Articles

PINIR: a comprehensive information resource for Pin-II type protease inhibitors

Serine protease inhibitors belonging to the Potato type-II Inhibitor family Protease Inhibitors (Pin-II type PIs) are essential plant defense molecules. They are characterized by multiple inhibitory repeat domain...

Authors: Nikhilesh K. Yadav, Nidhi S. Saikhedkar and Ashok P. Giri

Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

Long non-coding RNAs (lncRNAs) are regulatory transcripts of length > 200 nt. Owing to the rapidly progressing RNA-sequencing technologies, lncRNAs are emerging as considerable nodes in the plant antifungal de...

Authors: Garima Bhatia, Santosh K. Upadhyay, Anuradha Upadhyay and Kashmir Singh

Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers

Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant...

Authors: Ming Sun, Zhixiao Dong, Jian Yang, Wendan Wu, Chenglin Zhang, Jianbo Zhang, Junming Zhao, Yi Xiong, Shangang Jia and Xiao Ma

Screening and identification of genes affecting grain quality and spikelet fertility during high-temperature treatment in grain filling stage of rice

Recent temperature increases due to rapid climate change have negatively affected rice yield and grain quality. Particularly, high temperatures during right after the flowering stage reduce spikelet fertility,...

Authors: Jae-Ryoung Park, Eun-Gyeong Kim, Yoon-Hee Jang and Kyung-Min Kim

Genome-wide identification of the Capsicum bHLH transcription factor family: discovery of a candidate regulator involved in the regulation of species-specific bioactive metabolites

The basic helix–loop–helix (bHLH) transcription factors (TFs) serve crucial roles in regulating plant growth and development and typically participate in biological processes by interacting with other TFs. Cap...

Authors: Renjian Liu, Jiali Song, Shaoqun Liu, Changming Chen, Shuanglin Zhang, Juntao Wang, Yanhui Xiao, Bihao Cao, Jianjun Lei and Zhangsheng Zhu

Differential transcription pathways associated with rootstock-induced dwarfing in breadfruit (Artocarpus altilis) scions

Breadfruit (Artocarpus altilis) is a traditional staple tree crop throughout the tropics. Through interspecific grafting, a dwarf phenotype with over 50% reduction in plant height was identified when marang (Arto...

Authors: Yuchan Zhou and Steven J. R. Underhill

Effect of graphene / metal nanocomposites on the key genes involved in rosmarinic acid biosynthesis pathway and its accumulation in Melissa officinalis

Recently, numerous investigations have been done to study graphene and silver nanoparticle in the fields of agriculture and medicine. In the present study, the green synthesis of nanoparticles with two concentrat...

Authors: Roya Karimi Soraki, Mahyar Gerami and Moazzameh Ramezani

Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.)

Nitrogen (N) and phosphorus (P) are macronutrients essential for crop growth and productivity. In cultivated fields, N and P levels are rarely sufficient, contributing to the gap between realized and potential...

Authors: J. Vladimir Torres-Rodríguez, M. Nancy Salazar-Vidal, Ricardo A. Chávez Montes, Julio A. Massange-Sánchez, C. Stewart Gillmor and Ruairidh J. H. Sawers

Integrated metabolome and transcriptome analysis of the anthocyanin biosynthetic pathway in relation to color mutation in miniature roses

Roses are famous ornamental plants worldwide. Floral coloration is one of the most prominent traits in roses and is mainly regulated through the anthocyanin biosynthetic pathway. In this study, we investigated...

Authors: Jiaojiao Lu, Qing Zhang, Lixin Lang, Chuang Jiang, Xiaofeng Wang and Hongmei Sun

Study on the differences of gene expression between pear and apple wild cultivation materials based on RNA-seq technique

Pears and apples are both perennial deciduous trees of the Rosaceae family, and both are important economic fruit trees worldwide. The emergence of many varieties in the market has been mostly domesticated from w...

Authors: Huangwei Zhang, Meng Li, Min Kong, Jim M. Dunwell, Yuyan Zhang, Chao Yue, Juyou Wu and Shaoling Zhang

Genome-wide association study and transcriptome analysis discover new genes for bacterial leaf blight resistance in rice (Oryza sativa L.)

