Articles

Genome-wide analysis and functional characterization of the DELLA gene family associated with stress tolerance in B. napus

Brassica napus is an essential crop for oil and livestock feed. Eventually, this crop's economic interest is at the most risk due to anthropogenic climate change. DELLA proteins constitute a significant repressor...

Authors: Rehman Sarwar, Ting Jiang, Peng Ding, Yue Gao, Xiaoli Tan and Keming Zhu

Insights into the mechanism of the effects of rhizosphere microorganisms on the quality of authentic Angelica sinensis under different soil microenvironments

Angelica sinensis (Oliv.) Diels (A. sinensis) is a Chinese herb grown in different geographical locations. It contains numerous active components with therapeutic value. Rhizosphere microbiomes affect various asp...

Authors: Lei Zhu, Hui Yan, Gui-sheng Zhou, Chun-hao Jiang, Pei Liu, Guang Yu, Sheng Guo, Qi-Nan Wu and Jin-ao Duan

A novel gene LbHLH from the halophyte Limonium bicolor enhances salt tolerance via reducing root hair development and enhancing osmotic resistance

Identifying genes involved in salt tolerance in the recretohalophyte Limonium bicolor could facilitate the breeding of crops with enhanced salt tolerance. Here we cloned the previously uncharacterized gene LbHLH ...

Authors: Xi Wang, Yingli Zhou, Yanyu Xu, Baoshan Wang and Fang Yuan

Genome-wide association study and its applications in the non-model crop Sesamum indicum

Sesame is a rare example of non-model and minor crop for which numerous genetic loci and candidate genes underlying features of interest have been disclosed at relatively high resolution. These progresses have...

Authors: Muez Berhe, Komivi Dossa, Jun You, Pape Adama Mboup, Idrissa Navel Diallo, Diaga Diouf, Xiurong Zhang and Linhai Wang

Characterization of contrasting rice (Oryza sativa L.) genotypes reveals the Pi-efficient schema for phosphate starvation tolerance

Phosphorus (P), being one of the essential components of nucleic acids, cell membranes and enzymes, indispensable for diverse cellular processes like photosynthesis/carbohydrate metabolism, energy production, ...

Authors: Suresh Kumar, Pallavi, Chetna Chugh, Karishma Seem, Santosh Kumar, K. K. Vinod and Trilochan Mohapatra

Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinases play important roles in plant growth, development and stress responses. ...

Authors: Xin Wang, Ming-Hua Wu, Dong Xiao, Ruo-Lan Huang, Jie Zhan, Ai-Qin Wang and Long-Fei He

TeaAS: a comprehensive database for alternative splicing in tea plants (Camellia sinensis)

Alternative splicing (AS) increases the diversity of transcripts and proteins through the selection of different splice sites and plays an important role in the growth, development and stress tolerance of plan...

Authors: Xiaozeng Mi, Yi Yue, Mengsha Tang, Yanlin An, Hui Xie, Dahe Qiao, Zhiyu Ma, Shengrui Liu and Chaoling Wei

Expressional diversity of grapevine 3-Hydroxy-3-methylglutaryl-CoA reductase (VvHMGR) in different grapes genotypes

3-Hydroxy-3-methylglutaryl-CoA reductase (HMGR) is a key enzyme in the mevalonate (MVA) pathway, which regulates the metabolism of terpenoids in the cytoplasm and determines the type and content of downstream ...

Authors: Ting Zheng, Lubin Guan, Kun Yu, Muhammad Salman Haider, Maazullah Nasim, Zhongjie Liu, Teng Li, Kekun Zhang, Songtao Jiu, Haifeng Jia and Jinggui Fang

Combining QTL-seq and linkage mapping to fine map a candidate gene in qCTS6 for cold tolerance at the seedling stage in rice

Cold stress caused by low temperatures is an important factor restricting rice production. Identification of cold-tolerance genes that can stably express in cold environments is crucial for molecular rice bree...

Authors: Luomiao Yang, Jingguo Wang, Zhenghong Han, Lei Lei, Hua Long Liu, Hongliang Zheng, Wei Xin and Detang Zou

Multi-omics analysis of the bioactive constituents biosynthesis of glandular trichome in Perilla frutescens

Perilla frutescens (L.) Britt is a medicinal and edible plant widely cultivated in Asia. Terpenoids, flavonoids and phenolic acids are the primary source of medicinal ingredients. Glandular trichomes with multice...

