Article
Plant Sciences
Xiuru Dai, Xiaoyu Tu, Baijuan Du, Pengfei Dong, Shilei Sun, Xianglan Wang, Jing Sun, Gang Li, Tiegang Lu, Silin Zhong, Pinghua Li
Summary: Through analyzing BS and M cells isolated from maize leaves using multiple techniques, it was found that chromatin accessibility coordinates with epigenetic features to regulate gene expression, and the preferential expression of genes in specific cell types is finely tuned by multiple chromatin features. This coordination is critical in ensuring the cell type-specific function of key C-4 genes.
Article
Biochemistry & Molecular Biology
Huan Ma, Wentao Ding, Yiqian Chen, Jingwei Zhou, Wei Chen, Caixia Lan, Hailiang Mao, Qiang Li, Wenhao Yan, Handong Su
Summary: In this study, we investigated the genetics and epigenetics of centromeres in a population of wheat lines. We found that the highly repetitive DNA sequences associated with CENH3 exhibit phylogenetic homogenization across different wheat lines, while the less-associated repeat sequences diverge on their own way in each wheat line. We also observed that CENH3 nucleosome structures show looser wrapping of DNA termini on complex centromeric repeats and that strict CENH3 nucleosome positioning and intrinsic DNA features play a role in determining centromere identity among different lines.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Agronomy
Daniela Simoes, Eugenio Diogo, Eugenia de Andrade
Summary: Maize is an important staple crop worldwide, but it is highly susceptible to fungal infections, particularly by certain species of Fusarium. These infections can lead to significant reductions in yield and quality, as well as the production of mycotoxins. In Portugal and similar Mediterranean countries, F. verticillioides and F. subglutinans are the most common species infecting maize. However, the incidence of diseases and mycotoxin levels have increased, suggesting the presence of other mycotoxigenic Fusarium species or changes in exogenous conditions. Monitoring Fusarium species occurrence in the field is crucial to address these threats. A recent survey in Portugal identified the presence of F. andiyazi in maize crops for the first time, highlighting the need for further studies to prevent its spread and mitigate its impact on maize production and farmers' livelihoods.
Article
Plant Sciences
Julio S. S. Bernal, Anjel M. M. Helms, Ana A. A. Fontes-Puebla, Thomas J. J. DeWitt, Michael V. V. Kolomiets, John M. M. Grunseich
Summary: Domestication has a greater impact on the abundances and diversity of maize root volatiles than northward spread and modern breeding. The preference of the herbivore for maize roots is correlated with volatile diversity and herbivore resistance. Changes in abundances of individual volatiles are evident at the level of volatile groups, and maize domestication has the greatest effects.
Article
Agronomy
Jingwei Yan, Jing Li, Heping Zhang, Ya Liu, Aying Zhang
Summary: This study identified the function of the Zea mays WRKY transcription factor, ZmWRKY104, in salt stress response. ZmWRKY104 increases the salt tolerance of maize by regulating the expression of ZmSOD4.
Article
Plant Sciences
Alden C. Perkins, Jonathan P. Lynch
Summary: The research shows that seminal roots can improve the acquisition of nitrogen and phosphorus in maize seedlings, with increased seed size associated with maize domestication possibly facilitating the increase in seminal root number. The study also suggests that the optimal number of seminal roots for nutrient acquisition in teosinte is constrained by its limited seed carbohydrate reserves.
Article
Biochemistry & Molecular Biology
Takaki Yamauchi, Mikio Nakazono
Summary: Aerenchyma formation is crucial for oxygen diffusion in rice roots under low-oxygen conditions. Both ethylene and auxin hormones are involved in regulating aerenchyma formation in rice roots. The study found that ethylene-dependent aerenchyma formation is faster and rice roots have more aerenchyma, enabling efficient oxygen diffusion under low-oxygen conditions. Additionally, in rice, the expression levels of ethylene biosynthesis and responsive genes rapidly increase after root-cell emergence, contributing to the rapid induction of ethylene-dependent aerenchyma formation.
Article
Biochemistry & Molecular Biology
Silin Wu, Steffen Greiner, Chongjian Ma, Jiaxin Zhong, Xiaojia Huang, Thomas Rausch, Hongbo Zhao
Summary: A Zm-6&1-FEH2 enzyme related to cell wall invertase has been identified in maize, showing substrate specificity for inulin and levan and being localized in the apoplast. The enzyme can hydrolyze 1-kestotriose, an oligofructan, and its expression is influenced by plant development, drought, and abscisic acid.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Haiyan Li, Huifang Tao, Yao Xiao, Li Qin, Chen Lan, Beijiu Cheng, Jeremy A. Roberts, Xuebin Zhang, Xiaoduo Lu
Summary: In this study, two dwarf mutants of Zea mays, xyl-1 and xyl-2, were identified and characterized. It was found that the mutated gene ZmXYL encodes an alpha-xylosidase which affects the xylose content and XXXG content in xyloglucan. The decreased xylose content and increased XXXG content led to reduced auxin levels, resulting in the dwarf phenotypes of the mutants.