Rice (Oryza sativa) bacterial leaf blight (BLB), caused by the hemibiotrophic Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases affecting the production of rice worldwide. The developme...

Authors: Xinyue Shu, Aijun Wang, Bo Jiang, Yuqi Jiang, Xing Xiang, Xiaoqun Yi, Shuangcheng Li, Qiming Deng, Shiquan Wang, Jun Zhu, Yueyang Liang, Huainian Liu, Ting Zou, Lingxia Wang, Ping Li and Aiping Zheng

FLA14 is required for pollen development and preventing premature pollen germination under high humidity in Arabidopsis

As an important subfamily of arabinogalactan proteins (AGPs), fasciclin-like AGPs (FLAs) contribute to various aspects of growth, development and adaptation, yet their function remains largely elusive. Despite...

Authors: Yingjing Miao, Jiashu Cao, Li Huang, Youjian Yu and Sue Lin

Poplar aquaporin PIP1;1 promotes Arabidopsis growth and development

Root hydraulic conductance is primarily determined by the conductance of living tissues to radial water flow. Plasma membrane intrinsic proteins (PIPs) in root cortical cells are important for plants to take u...

Authors: Huani Leng, Cheng Jiang, Xueqin Song, Mengzhu Lu and Xianchong Wan

Effect of chilling acclimation on germination and seedlings response to cold in different seed coat colored wheat (Triticum aestivum L.)

Flavonoids can protect plants against extreme temperatures and ROS due to their antioxidant activities. We found that deep-purple seed coat color was controlled by two gene interaction (12:3:1) from the cross ...

Authors: Paulina Calderon Flores, Jin Seok Yoon, Dae Yeon Kim and Yong Weon Seo

Elucidating the multifunctional role of the cell wall components in the maize exploitation

Besides the use of maize grain as food and feed, maize stover can be a profitable by-product for cellulosic ethanol production, whereas the whole plant can be used for silage production. However, yield is redu...

Authors: Ana López-Malvar, Rosa Ana Malvar, Xose Carlos Souto, Leonardo Dario Gomez, Rachael Simister, Antonio Encina, Jaime Barros-Rios, Sonia Pereira-Crespo and Rogelio Santiago

Genome-wide association analysis reveals quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum)

Numerous quantitative trait loci (QTLs) and candidate genes associated with yield-related traits have been identified in cotton by genome-wide association study (GWAS) analysis. However, most of the phenotypic...

Authors: Guozhong Zhu, Sen Hou, Xiaohui Song, Xing Wang, Wei Wang, Quanjia Chen and Wangzhen Guo

Transcriptome and proteome analysis of walnut (Juglans regia L.) fruit in response to infection by Colletotrichum gloeosporioides

Walnut anthracnose induced by Colletotrichum gloeosporioides is a disastrous disease affecting walnut production. The resistance of walnut fruit to C. gloeosporioides is a highly complicated and genetically progr...

Authors: Hongcheng Fang, Xia Liu, Yuhui Dong, Shan Feng, Rui Zhou, Changxi Wang, Xinmei Ma, Jianning Liu and Ke Qiang Yang

The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions

Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) ex...

Authors: Yan-Yan Guo, Jia-Xing Yang, Ming-Zhu Bai, Guo-Qiang Zhang and Zhong-Jian Liu

Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper

Peppers (Capsicum annuum L.) containing distinct capsaicinoids are the most widely cultivated spices in the world. However, extreme genomic diversity among species represents an obstacle to breeding pepper.

Authors: Myung-Shin Kim, Geun Young Chae, Soohyun Oh, Jihyun Kim, Hyunggon Mang, Seungill Kim and Doil Choi

Comparative transcriptomic analysis of seed coats with high and low lignin contents reveals lignin and flavonoid biosynthesis in Brassica napus

Brassica napus L. (2n = 38, AACC) is one of the most important oil crops and sources of protein for animal feed worldwide. Lignin is a large molecule aromatic polymer and a major cell wall component. However, lig...

Authors: Yiran Ding, Shizhou Yu, Jia Wang, Maoteng Li, Cunmin Qu, Jiana Li and Liezhao Liu

Two β-glucuronosyltransferases involved in the biosynthesis of type II arabinogalactans function in mucilage polysaccharide matrix organization in Arabidopsis thaliana

Arabinogalactan-proteins (AGPs) are heavily glycosylated with type II arabinogalactan (AG) polysaccharides attached to hydroxyproline residues in their protein backbone. Type II AGs are necessary for plant gro...

