Articles

The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray)

Entering and exiting winter dormancy present important trade-offs between growth and survival at northern latitudes. Many forest trees display local adaptation across latitude in traits associated with these p...

Authors: Rami-Petteri Apuli, Thomas Richards, Martha Rendón-Anaya, Almir Karacic, Ann-Christin Rönnberg-Wästljung and Pär K. Ingvarsson

Reprogramming of the wheat transcriptome in response to infection with Claviceps purpurea, the causal agent of ergot

Ergot, caused by the fungal pathogen Claviceps purpurea, infects the female flowers of a range of cereal crops, including wheat. To understand the interaction between C. purpurea and hexaploid wheat we undertook ...

Authors: Eleni Tente, Nelzo Ereful, Anyela Camargo Rodriguez, Paul Grant, Donal M. O’Sullivan, Lesley A. Boyd and Anna Gordon

Natural variation in wild tomato trichomes; selecting metabolites that contribute to insect resistance using a random forest approach

Plant-produced specialised metabolites are a powerful part of a plant’s first line of defence against herbivorous insects, bacteria and fungi. Wild ancestors of present-day cultivated tomato produce a plethora...

Authors: Ruy W. J. Kortbeek, Marc D. Galland, Aleksandra Muras, Frans M. van der Kloet, Bart André, Maurice Heilijgers, Sacha A. F. T. van Hijum, Michel A. Haring, Robert C. Schuurink and Petra M. Bleeker

Genetic mapping and QTL analysis for peanut smut resistance

Peanut smut is a disease caused by the fungus Thecaphora frezii Carranza & Lindquist to which most commercial cultivars in South America are highly susceptible. It is responsible for severely decreased yield and ...

Authors: Francisco J. de Blas, Cecilia I. Bruno, Renee S. Arias, Carolina Ballén-Taborda, Eva Mamani, Claudio Oddino, Melina Rosso, Beatriz P. Costero, Marina Bressano, Juan H. Soave, Sara J. Soave, Mario I. Buteler, J. Guillermo Seijo and Alicia N. Massa

Identification of novel genomic regions associated with nine mineral elements in Chinese winter wheat grain

Mineral elements are important for maintaining good human health besides heavy metals. Mining genes that control mineral elements are paramount for improving their accumulation in the wheat grain. Although pre...

Authors: Wei Wang, Hong Guo, Chongning Wu, Hui Yu, Xiaokang Li, Guangfeng Chen, Jichun Tian and Zhiying Deng

Chickpea shows genotype-specific nodulation responses across soil nitrogen environment and root disease resistance categories

The ability of chickpea to obtain sufficient nitrogen via its symbiotic relationship with Mesorhizobium ciceri is of critical importance in supporting growth and grain production. A number of factors can affect t...

Authors: Krista L. Plett, Sean L. Bithell, Adrian Dando and Jonathan M. Plett

Genome-wide identification of ZmSnRK2 genes and functional analysis of ZmSnRK2.10 in ABA signaling pathway in maize (Zea mays L)

Phytohormone abscisic acid (ABA) is involved in the regulation of a wide range of biological processes. In Arabidopsis, it has been well-known that SnRK2s are the central components of the ABA signaling pathwa...

Authors: Tiandan Long, Binjie Xu, Yufeng Hu, Yayun Wang, Changqing Mao, Yongbin Wang, Junjie Zhang, Hanmei Liu, Huanhuan Huang, Yinghong Liu, Guowu Yu, Chunzhao Zhao, Yangping Li and Yubi Huang

Dynamic formation and transcriptional regulation mediated by phytohormones during chalkiness formation in rice

Rice (Oryza sativa L.) Chalkiness, the opaque part in the kernel endosperm formed by loosely piled starch and protein bodies. Chalkiness is a complex quantitative trait regulated by multiple genes and various env...

Authors: Qin Xie, Jinke Xu, Ke Huang, Yi Su, Jianhua Tong, Zhigang Huang, Chao Huang, Manlin Wei, Wanhuang Lin and Langtao Xiao

qMrdd2, a novel quantitative resistance locus for maize rough dwarf disease

Maize rough dwarf disease (MRDD), a widespread disease caused by four pathogenic viruses, severely reduces maize yield and grain quality. Resistance against MRDD is a complex trait that controlled by many quan...

Authors: Weixiao Zhang, Suining Deng, Yan Zhao, Wei Xu, Qingcai Liu, Yongzhong Zhang, Chunmei Ren, Zhaobang Cheng, Mingliang Xu and Baoshen Liu

Transcriptomics identifies key defense mechanisms in rice resistant to both leaf-feeding and phloem feeding herbivores

Outbreaks of insect pests in paddy fields cause heavy losses in global rice yield annually, a threat projected to be aggravated by ongoing climate warming. Although significant progress has been made in the sc...

Authors: Yi Li, Boon Huat Cheah, Yu-Fu Fang, Yun-Hung Kuang, Shau-Ching Lin, Chung-Ta Liao, Shou-Horng Huang, Ya-Fen Lin and Wen-Po Chuang

Natural variations in the non-coding region of ZmNAC080308 contributes maintaining grain yield under drought stress in maize

Natural variations derived from both evolutionary selection and genetic recombination, presume to have important functions to respond to various abiotic stresses, which could be used to improve drought toleran...

