Plant Communications最新文献

{"title":"Mitochondrial support of high rates of photosynthesis.","authors":"Guillaume Decros, Youjun Zhang, Alisdair R Fernie","doi":"10.1016/j.xplc.2025.101285","DOIUrl":"10.1016/j.xplc.2025.101285","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101285"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426595","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}

{"title":"Cropformer: An interpretable deep learning framework for crop genomic prediction.","authors":"Hao Wang, Shen Yan, Wenxi Wang, Yongming Chen, Jingpeng Hong, Qiang He, Xianmin Diao, Yunan Lin, Yanqing Chen, Yongsheng Cao, Weilong Guo, Wei Fang","doi":"10.1016/j.xplc.2024.101223","DOIUrl":"10.1016/j.xplc.2024.101223","url":null,"abstract":"<p><p>Machine learning and deep learning are extensively employed in genomic selection (GS) to expedite the identification of superior genotypes and accelerate breeding cycles. However, a significant challenge with current data-driven deep learning models in GS lies in their low robustness and poor interpretability. To address these challenges, we developed Cropformer, a deep learning framework for predicting crop phenotypes and exploring downstream tasks. This framework combines convolutional neural networks with multiple self-attention mechanisms to improve accuracy. The ability of Cropformer to predict complex phenotypic traits was extensively evaluated on more than 20 traits across five major crops: maize, rice, wheat, foxtail millet, and tomato. Evaluation results show that Cropformer outperforms other GS methods in both precision and robustness, achieving up to a 7.5% improvement in prediction accuracy compared to the runner-up model. Additionally, Cropformer enhances the analysis and mining of genes associated with traits. We identified numerous single nucleotide polymorphisms (SNPs) with potential effects on maize phenotypic traits and revealed key genetic variations underlying these differences. Cropformer represents a significant advancement in predictive performance and gene identification, providing a powerful general tool for improving genomic design in crop breeding. Cropformer is freely accessible at https://cgris.net/cropformer.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101223"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956090/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848361","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}

{"title":"Creation of rapeseed germplasm with high polyunsaturated fatty acid content by wild-relative introgression from Brassica carinata.","authors":"Yan Niu, Wenwen Li, Yinghui Yang, Hao Wang, Zhesi He, Han Qin, Yikai Zhang, Dandan Hu, Jing Wang, Chunyu Zhang, Guangsheng Yang, Ian Bancroft, Jun Zou","doi":"10.1016/j.xplc.2024.101193","DOIUrl":"10.1016/j.xplc.2024.101193","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101193"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644675","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}

{"title":"MRBIGR: A versatile toolbox for genetic regulation inference from population-scale multi-omics data.","authors":"Feng Xu, Qian Cheng, Songyu Liu, Shuqin Jiang, Jianan Zhang, Xiaowei Mao, Xiangfeng Wang, Jinsheng Lai, Jun Yan","doi":"10.1016/j.xplc.2024.101197","DOIUrl":"10.1016/j.xplc.2024.101197","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101197"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711570","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}

{"title":"Cotton metabolism regulatory network: Unraveling key genes and pathways in fiber development and growth regulation.","authors":"Zhao Liu, Liqiang Fan, Sheng Shu, Ghulam Qanmber, Eryong Chen, Jinquan Huang, Fuguang Li, Zuoren Yang","doi":"10.1016/j.xplc.2024.101221","DOIUrl":"10.1016/j.xplc.2024.101221","url":null,"abstract":"<p><p>Cotton (Gossypium hirsutum L.) is one of the world's most important commercial crops. However, the dynamics of metabolite abundance and potential regulatory networks throughout its life cycle remain poorly understood. In this study, we developed a cotton metabolism regulatory network (CMRN) that spans various developmental stages and encompasses 2138 metabolites and 90 309 expressed genesin upland cotton. By integrating high-resolution spatiotemporal metabolome and transcriptome data, we identified 1958 differentially accumulated metabolites and 13 597 co-expressed differentially expressed genes between the dwarf mutant pagoda1 and its wild-type counterpart Zhongmiansuo 24. These metabolites and genes were categorized into seven clusters based on tissue-specific accumulation patterns and gene expression profiles across different developmental stages. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed significant differential enrichment in the fatty acid elongation pathway, particularly in fibers. The differential involvement of genes and metabolites in very-long-chain fatty acid (VLCFA) synthesis led to the identification of GhKCS1b_Dt as a key gene. Overexpression of GhKCS1b_Dt significantly promoted fiber elongation, while its silencing markedly inhibited cotton fiber growth, affirming its positive regulatory role in fiber elongation. This dataset provides a valuable resource for further research into metabolic pathways and gene regulatory networks, offering novel insights for advancing cotton breeding strategies.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101221"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824578","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}