Authors: Oyeyemi O. Ajayi, Michael A. Held and Allan M. Showalter

Comparative analysis of latex transcriptomes reveals the potential mechanisms underlying rubber molecular weight variations between the Hevea brasiliensis clones RRIM600 and Reyan7-33–97

The processabilities and mechanical properties of natural rubber depend greatly on its molecular weight (MW) and molecular weight distribution (MWD). However, the mechanisms underlying the regulation of molecu...

Authors: Shichao Xin, Yuwei Hua, Ji Li, Xuemei Dai, Xianfeng Yang, Jinu Udayabhanu, Huasun Huang and Tiandai Huang

CsLAZY1 mediates shoot gravitropism and branch angle in tea plants (Camellia sinensis)

Branch angle is a pivotal component of tea plant architecture. Tea plant architecture not only affects tea quality and yield but also influences the efficiency of automatic tea plant pruning. However, the mole...

Authors: Xiaobo Xia, Xiaozeng Mi, Ling Jin, Rui Guo, Junyan Zhu, Hui Xie, Lu Liu, Yanlin An, Cao Zhang, Chaoling Wei and Shengrui Liu

The transcription factor AtGLK1 acts upstream of MYBL2 to genetically regulate sucrose-induced anthocyanin biosynthesis in Arabidopsis

The regulation of anthocyanin biosynthesis by various factors including sugars, light and abiotic stresses is mediated by numerous regulatory factors acting at the transcriptional level. Here experimental evid...

Authors: Dongming Zhao, Yuxuan Zheng, lingjun Yang, Ziyu Yao, Jianfeng Cheng, Fang Zhang, Haiyan Jiang and Dong Liu

Impact of water deficit on the development and senescence of tomato roots grown under various soil textures of Shaanxi, China

Water scarcity is expected to extend to more regions of the world and represents an alarming threat to food security worldwide. Under such circumstances, water holding capacity is an important agronomic trait,...

Authors: Husain Ahmad and Jianming Li

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

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

Differences in morphological and physiological features of citrus seedlings are related to Mg transport from the parent to branch organs

In this study, we aimed to test the hypothesis that magnesium (Mg) remobilization in citrus plants is regulated by Mg supply and contributes to differences in the growth of the parent and branch organs. Citrus...

Authors: Yamin Jia, Hao Xu, Yuwen Wang, Xin Ye, Ningwei Lai, Zengrong Huang, Lintong Yang, Yan Li, Li-Song Chen and Jiuxin Guo

The NAC side of the fruit: tuning of fruit development and maturation

Fruits and seeds resulting from fertilization of flowers, represent an incredible evolutionary advantage in angiosperms and have seen them become a critical element in our food supply.

Authors: Sara Forlani, Chiara Mizzotti and Simona Masiero

The genetic basis of water‐use efficiency and yield in lettuce

Water supply limits agricultural productivity of many crops including lettuce. Identifying cultivars within crop species that can maintain productivity with reduced water supply is a significant challenge, but...

Authors: Annabelle Damerum, Hazel K. Smith, GJJ Clarkson, Maria José Truco, Richard W. Michelmore and Gail Taylor

Inhibition of lateral shoot formation by RNA interference and chemically induced mutations to genes expressed in the axillary meristem of Nicotiana tabacum L.

Lateral branches vigorously proliferate in tobacco after the topping of the inflorescence portions of stems for the maturation of the leaves to be harvested. Therefore, tobacco varieties with inhibited lateral...

Authors: Kaori Hamano, Seiki Sato, Masao Arai, Yuta Negishi, Takashi Nakamura, Tomoyuki Komatsu, Tsuyoshi Naragino and Shoichi Suzuki

Genome-wide identification and functional analysis of U-box E3 ubiquitin ligases gene family related to drought stress response in Chinese white pear (Pyrus bretschneideri)

The plant U-box (PUB) proteins are a family of ubiquitin ligases (E3) enzymes that involved in diverse biological processes, as well as in responses to plant stress response. However, the characteristics and f...

