract":"The expression of double-stranded RNAs (dsRNAs) from the plastid genome has been proven to be an effective method for controlling herbivorous pests by targeting essential insect genes. However, there are limitations to the efficiency of plastid-mediated RNA interference (PM-RNAi) due to the initial damage caused by the insects and their slow response to RNA interference. In this study, we developed transplastomic poplar plants that express dsRNAs targeting the β-Actin (dsACT) and Srp54k (dsSRP54K) genes of Plagiodera versicolora. Feeding experiments showed that transplastomic poplar plants can cause significantly higher mortality in P. versicolora larvae compared with nuclear transgenic or wild-type poplar plants. The efficient killing effect of PM-RNAi on P. versicolora larvae was found to be dependent on the presence of gut bacteria. Importantly, foliar application of a gut bacterial strain, Pseudomonas putida, will induce dysbiosis in the gut bacteria of P. versicolora larvae, leading to a significant acceleration in the speed of killing by PM-RNAi. Overall, our findings suggest that interfering with gut bacteria could be a promising strategy to enhance the effectiveness of PM-RNAi for insect pest control, offering a novel and effective approach for crop protection based on RNAi technology.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":10.5,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140946392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An improved plant prime editor for efficient generation of multiple-nucleotide variations and structural variations in rice. 用于高效生成水稻多核苷酸变异和结构变异的改进型植物素编辑器。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-05-14 DOI: 10.1016/j.xplc.2024.100976

Zhaohui Zhong, Tingting Fan, Yao He, Shishi Liu, Xuelian Zheng, Yang Xu, Jingqi Ren, Hua Yuan, Zhengyan Xu, Yong Zhang

引用次数: 0

Whole-genome resequencing identifies candidate genes and allelic variation in the MdNADP-ME promoter that regulate fruit malate and fructose contents in apple. 全基因组重测序确定了调控苹果果实苹果酸盐和果糖含量的候选基因和 MdNADP-ME 启动子中的等位基因变异。

IF 9.4 1区生物学

Plant Communications Pub Date : 2024-05-14 DOI: 10.1016/j.xplc.2024.100973

Weihong Fu, Lin Zhao, Wanjun Qiu, Xu Xu, Meng Ding, Liming Lan, Shenchun Qu, Sanhong Wang

{"title":"Whole-genome resequencing identifies candidate genes and allelic variation in the MdNADP-ME promoter that regulate fruit malate and fructose contents in apple.","authors":"Weihong Fu, Lin Zhao, Wanjun Qiu, Xu Xu, Meng Ding, Liming Lan, Shenchun Qu, Sanhong Wang","doi":"10.1016/j.xplc.2024.100973","DOIUrl":"10.1016/j.xplc.2024.100973","url":null,"abstract":"Soluble sugar and organic acids are key determinants of fruit organoleptic quality and directly affect the commodity value and economic returns of fruit crops. We performed whole-genome sequencing of the apple varieties Gala and Xiahongrou, along with their F1 hybrids, to construct a high-density bin map. Our quantitative genetic analysis pinpointed 53 quantitative trait loci (QTLs) related to 11 sugar and acid traits. We identified a candidate gene, MdNADP-ME, responsible for malate degradation, in a stable QTL on linkage group 15. Sequence analysis revealed an A/C SNP in the promoter region (MEp-799) that influences binding of the MdMYB2 transcription factor, thereby affecting MdNADP-ME expression. In our study of various apple genotypes, this SNP has been demonstrated to be linked to malate and fructose levels. We also developed a dCAPS marker associated with fruit fructose content. These results substantiate the role of MdNADP-ME in maintaining the equilibrium between sugar and acid contents in apple fruits.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140946401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Plant Stem Cell Informatics Database (PSCIdb): A comprehensive computational platform for identifying and analyzing genes related to plant stem cells. 植物干细胞信息学数据库（PSCIdb）：一个用于识别和分析植物干细胞相关基因的综合计算平台。

IF 10.5 1区生物学

Plant Communications Pub Date : 2024-05-13 Epub Date: 2024-01-12 DOI: 10.1016/j.xplc.2024.100818

Xiao Wu, Yubo Yuan, Siyuan Zhou, Zewen Wang, Hongxiang Li, Wanping Wu, Zhijie Lei, Siyao Liu, Kaijie Qi, Hao Yin, Yun Zhou, Shaoling Zhang

引用次数: 0

Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat. 通过整合小麦基因调控网络和遗传变异，剖析穗状性状的分子基础。

IF 10.5 1区生物学

Plant Communications Pub Date : 2024-05-13 Epub Date: 2024-03-14 DOI: 10.1016/j.xplc.2024.100879

Guo Ai, Chao He, Siteng Bi, Ziru Zhou, Ankui Liu, Xin Hu, Yanyan Liu, Liujie Jin, JiaCheng Zhou, Heping Zhang, Dengxiang Du, Hao Chen, Xin Gong, Sulaiman Saeed, Handong Su, Caixia Lan, Wei Chen, Qiang Li, Hailiang Mao, Lin Li, Hao Liu, Dijun Chen, Kerstin Kaufmann, Khaled F Alazab, Wenhao Yan

{"title":"Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat.","authors":"Guo Ai, Chao He, Siteng Bi, Ziru Zhou, Ankui Liu, Xin Hu, Yanyan Liu, Liujie Jin, JiaCheng Zhou, Heping Zhang, Dengxiang Du, Hao Chen, Xin Gong, Sulaiman Saeed, Handong Su, Caixia Lan, Wei Chen, Qiang Li, Hailiang Mao, Lin Li, Hao Liu, Dijun Chen, Kerstin Kaufmann, Khaled F Alazab, Wenhao Yan","doi":"10.1016/j.xplc.2024.100879","DOIUrl":"10.1016/j.xplc.2024.100879","url":null,"abstract":"Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits. Here, we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat. We identified 170 loci that are responsible for variations in spike length, spikelet number per spike, and grain number per spike through genome-wide association study and meta-QTL analyses. We constructed gene regulatory networks for young inflorescences at the double ridge stage and the floret primordium stage, in which the spikelet meristem and the floret meristem are predominant, respectively, by integrating transcriptome, histone modification, chromatin accessibility, eQTL, and protein-protein interactome data. From these networks, we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits. The functions of TaZF-B1, VRT-B2, and TaSPL15-A/D in establishment of wheat spike architecture were verified. This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":null,"pages":null},"PeriodicalIF":10.5,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11121755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140133168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0