Review
Biochemistry & Molecular Biology
Arzoo Ahad, Alvina Gul, Tuba Sharf Batool, Noor-ul Noor-ul Huda, Faiza Naseeer, Uzma Abdul Salam, Maria Abdul Salam, Mahnoor Ilyas, Bengu Turkyilmaz Unal, Munir Ozturk
Summary: Environmental variation is a crucial problem that negatively affects food availability and leads to food insecurity. Wheat, being the largest staple food crop, is severely threatened by abiotic stresses such as salinity, heavy metal toxicity, drought, extreme temperatures, and oxidative stresses. Cold stress is a significant ecological constraint that hampers the development and yield of plants. Understanding cold tolerance and improving it in wheat is critical for expanding the adaptability of perennial grasses.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Genetics & Heredity
Collin L. Juurakko, Melissa Bredow, Takato Nakayama, Hiroyuki Imai, Yukio Kawamura, George C. diCenzo, Matsuo Uemura, Virginia K. Walker
Summary: Research has shown that two days of cold acclimation are sufficient to protect the plasma membrane, leading to an initial increase in sugar levels and significant changes in the abundance of 154 proteins, while prolonged cold acclimation results in further increases in soluble sugars and abundance changes in over 680 proteins. The identified plasma membrane proteins play roles in low-temperature tolerance, metabolism, transport, pathogen defense, as well as various stress responses, suggesting crosstalk between different stress pathways.
G3-GENES GENOMES GENETICS
(2021)
Article
Plant Sciences
Boris F. Mayer, Jean-Benoit Charron
Summary: The study reveals that plants adjust transcriptional responses through transcriptional memory during cold acclimation, providing plasticity to stress responses and promoting growth resumption and stress adaptation. Chromatin-associated TMs are involved in tuning plant responses to environmental change, regulating both stress and developmental components in cold-climate adaptation.
Article
Plant Sciences
Sixuan Zhao, Xiangli Ou, Yidan Zhang, Yingwen Wei, Xiule Yue, Zhiguang Zhao
Summary: This study compared the carbohydrate metabolism and transcriptome of Arabidopsis and Chorispora bungeana during cold acclimation. The results showed that Arabidopsis experienced a shortage of carbohydrates during cold acclimation, while Chorispora bungeana had increased starch accumulation. Transcriptome analysis revealed that genes for photosynthesis antenna proteins were repressed by cold stress in both species, but cold-up-regulated genes were enriched in different pathways. These findings uncovered the drawback of cold acclimation in improving freezing tolerance and highlighted the importance of photoprotective mechanisms in Chorispora bungeana's cold adaptation.
JOURNAL OF PLANT PHYSIOLOGY
(2023)
Article
Agronomy
Jessica M. Brown, Xingwang Yu, H. McCamy P. Holloway, Tan D. Tuong, Brian M. Schwartz, Aaron J. Patton, Consuelo Arellano, David P. Livingston, Susana R. Milla-Lewis
Summary: Zoysiagrasses, popular low-input and warm-season turfgrasses in the US, have limited freezing tolerance. A study identified QTL related to freezing tolerance, providing a basis for breeding efforts to develop zoysiagrass cultivars capable of surviving in cold climates.
Article
Cell Biology
Wen-Cheng Liu, Ru-Feng Song, Yi-Mi Qiu, Si-Qiu Zheng, Ting-Ting Li, Yan Wu, Chun-Peng Song, Ying-Tang Lu, Hong-Mei Yuan
Summary: H2O2 activates plant cold responses by sulfenylating ENO2 and promoting its oligomerization, leading to enhanced nuclear translocation and transcriptional activation of CBF1.
DEVELOPMENTAL CELL
(2022)
Article
Plant Sciences
Haifang Jiang, Yiting Shi, Jingyan Liu, Zhen Li, Diyi Fu, Shifeng Wu, Minze Li, Zijia Yang, Yunlu Shi, Jinsheng Lai, Xiaohong Yang, Zhizhong Gong, Jian Hua, Shuhua Yang
Summary: This study unravels the mechanism of cold tolerance in maize, showing that the transcription factor ZmICE1 plays a significant role in reprogramming amino acid metabolism and regulating the expression of specific genes involved in cold stress response, thus affecting cold tolerance in maize.