Authors: Nan Wang, Ming Cheng, Yong Chen, Bojuan Liu, Xiaonan Wang, Guojun Li, Yueheng Zhou, Ping Luo, Zhangying Xi, Hongjun Yong, Degui Zhang, Mingshun Li, Xuecai Zhang, Felix San Vicente, Zhuanfang Hao and Xinhai Li

Comparative transcriptome analysis reveals distinct gene expression profiles in Brachypodium distachyon infected by two fungal pathogens

The production of cereal crops is frequently affected by diseases caused by Fusarium graminearum and Magnaporthe oryzae, two devastating fungal pathogens. To improve crop resistance, many studies have focused on ...

Authors: Gengrui Zhu, Chengyu Gao, Chenyu Wu, Mu Li, Jin-Rong Xu, Huiquan Liu and Qinhu Wang

Evaluation of Jatropha curcas L. leaves mulching on wheat growth and biochemical attributes under water stress

Organic mulches are widely used in crop production systems. Due to their benefits in improving soil fertility, retention of soil moisture and weed control. Field experiments were conducted during wheat growing...

Authors: Muhammad Irshad, Faizan Ullah, Shah Fahad, Sultan Mehmood, Asif Ullah Khan, Martin Brtnicky, Antonin Kintl, Jiri Holatko, Inam Irshad, Mohamed El-Sharnouby, Ayman EL Sabagh, Rahul Datta and Subhan Danish

Reduced free asparagine in wheat grain resulting from a natural deletion of TaASN-B2: investigating and exploiting diversity in the asparagine synthetase gene family to improve wheat quality

Understanding the determinants of free asparagine concentration in wheat grain is necessary to reduce levels of the processing contaminant acrylamide in baked and toasted wheat products. Although crop manageme...

Authors: Joseph Oddy, Rocío Alarcón-Reverte, Mark Wilkinson, Karl Ravet, Sarah Raffan, Andrea Minter, Andrew Mead, J. Stephen Elmore, Isabel Moreira de Almeida, Nicholas C. Cryer, Nigel G. Halford and Stephen Pearce

Frequent gain- and loss-of-function mutations of the BjMYB113 gene accounted for leaf color variation in Brassica juncea

Mustard (Brassica juncea) is an important economic vegetable, and some cultivars have purple leaves and accumulate more anthocyanins than the green. The genetic and evolution of purple trait in mustard has not be...

Authors: Guanghui An and Jiongjiong Chen

Enhanced aluminum tolerance in sugarcane: evaluation of SbMATE overexpression and genome-wide identification of ALMTs in Saccharum spp.

A major limiting factor for plant growth is the aluminum (Al) toxicity in acidic soils, especially in tropical regions. The exclusion of Al from the root apex through root exudation of organic acids such as ma...

Authors: Ana Paula Ribeiro, Felipe Vinecky, Karoline Estefani Duarte, Thaís Ribeiro Santiago, Raphael Augusto das Chagas Noqueli Casari, Aline Forgatti Hell, Bárbara Andrade Dias Brito da Cunha, Polyana Kelly Martins, Danilo da Cruz Centeno, Patricia Abrão de Oliveira Molinari, Geraldo Magela de Almeida Cançado, Jurandir Vieira de Magalhães, Adilson Kenji Kobayashi, Wagner Rodrigo de Souza and Hugo Bruno Correa Molinari

Reconstruction of the full-length transcriptome of cigar tobacco without a reference genome and characterization of anion channel/transporter transcripts

Cigar wrapper leaves are the most important raw material of cigars. Studying the genomic information of cigar tobacco is conducive to improving cigar quality from the perspective of genetic breeding. However, ...

Authors: Hui Zhang, Jingjing Jin, Guoyun Xu, Zefeng Li, Niu Zhai, Qingxia Zheng, Hongkun Lv, Pingping Liu, Lifeng Jin, Qiansi Chen, Peijian Cao and Huina Zhou

Identification and characterization of An-4, a potential quantitative trait locus for awn development in rice

Awn of rice is an important domestication trait closely associated with yield traits. Therefore, the identification of genes for awn development is of great significance for the elucidation of molecular mechan...

Authors: Baoxiang Qin, Taian Lu, Yibo Xu, Wei Shen, Fang Liu, Xuyang Xie, Yunzhen Li, Kejian Wang and Rongbai Li

The report of anthocyanins in the betalain-pigmented genus Hylocereus is not well evidenced and is not a strong basis to refute the mutual exclusion paradigm

Here we respond to the paper entitled “Contribution of anthocyanin pathways to fruit flesh coloration in pitayas” (Fan et al., BMC Plant Biol 20:361, 2020). In this paper Fan et al. 2020 propose that the anthocya...