Authors: Peina Zhou, Mengjiao Yin, Shilin Dai, Ke Bao, Chenglin Song, Chanchan Liu and Qinan Wu

Correction to: Conserved and non‑conserved functions of the rice homologs of the Arabidopsis trichome initiation‑regulating MBW complex proteins

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

Microscopy and chemical analyses reveal flavone-based woolly fibres extrude from micron-sized holes in glandular trichomes of Dionysia tapetodes

Dionysia tapetodes, a small cushion-forming mountainous evergreen in the Primulaceae, possesses a vast surface-covering of long silky fibres forming the characteristic “woolly” farina. This contrasts with some re...

Authors: Matthieu Bourdon, Josephine Gaynord, Karin H. Müller, Gareth Evans, Simon Wallis, Paul Aston, David R. Spring and Raymond Wightman

NtbHLH1, a JAF13-like bHLH, interacts with NtMYB6 to enhance proanthocyanidin accumulation in Chinese Narcissus

Flavonoid biosynthesis in plants is primarily regulated at the transcriptional level by transcription factors modulating the expression of genes encoding enzymes in the flavonoid pathway. One of the most studi...

Authors: Yuxin Fan, Jiayu Peng, Jiacheng Wu, Ping Zhou, Ruijie He, Andrew C. Allan and Lihui Zeng

An NADPH oxidase regulates carbon metabolism and the cell cycle during root nodule symbiosis in common bean (Phaseolus vulgaris)

Rhizobium–legume symbiosis is a specific, coordinated interaction that results in the formation of a root nodule, where biological nitrogen fixation occurs. NADPH oxidases, or Respiratory Burst Oxidase Homolog...

Authors: Citlali Fonseca-García, Noreide Nava, Miguel Lara and Carmen Quinto

Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia

Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology.

Authors: Yong Li, Long-Chen Shi, Nan-Cai Pei, Samuel A. Cushman and Yu-Tao Si

Transcriptome analysis of scions grafted to potato rootstock for improving late blight resistance

Late blight seriously threatens potato cultivation worldwide. The severe and widespread damage caused by the fungal pathogen can lead to drastic decreases in potato yield. Although grafting technology has been...

Authors: Yuexin Li and Degang Zhao

De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance

Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assemb...

Authors: Jie Wang, Shiming Li, Lei Lan, Mushan Xie, Shu Cheng, Xiaolong Gan, Gang Huang, Guohua Du, Kang Yu, Xuemei Ni, Baolong Liu and Guoxiong Peng

Transcriptome analysis of Cinnamomum migao seed germination in medicinal plants of Southwest China

Cinnamomum migao is an endangered evergreen woody plant species endemic to China. Its fruit is used as a traditional medicine by the Miao nationality of China and has a high commercial value. However, its seed g...

Authors: Xiaolong Huang, Tian Tian, Jingzhong Chen, Deng Wang, Bingli Tong and Jiming Liu

Biochar induced improvement in root system architecture enhances nutrient assimilation by cotton plant seedlings

Raising nitrogen use efficiency of crops by improving root system architecture is highly essential not only to reduce costs of agricultural production but also to mitigate climate change. The physiological mec...

Authors: Lei Feng, Wanli Xu, Guangmu Tang, Meiying Gu and Zengchao Geng

BRS1 mediates plant redox regulation and cold responses

Brassinosteroid-insensitive 1 suppressor 1 (BRS1) is a serine carboxypeptidase that mediates brassinosteroid signaling and participates in multiple developmental processes in Arabidopsis. However, little is kn...

Authors: Dongzhi Zhang, Yuqian Zhao, Junzhe Wang, Peng Zhao and Shengbao Xu

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

Hybridization and introgression in sympatric and allopatric populations of four oak species

Hybridization and introgression are vital sources of novel genetic variation driving diversification during reticulated evolution. Quercus is an important model clade, having extraordinary diverse and abundant me...

Authors: Xuan Li, Gaoming Wei, Yousry A. El-Kassaby and Yanming Fang

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

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