Articles

Metabolome and transcriptome analysis reveals the molecular profiles underlying the ginseng response to rusty root symptoms

Ginseng rusty root symptoms (GRS) is one of the primary diseases of ginseng. This disease leads to a severe decline in the quality of ginseng. It has been shown that the occurrence of GRS is associated with so...

Authors: Xingbo Bian, Yan Zhao, Shengyuan Xiao, He Yang, Yongzhong Han and Lianxue Zhang

Discovery of genes involved in anthocyanin biosynthesis from the rind and pith of three sugarcane varieties using integrated metabolic profiling and RNA-seq analysis

Sugarcane (Saccharum officinarum) is one of the most valuable feedstocks for sugar production. In addition to the production of industrial raw materials such as alcohol, papermaking, the fiber of livestock feed, ...

Authors: Yang Ni, Haimei Chen, Di Liu, Lihui Zeng, Pinghua Chen and Chang Liu

A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era

The identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization. However, the complicated results from several cytogenetic nomenclatures for identifying oat chromoso...

Authors: Wenxi Jiang, Chengzhi Jiang, Weiguang Yuan, Meijun Zhang, Zijie Fang, Yang Li, Guangrong Li, Juqing Jia and Zujun Yang

Genetic control of iron bioavailability is independent from iron concentration in a diverse winter wheat mapping population

Anemia is thought to affect up to 1.6 billion people worldwide. One of the major contributors to low iron (Fe) absorption is a higher proportion of cereals compared to meats and pulse crops in people’s diets. ...

Authors: Tally I.C. Wright, Keith A. Gardner, Raymond P. Glahn and Matthew J. Milner

Plant DNA methylation is sensitive to parent seed N content and influences the growth of rice

Nitrogen (N) is an important nutrient for plant growth, development, and agricultural production. Nitrogen stress could induce epigenetic changes in plants. In our research, overexpression of the OsNAR2.1 line wa...

Authors: Xiaoru Fan, Laihua Liu, Kaiyun Qian, Jingguang Chen, Yuyue Zhang, Peng Xie, Man Xu, Zhi Hu, WenKai Yan, Yufeng Wu, Guohua Xu and Xiaorong Fan

Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development

Kinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon,...

Authors: Shujuan Tian, Jiao Jiang, Guo-qi Xu, Tan Wang, Qiyan Liu, Xiner Chen, Man Liu and Li Yuan

Metabolomic insights into the browning of the peel of bagging ‘Rui Xue’ apple fruit

Bagging is one of the most important techniques for producting high-quality fruits. In the actual of cultivating, we found a new kind of browning in peel of apple fruit that occurs before harvest and worsen du...

Authors: Hui Wang, Shuang Wang, Miao-Miao Fan, Shu-Hui Zhang, Lu-Long Sun and Zheng-Yang Zhao

Simultaneous gene expression and multi-gene silencing in Zea mays using maize dwarf mosaic virus

Maize dwarf mosaic virus (MDMV), a member of the genus Potyvirus, infects maize and is non-persistently transmitted by aphids. Several plant viruses have been developed as tools for gene expression and gene silen...

Authors: Wenshuang Xie, Dee Marie Marty, Junhuan Xu, Nitika Khatri, Kristen Willie, Wanderson Bucker Moraes and Lucy R. Stewart

Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

Artificial synthesis of octoploid rapeseed double haploid (DH) induction lines Y3380 and Y3560 was made possible by interspecific hybridization and genome doubling techniques. Production of pure lines by DH in...

Authors: Wei Zhang, Yongting Ma, Zhendong Zhu, Liangjun Huang, Asif Ali, Xuan Luo, Ying Zhou, Yun Li, Peizhou Xu, Jin Yang, Zhuang Li, Haoran Shi, Jisheng Wang, Wanzhuo Gong, Qiong Zou, Lanrong Tao…

Comparative transcriptomic analysis reveals the regulatory mechanism of the gibberellic acid pathway of Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) dwarf mutants

Tartary buckwheat is an important minor crop species with high nutritional and medicinal value and is widely planted worldwide. Cultivated Tartary buckwheat plants are tall and have hollow stems that lodge eas...

Authors: Zhaoxia Sun, Xinfang Wang, Ronghua Liu, Wei Du, Mingchuan Ma, Yuanhuai Han, Hongying Li, Longlong Liu and Siyu Hou

Correction to: Photosynthesis acclimation under severely fluctuating light conditions allows faster growth of diatoms compared with dinoflagellates

Authors: Lu Zhou, Songcui Wu, Wenhui Gu, Lijun Wang, Jing Wang, Shan Gao and Guangce Wang

Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex

The Rhododendron sanguineum complex is endemic to alpine mountains of northwest Yunnan and southeast Tibet of China. Varieties in this complex exhibit distinct flower colors even at the bud stage. However, the un...