{"title":"Genomic analysis of Zhou8425B, a key founder parent, reveals its genetic contributions to elite agronomic traits in wheat breeding.","authors":"Guangwei Li, Yan Ren, Yuxin Yang, Shulin Chen, Jizhou Zheng, Xiaoqing Zhang, Junlong Li, Mengen Chen, Xiaonan Sun, Chunlei Lv, Xiaode Li, Bingbing Zhang, Xiao Sun, Yujia Li, Mingtian Zhao, Chunhao Dong, Jianwei Tang, Zhenpu Huang, Yanyan Peng, Dengbin Gu, Zhiyong Wang, Hongyuan Zheng, Cuilan Shi, Guozhang Kang, Tiancun Zheng, Feng Chen, Daowen Wang, Kunpu Zhang, Guihong Yin","doi":"10.1016/j.xplc.2024.101222","DOIUrl":"10.1016/j.xplc.2024.101222","url":null,"abstract":"<p><p>High-quality genome information is essential for efficiently deciphering and improving crop traits. Here, we report a highly contiguous and accurate hexaploid genome assembly for the key wheat breeding parent Zhou8425B, an elite 1BL/1RS translocation line with durable adult plant resistance (APR) against yellow rust (YR) disease. By integrating HiFi and Hi-C sequencing reads, we have generated a 14.75-Gb genome assembly for Zhou8425B with a contig N50 of 70.94 and a scaffold N50 of 735.11 Mb. Comparisons with previously sequenced common wheat cultivars shed light on structural changes in the 1RS chromosome arm, which has been extensively used in wheat improvement. Interestingly, Zhou8425B 1RS carries more genes encoding AP2/ERF-ERF or B3 transcription factors than its counterparts in four previously sequenced wheat and rye genotypes. The Zhou8425B genome assembly aided in the fine mapping of a new APR locus (YrZH3BS) that confers resistance to YR disease and promotes grain yield under field conditions. Notably, pyramiding YrZH3BS with two previously characterized APR loci (YrZH22 and YrZH84) can further reduce YR severity and enhance grain yield, with the triple combination (YrZH3B + YrZH22 + YrZH84) having the greatest effect. Finally, the founder genotype effects of Zhou8425B were explored using publicly available genome resequencing data, which reveals the presence of important Zhou8425B genomic blocks in its derivative cultivars. Our data demonstrate the value of the Zhou8425B genome assembly for further study of the structural and functional characteristics of 1RS, the genetic basis of durable YR resistance, and founder genotype effects in wheat breeding. Our resources will facilitate the development of elite wheat cultivars through genomics-assisted breeding.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101222"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848365","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}

{"title":"Gap-free genome assemblies of two Pyrus bretschneideri cultivars and GWAS analyses identify a CCCH zinc finger protein as a key regulator of stone cell formation in pear fruit.","authors":"Yunpeng Cao, Xiaofeng Feng, Baopeng Ding, Heqiang Huo, Muhammad Abdullah, Jiayi Hong, Lan Jiang, Han Wang, Risheng Li, Yongping Cai, Xiaoxu Li, Zhichao Xia, Rajeev K Varshney, Haifei Hu, Mengfei Lin, Fei Shen","doi":"10.1016/j.xplc.2024.101238","DOIUrl":"10.1016/j.xplc.2024.101238","url":null,"abstract":"<p><p>The Chinese white pear (Pyrus bretschneideri) is an economically significant fruit crop worldwide. Previous versions of the P. bretschneideri genome assembly contain numerous gaps and unanchored genetic regions. Here, we generated two high-quality, gap-free genome assemblies for 'Dangshansu' (DS; 503.92 Mb) and 'Lianglizaosu' (ZS; 509.01 Mb), each anchored to 17 chromosomes, achieving a benchmarking universal single-copy ortholog completeness score of nearly 99.0%. Our genome-wide association studies explored the associations between genetic variations and stone cell traits, revealing a significant association peak on DS chromosome 3 and identifying a novel non-tandem CCCH-type zinc finger gene, designated PbdsZF. Through genetic transformation, we verified the pivotal role of PbdsZF in regulation of both lignin biosynthesis and stone cell formation, as it transcriptionally activates multiple genes involved in these processes. By binding to the CT-rich motifs CT1 (CTTTTTTCT) and CT2 (CTCTTTTT), PbdsZF significantly influences the transcription of genes essential for lignin production, underscoring its regulatory importance in plant lignin metabolism. Our study illuminates the complex biology of fruit development and delineates the gene regulatory networks that influence stone cell and lignocellulose formation, thereby enriching genetic resources and laying the groundwork for the molecular breeding of perennial trees.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":"6 3","pages":"101238"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607232","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}

{"title":"Natural variation in TaERF-A1 confers semi-dwarf and lodging-resistant plant architecture in wheat.","authors":"Renhan Li, Jie Liu, Lingling Chai, Dejie Du, Wen Yang, Jun Zhu, Yaotian Gao, Yunjie Liu, Lingfeng Miao, Long Song, Xiaoming Xie, Yongming Chen, Zhaoheng Zhang, Pei Ni, Yidi Zhao, Zhaoju Li, Lahu Lu, Weilong Guo, Huiru Peng, Qixin Sun, Zhongfu Ni","doi":"10.1016/j.xplc.2024.101194","DOIUrl":"10.1016/j.xplc.2024.101194","url":null,"abstract":"<p><p>The introduction of Reduced height (Rht) genes into wheat varieties has been pivotal in developing semi-dwarf plant architectures, significantly improving lodging resistance and harvest indices. Therefore, identifying new Rht gene resources for breeding semi-dwarf wheat cultivars has been a key strategy for ensuring high and stable grain yields since the 1960s. In this study, we report the map-based cloning of TaERF-A1, which encodes an AP2/ERF (APETALA2/ethylene responsive factor) transcription factor that acts as a positive regulator of wheat stem elongation, as a novel gene that regulates plant height and spike length. The natural variant, TaERF-A1^JD6, features a Phe (derived from 'Nongda3338') to Ser (derived from 'Jingdong6') substitution at position 178, which significantly reduces the stability of the TaERF-A1 protein. This substitution leads to partially attenuated transcriptional activation of downstream target genes, including TaPIF4 (Triticum aestivum Phytochrome Interacting Factor 4), thereby restricting stem and spike elongation. Importantly, the introgression of the semi-dwarfing allele TaERF-A1^JD6 into wheat can significantly enhance lodging resistance, particularly in dense cropping systems. Therefore, our study identifies TaERF-A1^JD6 as a new Rht gene resource for breeding semi-dwarf wheat varieties with increased yield stability.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101194"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677168","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}