Authors: Chunmeng Wang, Bobo Song, Yuqin Dai, Shaoling Zhang and Xiaosan Huang

Conserved and non-conserved functions of the rice homologs of the Arabidopsis trichome initiation-regulating MBW complex proteins

Trichome initiation in Arabidopsis is regulated by a MYB-bHLH-WD40 (MBW) transcriptional activator complex formed by the R2R3 MYB transcription factor GLABRA1 (GL1), MYB23 or MYB82, the bHLH transcription fact...

Authors: Kaijie Zheng, Xutong Wang, Yating Wang and Shucai Wang

Lanthanum (La) improves growth, yield formation and 2-acetyl-1-pyrroline biosynthesis in aromatic rice (Oryza sativa L.)

Lanthanum (La) is a rare earth element that can influence plant growth and development. However, the effect of La on growth, yield formation and 2-acetyl-1-pyrroline (2-AP, a key compound responsible for the a...

Authors: Haowen Luo, Yulin Chen, Longxin He and Xiangru Tang

RUS6, a DUF647-containing protein, is essential for early embryonic development in Arabidopsis thaliana

The Arabidopsis RUS (ROOT UV-B SENSITIVE) gene family contains six members, each of which encodes a protein containing a DUF647 (domain of unknown function 647) that is commonly found in eukaryotes. Previous stud...

Authors: Nathaniel Perry, Colin D. Leasure, Hongyun Tong, Elias M. Duarte and Zheng-Hui He

Transcriptome and metabolite profiling analyses provide insight into volatile compounds of the apple cultivar ‘Ruixue’ and its parents during fruit development

Aroma is one the most crucial inherent quality attributes of fruit. ‘Ruixue’ apples were selected from a cross between ‘Pink Lady’ and ‘Fuji’, a later ripening yellow new cultivar. However, there is little kno...

Authors: Xiaojie Liu, Nini Hao, Ruifang Feng, Zhipeng Meng, Yanan Li and Zhengyang Zhao

Integrative analysis of transcriptome and proteome revealed nectary and nectar traits in the plant-pollinator interaction of Nitraria tangutorum Bobrov

Nitraria tangutorum is an important desert shrub that shows resistance to drought, salt and wind erosion stresses. It is a central ecological species in its area. Here, we have studied how N. tangutorum has adapt...

Authors: Tingting Chen, Yanwei Zhou, Jingbo Zhang, Ye Peng, Xiuyan Yang, Zhaodong Hao, Ye Lu, Weihuang Wu, Tielong Cheng, Jisen Shi and Jinhui Chen

Genome-wide identification, evolutionary estimation and functional characterization of two cotton CKI gene types

Casein kinase I (CKI) is a kind of serine/threonine protein kinase highly conserved in plants and animals. Although molecular function of individual member of CKI family has been investigated in Arabidopsis, litt...

Authors: Yanlong Li, Yaoyao Li, Yuanyuan Chen, Maojun Wang, Jing Yang, Xianlong Zhang, Longfu Zhu, Jie Kong and Ling Min

Characterization of full-length transcriptome in Saccharum officinarum and molecular insights into tiller development

Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, ...

Authors: Haifeng Yan, Huiwen Zhou, Hanmin Luo, Yegeng Fan, Zhongfeng Zhou, Rongfa Chen, Ting Luo, Xujuan Li, Xinlong Liu, Yangrui Li, Lihang Qiu and Jianming Wu

Ethylene enhances root water transport and aquaporin expression in trembling aspen (Populus tremuloides) exposed to root hypoxia

Root hypoxia has detrimental effects on physiological processes and growth in most plants. The effects of hypoxia can be partly alleviated by ethylene. However, the tolerance mechanisms contributing to the eth...

Authors: Xiangfeng Tan, Mengmeng Liu, Ning Du and Janusz J. Zwiazek

IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like peptides and HAE (HAESA)-like receptors regulate corolla abscission in Nicotiana benthamiana flowers

Abscission is an active, organized, and highly coordinated cell separation process enabling the detachment of aerial organs through the modification of cell-to-cell adhesion and breakdown of cell walls at spec...