Authors: Lin-Jiang Ye, Michael Mӧller, Ya-Huang Luo, Jia-Yun Zou, Wei Zheng, Yue-Hua Wang, Jie Liu, An-Dan Zhu, Jin-Yong Hu, De-Zhu Li and Lian-Ming Gao

Transcriptome regulation of carotenoids in five flesh-colored watermelons (Citrullus lanatus)

Fruit flesh color in watermelon (Citrullus lanatus) is a great index for evaluating the appearance quality and a key contributor influencing consumers’ preferences. But the molecular mechanism of this intricate t...

Authors: Pingli Yuan, Muhammad Jawad Umer, Nan He, Shengjie Zhao, Xuqiang Lu, Hongju Zhu, Chengsheng Gong, Weinan Diao, Haileslassie Gebremeskel, Hanhui Kuang and Wenge Liu

Transcriptome dynamic landscape underlying the improvement of maize lodging resistance under coronatine treatment

Lodging is one of the important factors causing maize yield. Plant height is an important factor in determining plant architecture in maize (Zea mays L.), which is closely related to lodging resistance under high...

Authors: Zhaobin Ren, Xing Wang, Qun Tao, Qing Guo, Yuyi Zhou, Fei Yi, Guanmin Huang, Yanxia Li, Mingcai Zhang, Zhaohu Li and Liusheng Duan

The physiological and molecular mechanisms of N transfer in Eucalyptus and Dalbergia odorifera intercropping systems using root proteomics

The mixing of Eucalyptus with N₂-fixing trees species (NFTs) is a frequently successful and sustainable cropping practice. In this study, we evaluated nitrogen (N) transfer and conducted a proteomic analysis of t...

Authors: Xianyu Yao, Liangning Liao, Yongzhen Huang, Ge Fan, Mei Yang and Shaoming Ye

Genetic diversity structure of western-type carrots

Carrot is a crop with a wide range of phenotypic and molecular diversity. Within cultivated carrots, the western gene pool comprises types characterized by different storage root morphology. First western carr...

Authors: Katarzyna Stelmach, Alicja Macko-Podgórni, Charlotte Allender and Dariusz Grzebelus

Freezing resistance evaluation of rose stems during frost dehardening using electrical impedance tomography

Electrical impedance tomography (EIT) has rarely been applied in plant science, particularly to study plant resistance to abiotic and biotic stresses. In this study, we evaluated the freezing resistance of flo...

Authors: Ji Qian, Juan Zhou, Ruijuan Gong, Yang Liu and Gang Zhang

Extracting knowledge networks from plant scientific literature: potato tuber flesh color as an exemplary trait

Scientific literature carries a wealth of information crucial for research, but only a fraction of it is present as structured information in databases and therefore can be analyzed using traditional data anal...

Authors: Gurnoor Singh, Evangelia A. Papoutsoglou, Frederique Keijts-Lalleman, Bilyana Vencheva, Mark Rice, Richard G.F. Visser, Christian W.B. Bachem and Richard Finkers

Highly efficient generation of bacterial leaf blight-resistant and transgene-free rice using a genome editing and multiplexed selection system

Rice leaf blight, which is a devastating disease worldwide, is caused by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). The upregulated by transcription activator-like 1 (UPT) effector box in the promoter reg...

Authors: Kun Yu, Zhiqiang Liu, Huaping Gui, Lizhao Geng, Juan Wei, Dawei Liang, Jian Lv, Jianping Xu and Xi Chen

BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon

The vascular system of plants consists of two main tissue types, xylem and phloem. These tissues are organized into vascular bundles that are arranged into a complex network running through the plant that is e...

Authors: Kaori Sakai, Sylvie Citerne, Sébastien Antelme, Philippe Le Bris, Sylviane Daniel, Axelle Bouder, Angelina D’Orlando, Amy Cartwright, Frédérique Tellier, Stéphanie Pateyron, Etienne Delannoy, Debbie Laudencia-Chingcuanco, Gregory Mouille, Jean Christophe Palauqui, John Vogel and Richard Sibout

Physiological and biochemical responses of soybean plants inoculated with Arbuscular mycorrhizal fungi and Bradyrhizobium under drought stress

The present study aims to study the effects of biofertilizers potential of Arbuscular Mycorrhizal Fungi (AMF) and Bradyrhizobium japonicum (B. japonicum) strains on yield and growth of drought stressed soybean (G...

