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Centromeres: from chromosome biology to biotechnology applications and synthetic genomes in plants Plant Biotech. J. (IF 9.803) Pub Date : 2022-06-20 Jingwei Zhou, Yang Liu, Xianrui Guo, James A. Birchler, Fangpu Han, Handong Su
Centromeres are the genomic regions that organize and regulate chromosome behaviors during cell cycle, and their variations are associated with genome instability, karyotype evolution, and speciation in eukaryotes. The highly repetitive and epigenetic nature of centromeres were documented during the past half century. With the aid of rapid expansion in genomic biotechnology tools, the complete sequence
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Expressed- genes and their new alleles identification during fibre elongation reveal the genetic factors underlying improvements of fibre length in cotton Plant Biotech. J. (IF 9.803) Pub Date : 2022-06-19 Jianjiang Ma, Yafei Jiang, Wenfeng Pei, Man Wu, Qifeng Ma, Ji Liu, Jikun Song, Bing Jia, Shang Liu, Jianyong Wu, Jinfa Zhang, Jiwen Yu
Interspecific breeding in cotton takes advantage of genetic recombination among desirable genes from different parental lines. However, expression new alleles (ENAs) from crossovers within genic regions and their significance in FL improvement are currently not understood. Here, we generated resequencing genomes of 191 interspecific backcross inbred lines derived from CRI36 (G. hirsutum) × Hai7124
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The transient expression of recombinant proteins in plant cell packs facilitates stable isotope labeling for NMR spectroscopy Plant Biotech. J. (IF 9.803) Pub Date : 2022-06-15 P. Opdensteinen, L. E. Sperl, M. Mohamadi, N. Kündgen-Redding, F. Hagn, J. F. Buyel
Nuclear magnetic resonance (NMR) spectroscopy can be used to determine the structure, dynamics and interactions of proteins. However, protein NMR requires stable isotope labeling for signal detection. The cells used for the production of recombinant proteins must therefore be grown in medium containing isotopically labeled substrates. Stable isotope labeling is well established in Escherichia coli
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Onsite detection of plant viruses using isothermal amplification assays Plant Biotech. J. (IF 9.803) Pub Date : 2022-06-11 A.I. Bhat, Rashid Aman, Magdy Mahfouz
Plant diseases caused by viruses limit crop production and quality, resulting in significant losses. However, options for managing viruses are limited; for example, as systemic obligate parasites, they cannot be killed by chemicals. Sensitive, robust, affordable diagnostic assays are needed to detect the presence of viruses in plant materials such as seeds, vegetative parts, insect vectors, or alternative
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Genome sequencing reveals chromosome fusion and extensive expansion of genes related to secondary metabolism in Artemisia argyi Plant Biotech. J. (IF 9.803) Pub Date : 2022-06-11 Yuhuan Miao, Dandan Luo, Tingting Zhao, Hongzhi Du, Zhenhua Liu, Zhongping Xu, Lanping Guo, Changjie Chen, Sainan Peng, Jin Xin Li, Lin Ma, Guogui Ning, Dahui Liu, Luqi Huang
Artemisia argyi, as famous as Artemisia annua, is a medicinal plant with huge economic value in the genus of Artemisia and has been widely used in the world for about three thousand years. However, a lack of the reference genome severely hinders the understanding of genetic basis for the active ingredient synthesis of A. argyi. Here, we firstly report a complex chromosome-level genome assembly of A
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CRISPR RNA-guided integrase enables high-efficiency targeted genome engineering in Agrobacterium tumefaciens Plant Biotech. J. (IF 9.803) Pub Date : 2022-06-11 Ephraim Aliu, Keunsub Lee, Kan Wang
Agrobacterium tumefaciens, the causal agent of plant crown gall disease, has been widely used to genetically transform many plant species. The inter-kingdom gene transfer capability made Agrobacterium an essential tool and model system to study the mechanism of exporting and integrating a segment of bacterial DNA into the plant genome. However, many biological processes such as Agrobacterium-host recognition
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An amino acid transporter-like protein (OsATL15) facilitates the systematic distribution of thiamethoxam in rice for controlling the brown planthopper Plant Biotech. J. (IF 9.803) Pub Date : 2022-06-09 Yuyan Xiao, Hanlin Zhang, Zhiwei Li, Tinghong Huang, Takashi Akihiro, Jian Xu, Hanhong Xu, Fei Lin
Characterisation and genetic engineering of plant transporters involved in the pesticide uptake and translocation facilitate pesticide relocation to the tissue where the pests feed, thus improving the bioavailability of the agrichemicals. We aimed to identify thiamethoxam (THX) transporters in rice and modify their expression for better brown planthopper (BPH) control with less pesticide application
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Multi-omics profiling reveals comprehensive microbe-plant-metabolite regulation patterns for medicinal plant Glycyrrhiza uralensis Fisch Plant Biotech. J. (IF 9.803) Pub Date : 2022-06-06 Chaofang Zhong, Chaoyun Chen, Xi Gao, Chongyang Tan, Hong Bai, Kang Ning
Glycyrrhiza uralensis Fisch is a medicinal plant widely used to treat multiple diseases in Europe and Asia, and its efficacy largely depends on liquiritin and glycyrrhizic acid. The regulatory pattern responsible for the difference in efficacy between wild and cultivated G. uralensis remains largely undetermined. Here, we collected roots and rhizosphere soils from wild (WT) G. uralensis as well as
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Using field evaluation and systematic iteration to rationalise the accumulation of omega-3 long chain polyunsaturated fatty acids in transgenic Camelina sativa Plant Biotech. J. (IF 9.803) Pub Date : 2022-06-02 Lihua Han, Susana Silvestre, Olga Sayanova, Richard P. Haslam, Johnathan A. Napier
The Brassicaceae Camelina sativa (Gold-of-pleasure) is now an established niche crop, as well as being used as a transgenic host for a range of novel seed traits. Most notable of these is the accumulation of omega-3 long chain polyunsaturates such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), fatty acids normally only found in marine organisms. As part of continued efforts to optimise
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Redox-engineering enhances maize thermotolerance and grain yield in the field Plant Biotech. J. (IF 9.803) Pub Date : 2022-06-02 Stuart A Sprague, Tej Man Tamang, Trevor Steiner, Qingyu Wu, Ying Hu, Tayebeh Kakeshpour, Jungeun Park, Jian Yang, Zhao Peng, Blake Bergkamp, Impa Somayanda, Morgan Peterson, Ely Oliveira Garcia, Yangfan Hao, Paul St. Amand, Guihua Bai, Paul A Nakata, Ivo Rieu, David P Jackson, Ninghui Cheng, Barbara Valent, Kendal D Hirschi, SV Krishna Jagadish, Sanzhen Liu, Frank F White, Sunghun Park
Increasing populations and temperatures are expected to escalate food demands beyond production capacities, and the development of maize lines with better performance under heat stress is desirable. Here, we report that constitutive ectopic expression of a heterologous glutaredoxin S17 from Arabidopsis thaliana (AtGRXS17) can provide thermotolerance in maize through enhanced chaperone activity and
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Natural allelic variation of GmST05 controlling seed size and quality in soybean Plant Biotech. J. (IF 9.803) Pub Date : 2022-06-01 Zongbiao Duan, Min Zhang, Zhifang Zhang, Shan Liang, Lei Fan, Xia Yang, Yaqin Yuan, Yi Pan, Guoan Zhou, Shulin Liu, Zhixi Tian
Seed size is one of the most important agronomic traits determining the yield of crops. Cloning the key genes controlling seed size and pyramiding their elite alleles will facilitate yield improvement. To date, few genes controlling seed size have been identified in soybean, a major crop that provides half of the plant oil and one quarter of the plant protein globally. Here, through a genome-wide association
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A whiff of the future: functions of phenylalanine-derived aroma compounds and advances in their industrial production Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-31 Oded Skaliter, Yarin Livneh, Shani Agron, Sharoni Shafir, Alexander Vainstein
Plants produce myriad aroma compounds—odorous molecules that are key factors in countless aspects of the plant's life cycle, including pollinator attraction, and communication within and between plants. For humans, aroma compounds convey accurate information on food type, and are vital for assessing the environment. The phenylpropanoid pathway is the origin of notable aroma compounds, such as raspberry
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A single promoter-TALE system for tissue-specific and tuneable expression of multiple genes in rice Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-31 Florence Danila, