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Cotton metabolism regulatory network: Unraveling key genes and pathways in fiber development and growth regulation. 棉花代谢调控网络:揭示纤维发育和生长调控的关键基因和途径。
IF 9.4 1区 生物学
Plant Communications Pub Date : 2025-03-10 Epub Date: 2024-12-12 DOI: 10.1016/j.xplc.2024.101221
Zhao Liu, Liqiang Fan, Sheng Shu, Ghulam Qanmber, Eryong Chen, Jinquan Huang, Fuguang Li, Zuoren Yang
{"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}
引用次数: 0
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. 两个梨品种的无间隙基因组组装和GWAS分析发现CCCH锌指蛋白是梨果实石细胞形成的关键调节因子。
IF 9.4 1区 生物学
Plant Communications Pub Date : 2025-03-10 Epub Date: 2024-12-31 DOI: 10.1016/j.xplc.2024.101238
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
{"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}
引用次数: 0
Genomic analysis of Zhou8425B, a key founder parent, reveals its genetic contributions to elite agronomic traits in wheat breeding. 对小麦主要创始亲本周8425b的基因组分析揭示了其对小麦优良农艺性状的遗传贡献。
IF 9.4 1区 生物学
Plant Communications Pub Date : 2025-03-10 Epub Date: 2024-12-16 DOI: 10.1016/j.xplc.2024.101222
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
{"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}
引用次数: 0
Natural variation in TaERF-A1 confers semi-dwarf and lodging-resistant plant architecture in wheat. 编码 AP2/ERF 转录因子的 TaERF-A1 的自然变异赋予小麦半矮植株结构和更强的抗倒伏性。
IF 9.4 1区 生物学
Plant Communications Pub Date : 2025-03-10 Epub Date: 2024-11-19 DOI: 10.1016/j.xplc.2024.101194
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
{"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<sup>JD6</sup>, 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<sup>JD6</sup> into wheat can significantly enhance lodging resistance, particularly in dense cropping systems. Therefore, our study identifies TaERF-A1<sup>JD6</sup> 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}
引用次数: 0
Competitive binding of small antagonistic peptides to the OsER1 receptor optimizes rice panicle architecture. 小拮抗肽与OsER1受体的竞争性结合优化了水稻穗结构。
IF 9.4 1区 生物学
Plant Communications Pub Date : 2025-03-10 Epub Date: 2024-12-06 DOI: 10.1016/j.xplc.2024.101204
Tao Guo, Fuyan Si, Fei Lu, Lianlian Yang, Ke Chen, Xiaopan Wang, Guanglin Li, Zi-Qi Lu, Hong-Xuan Lin
{"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}
引用次数: 0
The integration of quantile regression with 3VmrMLM identifies more QTNs and QTN-by-environment interactions using SNP- and haplotype-based markers. 量子回归与 3VmrMLM 的整合利用基于 SNP 和单体型的标记物识别出更多的 QTN 和 QTN 与环境的相互作用。
IF 9.4 1区 生物学
Plant Communications Pub Date : 2025-03-10 Epub Date: 2024-11-23 DOI: 10.1016/j.xplc.2024.101196
Wen-Xian Sun, Xiao-Yu Chang, Ying Chen, Qiong Zhao, Yuan-Ming Zhang
{"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}
引用次数: 0
The OsMAPK6-OsWRKY72 module positively regulates rice leaf angle through brassinosteroid signals. OsMAPK6-OsWRKY72模块通过油菜素内酯信号正向调节水稻叶片角度。
IF 9.4 1区 生物学
Plant Communications Pub Date : 2025-03-10 Epub Date: 2024-12-26 DOI: 10.1016/j.xplc.2024.101236
Fuxiang Wang, Ling Zhang, Lili Cui, Yongchao Zhao, Yi Huang, Minrong Jiang, Qiuhua Cai, Ling Lian, Yongsheng Zhu, Hongguang Xie, Liping Chen, Yanjia Xiao, Huaan Xie, Jianfu Zhang
{"title":"The OsMAPK6-OsWRKY72 module positively regulates rice leaf angle through brassinosteroid signals.","authors":"Fuxiang Wang, Ling Zhang, Lili Cui, Yongchao Zhao, Yi Huang, Minrong Jiang, Qiuhua Cai, Ling Lian, Yongsheng Zhu, Hongguang Xie, Liping Chen, Yanjia Xiao, Huaan Xie, Jianfu Zhang","doi":"10.1016/j.xplc.2024.101236","DOIUrl":"10.1016/j.xplc.2024.101236","url":null,"abstract":"<p><p>Leaf angle is a major agronomic trait that determines plant architecture, which directly affects rice planting density, photosynthetic efficiency, and yield. The plant phytohormones brassinosteroids (BRs) and the MAPK signaling cascade are known to play crucial roles in regulating leaf angle, but the underlying molecular mechanisms are not fully understood. Here, we report a rice WRKY family transcription factor gene, OsWRKY72, which positively regulates leaf angle by affecting lamina joint development and BR signaling. Phenotypic analysis showed that oswrky72 mutants have smaller leaf angles and exhibit insensitivity to exogenous BRs, whereas OsWRKY72 overexpression lines show enlarged leaf angles and are hypersensitive to exogenous BRs. Histological sections revealed that the change in leaf inclination is due to asymmetric cell proliferation and growth at the lamina joint. Further investigation showed that OsWRKY72 binds directly to the promoter region of BR receptor kinase (OsBRI1), a key gene in the BR signaling pathway, and activates its expression to positively regulate rice BR signaling. In addition, we discovered that OsWRKY72 interacts with and is phosphorylated by OsMAPK6, and this phosphorylation event can enhance OsWRKY72 activity in promoting OsBRI1 expression. Genetic evidence confirmed that OsMAPK6, OsWRKY72, and OsBRI1 function in a common pathway to regulate leaf angle. Collectively, our findings clarify the critical role of the OsWRKY72 transcription factor in regulating rice leaf angle. These results provide valuable insights into the molecular regulatory networks that govern plant architecture in rice.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101236"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956091/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900339","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
A comprehensive map of DNA-segment copy number variation in 491 genomes of common wheat uncovers genes associated with multiple agronomic traits. 普通小麦 491 个基因组中 DNA 片段拷贝数变异的综合图谱揭示了与多种农艺性状相关的基因。
IF 9.4 1区 生物学
Plant Communications Pub Date : 2025-03-10 Epub Date: 2024-12-19 DOI: 10.1016/j.xplc.2024.101226
Shengwei Ma, Jianqing Niu, Yaoqi Si, Shusong Zheng, Yaru Lu, Shuiquan Tian, Xiaoli Shi, Zedong Chen, Cong Sun, Ziyi Qin, Xiaolin Liu, Huilan Wu, Mengjun Gu, Man Cui, Qiao Lu, Wenjuan Zhou, Weiming He, Chi Zhang, Fei He, Hong-Qing Ling
{"title":"A comprehensive map of DNA-segment copy number variation in 491 genomes of common wheat uncovers genes associated with multiple agronomic traits.","authors":"Shengwei Ma, Jianqing Niu, Yaoqi Si, Shusong Zheng, Yaru Lu, Shuiquan Tian, Xiaoli Shi, Zedong Chen, Cong Sun, Ziyi Qin, Xiaolin Liu, Huilan Wu, Mengjun Gu, Man Cui, Qiao Lu, Wenjuan Zhou, Weiming He, Chi Zhang, Fei He, Hong-Qing Ling","doi":"10.1016/j.xplc.2024.101226","DOIUrl":"10.1016/j.xplc.2024.101226","url":null,"abstract":"<p><p>DNA-segment copy number variations (DSCNVs), such as deletions and duplications, are important sources of genomic structural variation. However, the types and sizes of DSCNVs, as well as their genome-wide distribution and potential functions, are poorly understood in wheat. Here, we identified 198 985 DSCNVs by investigating 491 genomes of common wheat and found that they account for 20% of the entire genome. Interestingly, approximately 38% of genes are linked to DSCNVs. The number of DSCNVs within each accession ranges from 47 366 to 96 342, and their total sizes vary from 421.3 to 1267.9 Mb. We found that 957 and 1304 DSCNVs have been favored by breeders in China and the United States, respectively. By conducting DSCNV-based genome-wide association studies for the principal components of plant developmental and yield-component traits, we identified 34 loci as directly or indirectly involved in controlling the formation of multiple traits. Notably, a newly discovered DSCNV covering TaFT-D1 is significantly associated with flowering time and other agronomic traits. Overall, our findings highlight the potential of DSCNVs to drive fundamental discoveries in plant science. The comprehensive DSCNV map and the DSCNV-associated genes will also facilitate future research efforts to improve wheat yield, quality, and adaptation.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101226"},"PeriodicalIF":9.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142866258","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
Gap-free genome assembly and pan-genome of Brassica juncea provide insights into seed quality improvement and environmental adaptation. 芥菜无间隙基因组组装和泛基因组研究为芥菜种子品质改良和环境适应提供了新的思路。
IF 9.4 1区 生物学
Plant Communications Pub Date : 2025-03-06 DOI: 10.1016/j.xplc.2025.101298
Ru Zhang, Chunyan Dai, Ruolin Gong, Keqi Li, Cuiping Zhang, Zhanling An, Aixia Xu, Han Wang, Jungang Dong, Zhen Huang, Jihong Hu
{"title":"Gap-free genome assembly and pan-genome of Brassica juncea provide insights into seed quality improvement and environmental adaptation.","authors":"Ru Zhang, Chunyan Dai, Ruolin Gong, Keqi Li, Cuiping Zhang, Zhanling An, Aixia Xu, Han Wang, Jungang Dong, Zhen Huang, Jihong Hu","doi":"10.1016/j.xplc.2025.101298","DOIUrl":"10.1016/j.xplc.2025.101298","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101298"},"PeriodicalIF":9.4,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143587994","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 wheat Sr8155B1 gene encodes a typical NLR protein that confers resistance to the Ug99 stem rust race group. 小麦基因Sr8155B1编码一种典型的NLR蛋白,该蛋白赋予小麦对Ug99茎锈病的抗性。
IF 9.4 1区 生物学
Plant Communications Pub Date : 2025-03-03 DOI: 10.1016/j.xplc.2025.101296
Tao Shen, Xiaohua Hao, Guiping Wang, Hongna Li, Jian Wang, Shikai Lyu, Shams Ur Rehman, Yanyan Liang, Lei Hua, Wenjun Zhang, Zhiyong Liu, Shisheng Chen
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引用次数: 0
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