{"title":"Competitive binding of small antagonistic peptides to the OsER1 receptor optimizes rice panicle architecture.","authors":"Tao Guo, Fuyan Si, Fei Lu, Lianlian Yang, Ke Chen, Xiaopan Wang, Guanglin Li, Zi-Qi Lu, Hong-Xuan Lin","doi":"10.1016/j.xplc.2024.101204","DOIUrl":"10.1016/j.xplc.2024.101204","url":null,"abstract":"<p><p>Rice panicle architecture is a pivotal trait that strongly contributes to grain yield. Small peptide ligands from the OsEPF/EPFL family synergistically control panicle architecture by recognition of the OsER1 receptor and subsequent activation of the OsMKKK10-OsMKK4-OsMPK6 cascade, indicating that specific ligand-receptor pairs orchestrate rice panicle development. However, how small homologous peptides fine-tune organ morphogenesis by targeting a common receptor remains to be clarified. Here, we report that the small peptide OsEPFL5 acts as a ligand of the OsER1 receptor that inactivates the OsMKKK10-OsMKK4-OsMPK6 cascade, suggesting that OsEPFL5 plays a role opposite to that of the OsEPFL6/7/8/9 subfamily in regulating spikelet number per panicle and grain size. Notably, OsEPFL5 competitively replaces binding of OsEPFL6, OsEPFL7, OsEPFL8, or OsEPFL9 to the OsER1 receptor, revealing antagonistic competition between these small homologous peptides. Specifically enhancing the expression of OsEPFL5 can significantly improve grain yield by suppressing functions of the ligand-receptor pairs OsEPFL6-OsER1, OsEPFL7-OsER1, OsEPFL8-OsER1, and OsEPFL9-OsER1, suggesting that competitive binding to the OsER1 receptor by small antagonistic peptides can optimize rice panicle architecture. Our findings clarify how a receptor agonist and antagonist define inductive and inhibitory cues to shape rice panicle architecture, thus providing a new method for rationally breaking yield-trait coupling by manipulating small antagonistic peptides.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101204"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956112/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792187","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}

{"title":"The integration of quantile regression with 3VmrMLM identifies more QTNs and QTN-by-environment interactions using SNP- and haplotype-based markers.","authors":"Wen-Xian Sun, Xiao-Yu Chang, Ying Chen, Qiong Zhao, Yuan-Ming Zhang","doi":"10.1016/j.xplc.2024.101196","DOIUrl":"10.1016/j.xplc.2024.101196","url":null,"abstract":"<p><p>Current methods used in genome-wide association studies frequently lack power owing to their inability to detect heterogeneous associations and rare and multiallelic variants. To address these issues, quantile regression is integrated with a three (compressed) variance component multi-locus random-SNP-effect mixed linear model (3VmrMLM) to propose q3VmrMLM for detecting heterogeneous quantitative trait nucleotides (QTNs) and QTN-by-environment interactions (QEIs), and then design haplotype-based q3VmrMLM (q3VmrMLM-Hap) for identifying multiallelic haplotypes and rare variants. In Monte Carlo simulation studies, q3VmrMLM had higher power than 3VmrMLM, sequence kernel association test (SKAT), and integrated quantile rank test (iQRAT). In a re-analysis of 10 traits in 1439 rice hybrids, 261 known genes were identified only by q3VmrMLM and q3VmrMLM-Hap, whereas 175 known genes were detected by both the new and existing methods. Of all the significant QTNs with known genes, q3VmrMLM (179: 140 variance heterogeneity and 157 quantile effect heterogeneity) found more heterogeneous QTNs than 3VmrMLM (123), SKAT (27), and iQRAT (29); q3VmrMLM-Hap (121) mapped more low-frequency (<0.05) QTNs than q3VmrMLM (51), 3VmrMLM (43), SKAT (11), and iQRAT (12); and q3VmrMLM-Hap (12), q3VmrMLM (16), and 3VmrMLM (12) had similar power in identifying gene-by-environment interactions. All significant and suggested QTNs achieved the highest predictive accuracy (r = 0.9045). In conclusion, this study describes a new and complementary approach to mining genes and unraveling the genetic architecture of complex traits in crops.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101196"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956104/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711580","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}