Article
Food Science & Technology
Aldo Rosales, Aide Molina-Macedo, Mayolo Leyva, Felix San Vicente, Natalia Palacios-Rojas
Summary: Zinc deficiency is a major health challenge globally, especially in areas with limited access to diverse diets. This study examines the zinc content in maize kernels with different genetic backgrounds during kernel development. It is found that high-zinc kernel genotypes have higher zinc and iron contents during the milky stage. By consuming fresh maize biofortified with zinc, a significant portion of the nutrient needs for pregnant women and children can be fulfilled. These results highlight the potential of fresh high-zinc maize as a valuable source for addressing zinc deficiency.
Article
Plant Sciences
Hao Wu, Guosheng Li, Junpeng Zhan, Shanshan Zhang, Brandon D. Beall, Ramin Yadegari, Philip W. Becraft
Summary: This study discovered an intrachromosomal rearrangement between the r1 and nkd2 genes, and identified the effects of related expression patterns and mutant alleles on gene expression. Furthermore, it revealed that the regulatory sequences of the nkd2 gene may influence the expression of the r1 gene.
Article
Agronomy
Zalak Y. Chauhan, Sanjay N. Shah, Hiren K. Patel
Summary: Excessive use of chemical fertilizers leads to losses, inefficient utilization, and nutritional imbalance, while integrated nutrient management is the best alternative for repairing soil nutrient depletion.
Article
Biochemistry & Molecular Biology
Eduardo Lujan-Soto, Paola Aguirre de la Cruz, Vasti T. Juarez-Gonzalez, Jose L. Reyes, Maria de la Paz Sanchez, Tzvetanka D. Dinkova
Summary: In recent years, miR528 has been found to play important roles in plant development and stress response. This study examined the transcription regulation and molecular mechanisms of MIR528 expression in maize, revealing conserved transcription factor binding sites and demonstrating the up-regulation of miR528 expression by exogenous nitrate and auxin treatments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Ruiqiang Lai, Jieming Jiang, Jun Wang, Jinju Du, Jianbin Lai, Chengwei Yang
Summary: SUMOylation is a crucial post-translational modification that regulates protein substrates. The maize SIZ1 homologs ZmSIZ1a, ZmSIZ1b, and ZmSIZ1c were functionally characterized in this study, showing potential roles in development regulation and stress responses. Overexpression of ZmSIZ1c in Arabidopsis resulted in early flowering and improved salt tolerance, suggesting distinct functions among the ZmSIZ1 members.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ryan N. Douglas, Hua Yang, Bing Zhang, Chen Chen, Fangpu Han, Jianlin Cheng, James A. Birchler
Summary: Research on maize B chromosomes shows that they undergo nondisjunction during the second pollen mitosis as part of their accumulation mechanism. The study identified 9-Bic-1 as an epigenetically silenced B chromosome centromere that may undergo both centromere reactivation and de novo centromere formation. Breakpoint determination revealed the potential for these processes to occur on fragments derived from the progenitor.
CHROMOSOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Qian Liu, Yang Liu, Qinghua Shi, Handong Su, Chunhui Wang, James A. Birchler, Fangpu Han
Summary: This article provides a comprehensive overview of the roles of cenRNAs in centromere formation and function, describing their structure, DNA sequence, transcription products, as well as their roles in kinetochore structure, accurate chromosome segregation, and pericentromeric heterochromatin assembly. The rising stars in centromere function, cenRNAs and R-loops are introduced, including their identification methods and ongoing investigations into their molecular features and functions. This review summarizes recent findings on the epigenetic regulation of cenRNAs across species, providing useful information and potential directions for further studies.
Article
Multidisciplinary Sciences
Handong Su, Yang Liu, Chunhui Wang, Yalin Liu, Chao Feng, Yishuang Sun, Jing Yuan, James A. Birchler, Fangpu Han
Summary: The study identified a maize Knl1 homolog as a constitutive central kinetochore component that plays a conserved role in chromosomal congression and segregation, with an interaction with spindle assembly checkpoint components Bub1/Mad3 family proteins 1 and 2. This highlights distinct modes of SAC to kinetochore connection within plant lineages and sheds light on evolutionary patterns in SAC signaling and kinetochore network.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Yuhong Huang, Yang Liu, Chang Liu, James A. Birchler, Fangpu Han
Summary: This paper reviews recent advances in epigenomics research of rice, maize, and wheat, and projects the development trends of epigenomics of major crops in the coming years. It highlights the role of epigenomics in regulating growth and development and identifying potential distal cis-regulatory elements in three major crops, and discusses the prospects and challenges for new epigenetics-mediated breeding technologies in crop improvement. The review summarizes and analyzes recent epigenomic advances in three major crops epigenomics and discusses possibilities and challenges for future research in the field.