Authors: Mohamed S. Sheteiwy, Dina Fathi Ismail Ali, You-Cai Xiong, Marian Brestic, Milan Skalicky, Yousef Alhaj Hamoud, Zaid Ulhassan, Hiba Shaghaleh, Hamada AbdElgawad, Muhammad Farooq, Anket Sharma and Ahmed M. El-Sawah

The role of RNA-binding protein, microRNA and alternative splicing in seed germination: a field need to be discovered

Seed germination is the process through which a quiescent organ reactivates its metabolism culminating with the resumption cell divisions. It is usually the growth of a plant contained within a seed and result...

Authors: Xiaofei Xue, Fuchao Jiao, Haicheng Xu, Qiqing Jiao, Xin Zhang, Yong Zhang, Shangyi Du, Menghan Xi, Aiguo Wang, Jingtang Chen and Ming Wang

Genome-wide identification and functional characterization of LEA genes during seed development process in linseed flax (Linum usitatissimum L.)

LEA proteins are widely distributed in the plant and animal kingdoms, as well as in micro-organisms. LEA genes make up a large family and function in plant protection against a variety of adverse conditions.

Authors: Zhen Li, Hui Chi, Caiyue Liu, Tianbao Zhang, Lida Han, Liang Li, Xinwu Pei and Yan Long

Mass propagation of Juniperus procera Hoechst. Ex Endl. From seedling and screening of bioactive compounds in shoot and callus extract

Juniperus procera Hoechst. ex Endl. is a medicinal tree in Saudi Arabia, primarily in the Enemas region, but it is locally threatened due to die-back disease and difficulties regarding seed reproduction (seed dor...

Authors: Abdalrhaman M. Salih, Fahad Al-Qurainy, Salim Khan, Mohamed Tarroum, Mohammad Nadeem, Hassan O. Shaikhaldein, Nadiyah M. Alabdallah, Saleh Alansi and Aref Alshameri

The P450 multigene family of Fontainea and insights into diterpenoid synthesis

Cytochrome P450s (P450s) are enzymes that play critical roles in the biosynthesis of physiologically important compounds across all organisms. Although they have been characterised in a large number of plant s...

Authors: Shahida A. Mitu, Steven M. Ogbourne, Anne H. Klein, Trong D. Tran, Paul W. Reddell and Scott F. Cummins

Analysis of miRNA-mediated regulation of flowering induction in Lilium × formolongi

MicroRNAs play pivotal roles in plant vegetative phase change and flowering induction via integrating into multiple flowering pathways. Lilium × formolongi is an important ornamental lily cultivar that can flower...

Authors: Qian Zhang, Yu-Qian Zhao, Xue Gao and Gui-Xia Jia

Adaptation of cucumber seedlings to low temperature stress by reducing nitrate to ammonium during it’s transportation

Low temperature severely depresses the uptake, translocation from the root to the shoot, and metabolism of nitrate and ammonium in thermophilic plants such as cucumber (Cucumis sativus). Plant growth is inhibited...

Authors: Yumei Liu, Longqiang Bai, Mintao Sun, Jun Wang, Shuzhen Li, Li Miao, Yan Yan, Chaoxing He, Xianchang Yu and Yansu Li

Character changes and Transcriptomic analysis of a cassava sexual Tetraploid

Cassava (Manihot esculenta Crantz) is an important food crop known for its high starch content. Polyploid breeding is effective in its genetic improvement, and use of 2n gametes in sexual polyploid breeding is on...

Authors: Xia Chen, Hanggui Lai, Ruimei Li, Yuan Yao, Jiao Liu, Shuai Yuan, Shaoping Fu, Xinwen Hu and Jianchun Guo

A comparative study on the reproductive success of two rewarding Habenaria species (Orchidaceae) occurring in roadside verge habitats

Most orchid species have been shown to be severely pollination limited, and the factors affecting reproductive success have been widely studied. However, the factors determining the reproductive success vary f...

Authors: Wenliu Zhang and Jiangyun Gao

Identification of consistent QTL for time to maturation in Virginia-type Peanut (Arachis hypogaea L.)

Time-to-maturation (TTM) is an important trait contributing to adaptability, yield and quality in peanut (Arachis hypogaea L). Virginia market-type peanut belongs to the late-maturing A. hypogaea subspecies with ...