Authors: Daniel Ventimilla, Karelia Velázquez, Susana Ruiz-Ruiz, Javier Terol, Miguel A. Pérez-Amador, Mª. Carmen Vives, José Guerri, Manuel Talon and Francisco R. Tadeo

Retraction Note: Contribution of anthocyanin pathways to fruit flesh coloration in pitayas

This article has been retracted. Please see the Retraction Notice for more detail: https://​doi.​org/​10.​1186/​s12870-020–02566-2

Authors: Ruiyi Fan, Qingming Sun, Jiwu Zeng and Xinxin Zhang

Comparative transcriptomic analysis of candidate effectors to explore the infection and survival strategy of Bursaphelenchus xylophilus during different interaction stages with pine trees

The pine wood nematode (PWN), Bursaphelenchus xylophilus, is a devastating pathogen of many Pinus species in China. The aim of this study was to understand the interactive molecular mechanism of PWN and its host ...

Authors: Long-Jiao Hu, Xiao-Qin Wu, Xiao-Lei Ding and Jian-Ren Ye

RcTGA1 and glucosinolate biosynthesis pathway involvement in the defence of rose against the necrotrophic fungus Botrytis cinerea

Rose is an important economic crop in horticulture. However, its field growth and postharvest quality are negatively affected by grey mould disease caused by Botrytis c. However, it is unclear how rose plants def...

Authors: Penghua Gao, Hao Zhang, Huijun Yan, Qigang Wang, Bo Yan, Hongying Jian, Kaixue Tang and Xianqin Qiu

Half-leaf width symmetric distribution reveals buffering strategy of Cunninghamia lanceolata

Leaf length and width could be a functioning relationship naturally as plant designs. Single-vein leaves have the simplest symmetrical distribution and structural design, which means that fast-growing single-v...

Authors: Xi Peng, Meifang Zhao, Shuguang Liu and Wende Yan

LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome

Long Terminal Repeat retrotransposons (LTR-REs) are repetitive DNA sequences that constitute a large part of the genome. The improvement of sequencing technologies and sequence assembling strategies has achiev...

Authors: Alberto Vangelisti, Samuel Simoni, Gabriele Usai, Maria Ventimiglia, Lucia Natali, Andrea Cavallini, Flavia Mascagni and Tommaso Giordani

Identification of cell wall-associated kinases as important regulators involved in Gossypium hirsutum resistance to Verticillium dahliae

Verticillium wilt, caused by the soil borne fungus Verticillium dahliae, is a major threat to cotton production worldwide. An increasing number of findings indicate that WAK genes participate in plant−pathogen in...

Authors: Jun Yang, Meixia Xie, Xingfen Wang, Guoning Wang, Yan Zhang, Zhikun Li and Zhiying Ma

Comparative analysis of chloroplast genome structure and molecular dating in Myrtales

Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a co...

Authors: Xiao-Feng Zhang, Jacob B. Landis, Hong-Xin Wang, Zhi-Xin Zhu and Hua-Feng Wang

Inter-species functional compatibility of the Theobroma cacao and Arabidopsis FT orthologs: 90 million years of functional conservation of meristem identity genes

In angiosperms the transition to flowering is controlled by a complex set of interacting networks integrating a range of developmental, physiological, and environmental factors optimizing transition time for m...

Authors: S. F. Prewitt, A. Shalit-Kaneh, S. N. Maximova and M. J. Guiltinan

Combining targeted metabolite analyses and transcriptomics to reveal the specific chemical composition and associated genes in the incompatible soybean variety PI437654 infected with soybean cyst nematode HG1.2.3.5.7

Soybean cyst nematode, Heterodera glycines, is one of the most devastating pathogens of soybean and causes severe annual yield losses worldwide. Different soybean varieties exhibit different responses to H. glyci...

Authors: Xue Shi, Qiansi Chen, Shiming Liu, Jiajun Wang, Deliang Peng and Lingan Kong

Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated withearly-stage resistance to Aspergillus flavus in maize

The fungus Aspergillus flavus (A. flavus) is a serious threat to maize (Zea mays) production worldwide. It causes considerable yield and economic losses, and poses a health risk to humans and livestock due to the...

Authors: Huanhuan Liu, Haofeng Wu, Yan Wang, Huan Wang, Saihua Chen and Zhitong Yin