Authors: Boas Pucker, Hidam Bishworjit Singh, Monika Kumari, Mohammad Imtiyaj Khan and Samuel F. Brockington

Genome-wide identification and expression analysis of LBD transcription factor genes in Moso bamboo (Phyllostachys edulis)

Moso bamboo, the fastest growing plant on earth, is an important source for income in large areas of Asia, mainly cultivated in China. Lateral organ boundaries domain (LBD) proteins, a family of transcription ...

Authors: Bin Huang, Zhinuo Huang, Ruifang Ma, Muthusamy Ramakrishnan, Jialu Chen, Zhijun Zhang and Kim Yrjälä

Genome-wide identification of AP2/EREBP in Fragaria vesca and expression pattern analysis of the FvDREB subfamily under drought stress

Drought is a common phenomenon worldwide. It is also one of the main abiotic factors that affect the growth and quality of strawberry. The dehydration-responsive element binding protein (DREB) members that bel...

Authors: Chao Dong, Yue Xi, Xinlu Chen and Zong-Ming Cheng

The characterization of key physiological traits of medicinal cannabis (Cannabis sativa L.) as a tool for precision breeding

For millennia, drug-type cannabis strains were extensively used for various medicinal, ritual, and inebriant applications. However, cannabis prohibition during the last century led to cultivation and breeding ...

Authors: Erez Naim-Feil, Luke W. Pembleton, Laura E. Spooner, Alix L. Malthouse, Amy Miner, Melinda Quinn, Renata M. Polotnianka, Rebecca C. Baillie, German C. Spangenberg and Noel O. I. Cogan

Effect of drought on photosynthesis, total antioxidant capacity, bioactive component accumulation, and the transcriptome of Atractylodes lancea

Atractylodes lancea (Thunb.) DC, a medicinal herb belonging to the Asteraceae family, often faces severe drought stress during its growth. Until now, there has been no research on the effect of drought stress on ...

Authors: Aqin Zhang, Mengxue Liu, Wei Gu, Ziyun Chen, Yuchen Gu, Lingfeng Pei and Rong Tian

Downstream of GA₄, PbCYP78A6 participates in regulating cell cycle-related genes and parthenogenesis in pear (Pyrus bretshneideri Rehd.)

Parthenocarpy results in traits attractive to both consumers and breeders, and it overcomes the obstacle of self-incompatibility in the fruit set of horticultural crops, including pear (Pyrus bretshneider). Howev...

Authors: Haiqi Zhang, Wei Han, Huibin Wang, Liu Cong, Rui Zhai, Chengquan Yang, Zhigang Wang and Lingfei Xu

Evolutionary analysis and functional characterization of SiBRI1 as a Brassinosteroid receptor gene in foxtail millet

Brassinosteroids (BRs) play important roles in plant growth and development. Although BR receptors have been intensively studied in Arabidopsis, those in foxtail millet remain largely unknown. Here, we show that ...

Authors: Zhiying Zhao, Sha Tang, Yiming Zhang, Jingjing Yue, Jiaqi Xu, Wenqiang Tang, Yanxiang Sun, Ruiju Wang, Xianmin Diao and Baowen Zhang

Quantitative trait loci (QTL) analysis of leaf related traits in spinach (Spinacia oleracea L.)

Spinach (Spinacia oleracea L.) is an important leafy vegetable crop, and leaf-related traits including leaf length, leaf width, and petiole length, are important commercial traits. However, the underlying genes r...

Authors: Zhiyuan Liu, Hongbing She, Zhaosheng Xu, Helong Zhang, Guoliang Li, Shifan Zhang and Wei Qian

Comparative anatomical and transcriptomic insights into Vaccinium corymbosum flower bud and fruit throughout development

Blueberry (Vaccinium spp.) is characterized by the production of berries that are smaller than most common fruits, and the underlying mechanisms of fruit size in blueberry remain elusive. V. corymbosum ‘O’Neal’ a...

Authors: Li Yang, Liangmiao Liu, Zhuoyi Wang, Yu Zong, Lei Yu, Yongqaing Li, Fanglei Liao, Manman Chen, Kailing Cai and Weidong Guo

Genome-wide identification of Brassicaceae B-BOX genes and molecular characterization of their transcriptional responses to various nutrient stresses in allotetraploid rapeseed

B-box (BBX) genes play important roles in plant growth regulation and responses to abiotic stresses. The plant growth and yield production of allotetraploid rapeseed is usually hindered by diverse nutrient stress...

Authors: Li-wei Zheng, Sheng-jie Ma, Ting Zhou, Cai-peng Yue, Ying-peng Hua and Jin-yong Huang

PEPC of sugarcane regulated glutathione S-transferase and altered carbon–nitrogen metabolism under different N source concentrations in Oryza sativa

Phosphoenolpyruvate carboxylase (PEPC) plays an important role in the primary metabolism of higher plants. Several studies have revealed the critical importance of PEPC in the interaction of carbon and nitroge...

Authors: Ling Lian, Yuelong Lin, Yidong Wei, Wei He, Qiuhua Cai, Wei Huang, Yanmei Zheng, Huibin Xu, Fuxiang Wang, Yongsheng Zhu, Xi Luo, Huaan Xie and Jianfu Zhang

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

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