Authors: Srinivas Kunta, Sara Agmon, Ilan Chedvat, Yael Levy, Ye Chu, Peggy Ozias-Akins and Ran Hovav

Genome-wide identification of heat shock factors and heat shock proteins in response to UV and high intensity light stress in lettuce

Heat shock factors (Hsfs) and Heat shock proteins (Hsps) belong to an essential group of molecular regulators involved in controlling cellular processes under normal and stress conditions. The role of Hsfs and...

Authors: Taehoon Kim, Shafina Samraj, Juan Jiménez, Celina Gómez, Tie Liu and Kevin Begcy

GWAS of pod morphological and color characters in common bean

Common bean (Phaseolus vulgaris L.) is an important legume species which can be consumed as immature pods and dry seeds after re-hydration and cooking. Many genes and QTL, and epistatic interactions among them, c...

Authors: Carmen García-Fernández, Ana Campa, Alvaro Soler Garzón, Phil Miklas and Juan Jose Ferreira

Pinpointing regulatory protein phosphatase 2A subunits involved in beneficial symbiosis between plants and microbes

PROTEIN PHOSPHATASE 2A (PP2A) expression is crucial for the symbiotic association between plants and various microbes, and knowledge on these symbiotic processes is important for sustainable agriculture. Here ...

Authors: Irina O. Averkina, Muhammad Harris, Edward Ohene Asare, Berenice Hourdin, Ivan A. Paponov and Cathrine Lillo

A SNP of HD-ZIP I transcription factor leads to distortion of trichome morphology in cucumber (Cucumis sativus L.)

Trichomes are excellent model systems for the analysis of cell differentiation and play essential roles in plant protection. From cucumber inbred line ‘WD1’, we identified an EMS-induced trichome abnormally de...

Authors: Leyu Zhang, Duo Lv, Jian Pan, Keyan Zhang, Haifan Wen, Yue Chen, Hui Du, Huanle He, Run Cai, Junsong Pan and Gang Wang

Temporal transcriptome profiling of developing seeds reveals candidate genes involved in oil accumulation in safflower (Carthamus tinctorius L.)

The investigation of molecular mechanisms involved in lipid metabolism plays a critical role for the genetic engineering of safflower (Carthamus tinctorius L.) to increase the oil accumulation level or to change ...

Authors: Dandan Li, Qing Wang, Xin Xu, Jingsheng Yu, Zhiyu Chen, Bo Wei and Wei Wu

Comparative physiological and full-length transcriptome analyses reveal the molecular mechanism of melatonin-mediated salt tolerance in okra (Abelmoschus esculentus L.)

Melatonin, a multifunctional signal molecule, has been reported to play crucial roles in growth and development and stress responses in various plant species. Okra (Abelmoschus esculentus L.) is a food crop with ...

Authors: Yihua Zhan, Tingting Wu, Xuan Zhao, Zhanqi Wang and Yue Chen

Transcriptome architecture reveals genetic networks of bolting regulation in spinach

Bolting refers to the early flowering stem production on agricultural and horticultural crops before harvesting. Indeed, bolting is an event induced by the coordinated effects of various environmental factors ...

Authors: Reza Abolghasemi, Maryam Haghighi, Nematollah Etemadi, Shui Wang and Aboozar Soorni

Small RNA sequencing provides candidate miRNA-target pairs for revealing the mechanism of apomixis in Zanthoxylum bungeanum

Apomixis is a form of asexual reproduction that produces offspring without the need for combining male and female gametes, and the offspring have the same genetic makeup as the mother. Therefore, apomixis tech...

Authors: Xitong Fei, Yu Lei, Yichen Qi, Shujie Wang, Haichao Hu and Anzhi Wei

Explore the gene network regulating the composition of fatty acids in cottonseed

Cottonseed is one of the major sources of vegetable oil. Analysis of the dynamic changes of fatty acid components and the genes regulating the composition of fatty acids of cottonseed oil is of great significa...

Authors: Lihong Ma, Xinqi Cheng, Chuan Wang, Xinyu Zhang, Fei Xue, Yanjun Li, Qianhao Zhu, Jie Sun and Feng Liu

Halotolerant bacteria mitigate the effects of salinity stress on soybean growth by regulating secondary metabolites and molecular responses

Salinity is a major threat to the agriculture industry due to the negative impact of salinity stress on crop productivity. In the present study, we isolated rhizobacteria and evaluated their capacities to prom...