Article
Plant Sciences
Xiaoqin Liao, Xingsu Zhang, Xin Li, Yuchen Tian, Qing Yang, Yongyan Wang, Si Tang, Xuanling Luo, Fan Zhang, Lei Zhang, Beibei Jiang, Qinglin Liu
Summary: This study reports the discovery of a newly identified posttranslational modification called lysine malonylation (Kmal), and its role in the response to abiotic stress in plants. By overexpressing and CRISPR-Cas9-mediated gene editing of DgnsLTP1, a nonspecific lipid transfer protein, it was found to confer cold tolerance in chrysanthemum. Further investigation revealed that DgnsLTP1 interacts with a plasma membrane intrinsic protein (PIP) called DgPIP, and through the regulation of DgGPX expression and activity, it enhances chrysanthemum's low-temperature stress tolerance.
Article
Plant Sciences
Jahad Soorni, Seyed Kamal Kazemitabar, Danial Kahrizi, Ali Dehestani, Nadali Bagheri, Attila Kiss, Peter Gergo Kovacs, Istvan Papp, Iman Mirmazloum
Summary: In this study, cold-acclimated and non-acclimated Camelina biotypes were compared for stress-associated biomarkers and gene expression. The results showed that cold acclimation had a positive effect on freezing tolerance, increasing the protein and proline content in stressed plants. Freezing stress significantly affected antioxidant enzyme activity and gene expression.
Article
Plant Sciences
Xiaojing Duan, Zhonglong Zhu, Yang Yang, Jie Duan, Zhongkui Jia, Faju Chen, Ziyang Sang, Luyi Ma
Summary: The research found that salicylic acid can promote natural cold acclimation in Magnolia wufengensis, ultimately enhancing winter hardiness and improving freezing tolerance by increasing the accumulation of soluble sugars. The enhanced accumulation of glucose, fructose, and raffinose can contribute to the development of cold acclimation and improve plant cold resistance.
JOURNAL OF PLANT GROWTH REGULATION
(2022)
Article
Plant Sciences
Xin Zhang, Guangrun Yu, Yan Dai, Hui Zhang, Kai Wang, Jinlei Han
Summary: This study investigated the impact of cold stress on gene expression and genome structure using 3D genomic maps. The results showed that cold stress causes changes in chromosome organization, including A/B compartment transition, reduction in chromatin compartmentalization and TAD size, and loss of long-range chromatin loops. Transcriptional changes are associated with A/B compartment transition, while TAD reorganization requires transcriptional alterations. The loss of chromatin looping has a more significant impact on gene expression than loop formation in response to cold stress.
Article
Plant Sciences
Shanshan He, Xianxian Wang, Zhiyu Du, Pingping Liang, Yifan Zhong, Lin Wang, Yuan-Ye Zhang, Yingjia Shen
Summary: Kandelia obovata, the most cold-tolerant mangrove species, showed acclimation to cold waves through physiological changes and gene expression. We identified 1,135 cold acclimation-related genes (CARGs), which are involved in calcium signaling, cell wall modification, and ubiquitination pathways. CBFs and CBF-independent transcription factors played important roles in regulating the expression of CARGs.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Safia Saada, Charles Ugochukwu Solomon, Sinead Drea
Summary: The study found that programmed cell death (PCD) occurs in developing grains of the wild model species Brachypodium distachyon. Compared to domesticated species like barley and rice, the rate and pattern of PCD in Brachypodium differ, affecting grain size and shape. This suggests that the regulation of PCD may play a role in determining grain characteristics in different plant species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Yue Song, Xiaoyan Zhang, Minze Li, Hao Yang, Diyi Fu, Jian Lv, Yanglin Ding, Zhizhong Gong, Yiting Shi, Shuhua Yang
Summary: Cold acclimation in Arabidopsis thaliana triggers significant transcriptional reprogramming through the CBF-dependent pathway, involving CBF transcription factors binding to conserved sequences on target genes. CBF-target genes are enriched in functions related to hormones, light, and circadian rhythm signaling, indicating their role as key integrators of endogenous and external cues.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jaime Barros, Him K. Shrestha, Juan C. Serrani-Yarce, Nancy L. Engle, Paul E. Abraham, Timothy J. Tschaplinski, Robert L. Hettich, Richard A. Dixon
Summary: Ammonia-lyases play a key role in coordinating the allocation of carbon for lignin synthesis and nitrogen availability for plant growth.
Article
Biotechnology & Applied Microbiology
Hong Chen, Hao Feng, Xueyan Zhang, Chaojun Zhang, Tao Wang, Jiangli Dong
PLANT BIOTECHNOLOGY JOURNAL
(2019)
Review
Biochemistry & Molecular Biology
Lihua Zheng, Peng Liu, Qianwen Liu, Tao Wang, Jiangli Dong
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Plant Sciences
Rongxue Zhang, Hong Chen, Mei Duan, Fugui Zhu, Jiangqi Wen, Jiangli Dong, Tao Wang
Article
Biotechnology & Applied Microbiology
Jingjie Hao, Yen Ning Chai, Lucas Dantas Lopes, Raziel A. Ordonez, Emily E. Wright, Sotirios Archontoulis, Daniel P. Schachtman
Summary: This study investigated the differences in microbial community abundance, composition, and diversity in soils from corn and soybean fields in Iowa using 16S rRNA amplicon sequencing. The results revealed decreased richness and diversity in microbial communities with increasing soil depth, with Proteobacteria dominating deep agricultural soils. Soil organic matter showed the highest correlation with the exponential decrease in bacterial abundance with depth. Understanding how soil depth influences microbial communities is crucial for guiding sampling approaches in agricultural soils and enhancing soil sustainability for food security.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Lucas Dantas Lopes, Jingjie Hao, Daniel P. Schachtman
Summary: Soil pH significantly influences microbial communities in the rhizosphere, root endosphere, and bulk soil. Plant species have a stronger impact on belowground microbiomes in alkaline soils. Cation exchange capacity, in addition to pH, plays a significant role in shaping bulk soil microbial communities.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Michael A. Meier, Martha G. Lopez-Guerrero, Ming Guo, Marty R. Schmer, Joshua R. Herr, James C. Schnable, James R. Alfano, Jinliang Yang
Summary: Root-associated microbes play important roles in plant health, disease resistance, and nitrogen use efficiency. Environmental conditions, host plant species, and nitrogen fertilization have major effects on microbiomes associated with maize and soybean. Specific microbial taxa and functional groups show distinct responses to treatment factors, providing insights for harnessing soil microbes in crop systems.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Hong Chen, Jiangli Dong, Tao Wang
Summary: Plants, as an open system, exchange material, energy and information with the outside world throughout their life cycle. To maintain cellular homeostasis and cope with environmental changes, plants have developed sophisticated autophagy mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Zhikai Yang, Gen Xu, Qi Zhang, Toshihiro Obata, Jinliang Yang
Summary: Mapping genotype to phenotype is an important topic in genetics and genomics research. Current association methods suffer from low mapping resolution and unclear causality between genotype and phenotype. This study applies mediation analysis to connect genotype with phenotype using high-dimensional data, detecting 736 unique mediating genes and revealing the prevalence of pleiotropic effects.
Article
Biology
Michael A. Meier, Gen Xu, Martha G. Lopez-Guerrero, Guangyong Li, Christine Smith, Brandi Sigmon, Joshua R. Herr, James R. Alfano, Yufeng Ge, James C. Schnable, Jinliang Yang
Summary: The composition of the rhizobiome is influenced by host plant genetics, with a greater impact under low nitrogen conditions. This study also identifies genetic markers associated with the abundance of specific microbial groups in the maize rhizobiome and their correlation with plant vigor.
Article
Plant Sciences
Marcin W. Grzybowski, Ravi V. Mural, Gen Xu, Jonathan Turkus, Jinliang Yang, James C. Schnable
Summary: Maize populations show vast diversity in both genetic and phenotypic traits. Resequencing strategies have been used to identify millions of genetic variants within and between maize populations, but inconsistencies in analytical pipelines, reference genome assemblies, and minor allele frequency filtering often limit the reuse and remixing of genetic diversity data for new research questions. This study utilized resequencing data from published and newly sequenced maize samples to create a unified marker set of over 366 million segregating variants, providing increased power to identify known flowering-time genes and track changes in allele frequency across the global distribution of maize.
Article
Genetics & Heredity
Semra Palali Delen, Gen Xu, Jenifer Velazquez-Perfecto, Jinliang Yang
Summary: Understanding the genetic basis of nitrogen (N) fertilization response in crop production is an important research topic. However, the genetic parameters underlying N responses in maize are still unclear. This study phenotyped 230 maize inbred lines under high and low N conditions for 2 years and conducted genome-wide association study (GWAS) and genome-wide complex trait Bayesian (GCTB) analysis. The results revealed a complex genetic architecture for N responses and identified candidate genetic loci for N resilient maize improvement.
Article
Plant Sciences
Nuwan K. Wijewardane, Huichun Zhang, Jinliang Yang, James C. Schnable, Daniel P. Schachtman, Yufeng Ge
Summary: A spectral library of maize and sorghum is developed to estimate leaf properties and is effective in predictions for soybean and camelina using extra-weighted spiking. Leaf-level hyperspectral reflectance is an effective tool in plant leaf phenotyping. However, model transferability among different datasets is poor. This study aims to assemble a large leaf hyperspectral library, evaluate machine-learning approaches to estimate leaf properties, and investigate the usefulness of the library for predicting external datasets.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Chemistry, Analytical
Xinyan Xie, Yufeng Ge, Harkamal Walia, Jinliang Yang, Hongfeng Yu
Summary: Leaf numbers are crucial for estimating crop yield. Traditional manual counting methods are laborious and costly. Existing methods for counting leaves in rosette plants show promising results, but there is a lack of effective solutions for monocot plants. We propose a deep neural network-based method that achieves superior performance even with severe leaf occlusions. Our method extracts leaf skeletons and applies augmentation to enhance structural variety, resulting in improved accuracy and lower training cost compared to existing approaches.
Article
Agronomy
Chenyong Miao, Alejandro Pages, Zheng Xu, Eric Rodene, Jinliang Yang, James C. Schnable
Article
Multidisciplinary Sciences
Gen Xu, Jing Lyu, Qing Li, Han Liu, Dafang Wang, Mei Zhang, Nathan M. Springer, Jeffrey Ross-Ibarra, Jinliang Yang
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Yanru Feng, Muhammad Shahedul Alam, Feng Yan, Michael Frei
Summary: Tropospheric ozone has significant effects on the remobilization and allocation efficiency of aboveground biomass and nutrients in cereal crops. Long-term ozone exposure increases straw C:N ratio and affects grain C:N ratio. Grain N concentrations increase significantly under ozone stress, but N yield declines due to grain yield losses. Various indicators of N use efficiency are reduced, indicating reduced N absorption from soil and allocation from vegetative to reproductive organs. Straw C:N ratio is not suitable for predicting wheat productivity. Nitrogen harvest index (NHI) is not affected by ozone stress, but the relationship between harvest index (HI) and NHI is changed by elevated ozone concentration.
Article
Biochemistry & Molecular Biology
Cong Guan, Wei Li, Guoliang Wang, Ruimei Yang, Jinglei Zhang, Jinhong Zhang, Bo Wu, Run Gao, Chunlin Jia
Summary: This study characterized the expression profiles of mRNAs and ncRNAs in switchgrass under drought stress. The up-regulated mRNAs were enriched in starch and sucrose metabolism pathway, while the differentially expressed lncRNAs potentially regulated protein-coding genes. The study also constructed regulatory networks and validated the functionality of the target gene PvSS4 in enhancing drought tolerance.
Article
Biochemistry & Molecular Biology
Juan Nicolas-Espinosa, Lucia Yepes-Molina, Fuensanta Martinez-Bernal, Miriam Fernandez-Pozurama, Micaela Carvajal
Summary: This study aimed to investigate the physiological response of broccoli leaves to abiotic stresses such as salinity and boron toxicity/deficiency. The results showed that the combined stress of salinity and boron deficiency resulted in a significant reduction in plant biomass, and the adaptation mechanisms were associated with water and boron concentration in the leaves. The expression patterns of PIP aquaporins varied among the different stress treatments, and their presence in the plasma membrane and interaction with the lipid environment played potential regulatory roles in facilitating salinity-boron stress adaptation mechanisms.