Review
Biotechnology & Applied Microbiology
Jingwei Zhou, Yang Liu, Xianrui Guo, James A. Birchler, Fangpu Han, Handong Su
Summary: This article systematically summarizes the current knowledge of centromere biology, discussing the relationship between DNA compositions and the histone H3 variant in centromere establishment and identity. The roles of centromeres in cell division and three-dimensional genomic architecture are explored, along with potential applications in plant breeding and chromosome engineering. The challenges and strategies for de novo design and synthesis of centromeres are also assessed.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Plant Sciences
Stefan Steckenborn, Maria Cuacos, Mohammad A. Ayoub, Chao Feng, Veit Schubert, Iris Hoffie, Gotz Hensel, Jochen Kumlehn, Stefan Heckmann
Summary: In barley, MTOPVIB is critical for meiotic DSB and accompanied SC and CO formation while dispensable for meiotic bipolar spindle formation.
PLANT REPRODUCTION
(2022)
Article
Plant Sciences
Xianrui Guo, Mian Wang, Houyang Kang, Yonghong Zhou, Fangpu Han
Summary: The Fhb7 gene was found to originate from Triticeae plants rather than Thinopyrum, indicating a possible horizontal gene transfer before Triticeae differentiation. The different reactions to Fusarium head blight in some wheat-Thinopyrum derivatives raise questions about the ability of the GST-encoding Fhb7 to resist FHB.
Article
Biotechnology & Applied Microbiology
Xianrui Guo, Qinghua Shi, Mian Wang, Jing Yuan, Jing Zhang, Jing Wang, Yang Liu, Handong Su, Zhen Wang, Jinbang Li, Cheng Liu, Xingguo Ye, Fangpu Han
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Qinghua Shi, Xianrui Guo, Handong Su, Yingxin Zhang, Zanmin Hu, Jing Zhang, Fangpu Han
Summary: In this study, researchers found that the induced tetraploid Th. elongatum and the natural tetraploid Th. elongatum are morphologically similar, except for slower development and lower seed setting in the induced tetraploid. Using various molecular probes, the researchers identified differences between two chromosome sets of the natural tetraploid Th. elongatum, but not the induced one. Analysis of hybrid individuals and meiosis in the induced tetraploid revealed that chromosome pairing was successful, indicating rapid diploidization in the induced tetraploid.
Article
Multidisciplinary Sciences
Qian Liu, Congyang Yi, Zeyan Zhang, Handong Su, Chang Liu, Yuhong Huang, Wei Li, Xiaojun Hu, Cheng Liu, James A. Birchler, Yang Liu, Fangpu Han
Summary: Non-B-form DNA plays a crucial role in the oat genome, specifically in centromeres. Through systematic studies using the oat system, the presence and structural characteristics of non-B-form DNA in centromeres were identified and its potential role was revealed.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Yang Liu, Congyang Yi, Qian Liu, Chunhui Wang, Wenpeng Wang, Fangpu Han, Xiaojun Hu
Summary: This study investigated the mechanisms regulating seed size in peanut by using a multi-omics approach. Two mutants with bigger seed size were isolated and analyzed through whole genome sequencing and RNA-Seq analysis, leading to the identification of candidate genes associated with seed size.
Article
Biochemistry & Molecular Biology
Huan Ma, Wentao Ding, Yiqian Chen, Jingwei Zhou, Wei Chen, Caixia Lan, Hailiang Mao, Qiang Li, Wenhao Yan, Handong Su
Summary: In this study, we investigated the genetics and epigenetics of centromeres in a population of wheat lines. We found that the highly repetitive DNA sequences associated with CENH3 exhibit phylogenetic homogenization across different wheat lines, while the less-associated repeat sequences diverge on their own way in each wheat line. We also observed that CENH3 nucleosome structures show looser wrapping of DNA termini on complex centromeric repeats and that strict CENH3 nucleosome positioning and intrinsic DNA features play a role in determining centromere identity among different lines.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Chang Liu, Yuhong Huang, Xianrui Guo, Congyang Yi, Qian Liu, Kaibiao Zhang, Congle Zhu, Yang Liu, Fangpu Han
Summary: This study investigated the fine centromere structure of wheat-rye translocation chromosomes, revealing that only the rye-derived centromere is functional, while the wheat-derived centromere is inactive. The rye-derived centromere is enriched with specific retrotransposons and stable non-B DNA structures, contributing to its functionality. On the other hand, the wheat-derived centromere shows high levels of DNA methylation and H3K9me2, suggesting its role in maintaining the inactive status.
Article
Plant Sciences
Chao Feng, Elisabeth Roitinger, Otto Hudecz, Maria Cuacos, Jana Lorenz, Veit Schubert, Baicui Wang, Rui Wang, Karl Mechtler, Stefan Heckmann
Summary: During meiotic prophase I, the meiotic chromosome axis is essential for synapsis and meiotic recombination progression. TurboID-based proximity labelling enables the identification of proximate proteins in meiotic cells of A. thaliana. This proteomic profiling helps uncover known and new meiotic proteins in rare cell types like meiotic cells.