Authors: Muhammad Aaqil Khan, Atlaw Anbelu Sahile, Rahmatullah Jan, Sajjad Asaf, Muhammad Hamayun, Muhammad Imran, Arjun Adhikari, Sang-Mo Kang, Kyung-Min Kim and In-Jung Lee

Comprehensive transcriptional analysis reveals salt stress-regulated key pathways, hub genes and time-specific responsive gene categories in common bermudagrass (Cynodon dactylon (L.) Pers.) roots

Despite its good salt-tolerance level, key genes and pathways involved with temporal salt response of common bermudagrass (Cynodon dactylon (L.) Pers.) have not been explored. Therefore, in this study, to underst...

Authors: An Shao, Wei Wang, Shugao Fan, Xiao Xu, Yanling Yin, Amombo Erick, Xiaoning Li, Guangyang Wang, Hongli Wang and Jinmin Fu

Parallel analysis of global garlic gene expression and alliin content following leaf wounding

Allium sativum (garlic) is an economically important food source and medicinal plant rich in sulfides and other protective substances such as alliin, the precursor of allicin biosynthesis. Cysteine, serine and su...

Authors: Xuqin Yang, Yiren Su, Jiaying Wu, Wen Wan, Huijian Chen, Xiaoying Cao, Junjuan Wang, Zhong Zhang, Youzhi Wang, Deliang Ma, G. J. Loake and Jihong Jiang

Cross-talk between transcriptome, phytohormone and HD-ZIP gene family analysis illuminates the molecular mechanism underlying fruitlet abscission in sweet cherry (Prunus avium L)

The shedding of premature sweet cherry (Prunus avium L) fruitlet has significantly impacted production, which in turn has a consequential effect on economic benefits.

Authors: Zhilang Qiu, Zhuang Wen, Qiandong Hou, Guang Qiao, Kun Yang, Yi Hong and Xiaopeng Wen

Cold acclimation can specifically inhibit chlorophyll biosynthesis in young leaves of Pakchoi

Leaf color is an important trait in breeding of leafy vegetables. Y-05, a pakchoi (Brassica rapa ssp. chinensis) cultivar, displays yellow inner (YIN) and green outer leaves (GOU) after cold acclimation. However,...

Authors: Huiyu Wang, Zhubo Li, Lingyun Yuan, Hefang Zhou, Xilin Hou and Tongkun Liu

Effects of ectomycorrhizal fungi (Suillus variegatus) on the growth, hydraulic function, and non-structural carbohydrates of Pinus tabulaeformis under drought stress

A better understanding of non-structural carbohydrate (NSC) dynamics in trees under drought stress is critical to elucidate the mechanisms underlying forest decline and tree mortality from extended periods of ...

Authors: Jiaxing Wang, Haoqiang Zhang, Jing Gao, Yu Zhang, Yaqin Liu and Ming Tang

Poplar protease inhibitor expression differs in an herbivore specific manner

Protease inhibitors are defense proteins widely distributed in the plant kingdom. By reducing the activity of digestive enzymes in insect guts, they reduce the availability of nutrients and thus impair the gro...

Authors: Franziska Eberl, Thomas Fabisch, Katrin Luck, Tobias G. Köllner, Heiko Vogel, Jonathan Gershenzon and Sybille B. Unsicker

Uncovering salt tolerance mechanisms in pepper plants: a physiological and transcriptomic approach

Pepper is one of the most cultivated crops worldwide, but is sensitive to salinity. This sensitivity is dependent on varieties and our knowledge about how they can face such stress is limited, mainly according...

Authors: Lidia López-Serrano, Ángeles Calatayud, Salvador López-Galarza, Ramón Serrano and Eduardo Bueso

Correction to: Biochemical metabolism of young plants of Ucuúba (Virola surinamensis) in the presence of cadmium

An amendment to this paper has been published and can be accessed via the original article.

Authors: W. V. Andrade Júnior, C. F. Oliveira Neto, B. G. Santos Filho, E. D. Cruz, C. B. Amarante, A. V. C. Barbosa, G. A. S. Nogueira, V. R. Nascimento, D. J. P. Sousa and J. S. S. Teixeira

FISH landmarks reflecting meiotic recombination and structural alterations of chromosomes in wheat (Triticum aestivum L.)

DNA sequence composition affects meiotic recombination. However, the correlation between tandem repeat composition and meiotic recombination in common wheat (Triticum aestivum L.) is unclear.

Authors: Yang Zou, Linrong Wan, Jie Luo, Zongxiang Tang and Shulan Fu

Auxin regulated metabolic changes underlying sepal retention and development after pollination in spinach

Pollination accelerate sepal development that enhances plant fitness by protecting seeds in female spinach. This response requires pollination signals that result in the remodeling within the sepal cells for r...

Authors: Mahpara Fatima, Xiaokai Ma, Ping Zhou, Madiha Zaynab and Ray Ming