Review
Biochemistry & Molecular Biology
Wen-Feng Huang, Juan Li, Jian-An Huang, Zhong-Hua Liu, Li-Gui Xiong
Summary: This review examines the seasonal trends of phyllosphere microorganisms in woody and herbaceous plants and explores the factors influencing these trends. While herbaceous and woody plants share some similarities and differences in their phyllosphere microbiomes, further experimental validation is needed.
Article
Biochemistry & Molecular Biology
Changguang Liao, Hui Shen, Zihan Gao, Yunshu Wang, Zhiguo Zhu, Qiaoli Xie, Ting Wu, Guoping Chen, Zongli Hu
Summary: The novel CRF, SlCRF6, plays a crucial role in regulating tomato plant morphology, leaf development, and the accumulation of photosynthetic products.
Article
Biochemistry & Molecular Biology
Alok Madhu, Alok Sharma, Amandeep Kaur, Kashmir Singh, Santosh Kumar Upadhyay
Summary: In this study, 15 TaMDHAR genes were identified in bread wheat and their crucial roles in antioxidants, growth and development, and stress responses were revealed.
Article
Biochemistry & Molecular Biology
Kai Zheng, Yongsheng Cai, Yanying Qu, Lu Teng, Chaoyue Wang, Jie Gao, Quanjia Chen
Summary: In this study, the whole genome identification and bioinformatics analysis of the HCT gene family were performed in G. barbadense. The results showed that the GbHCT114 gene regulates plant trichome development, which is closely related to cotton fiber quality. Gene silencing and overexpression experiments confirmed the important role of GbHCT114 gene in cotton fiber morphology, lignin content, and secondary xylem duct cell wall development. Transcriptomic analysis identified differentially expressed genes associated with lignin synthesis and fiber development.
Review
Biochemistry & Molecular Biology
Tanashvi Seth, Sejal Asija, Shahid Umar, Ravi Gupta
Summary: Plants activate a sophisticated signaling cascade in response to pests and pathogens, with lipids playing a crucial role in mediating these defense responses. Different types of lipids are involved in cell signaling during plant-pathogen interaction and each lipid has specific relevance and contributes to specific signaling cascades. Lipid biosynthetic enzymes, including phospholipases, are involved in the production of defense signaling molecules. Lipids participate in stress signaling by mediating signal transduction, acting as precursors for bioactive molecules, regulating ROS formation, and interacting with phytohormones.
Article
Biochemistry & Molecular Biology
Yangyang Chen, Xiao Wu, Xiaohua Wang, Qionghou Li, Hao Yin, Shaoling Zhang
Summary: 'Nanguo' pears emit a rich aroma when fully ripe, and the important volatile components are the six-carbon compounds derived from the lipoxygenase pathway. This study identified a highly expressed bZIP transcription factor that is induced during the mature stage of 'Nanguo' pears, and demonstrated its regulatory role in fatty acid-derived volatile biosynthesis.
Article
Biochemistry & Molecular Biology
Zhao Geng, Haikuan Dou, Jianguang Liu, Guiyuan Zhao, Linlin Liu, Ning Zhao, Hanshuang Zhang, Yongqiang Wang, Zetong An
Summary: The overexpression of GhFB15 gene decreases the salt tolerance of Arabidopsis plants, while silencing the gene improves the salt tolerance of cotton plants. Furthermore, GhFB15 regulates the accumulation of flavonoids and the levels of ROS.
Article
Biochemistry & Molecular Biology
Linjun Cai, Ancheng Ma, Jiao Lei, Chongsheng He
Summary: METTL4 is identified as a plant DNA 6mA methyltransferase in Arabidopsis thaliana and plays a crucial role in regulating heat stress response.
Article
Biochemistry & Molecular Biology
Zailong Tian, Kun Li, Yaru Sun, Baojun Chen, Zhaoe Pan, Zhenzhen Wang, Baoyin Pang, Shoupu He, Yuchen Miao, Xiongming Du
Summary: Plants have evolved a mechanism called 'stress memory' to survive in various environmental stresses. This study reveals the physiological, biochemical, and molecular mechanisms underlying drought stress memory formation in cotton, highlighting the role of histone modification H3K4me3 in regulating transcriptional memory. It also investigates the intergenerational inheritance of drought stress memory in cotton, providing theoretical guidance for cotton breeding.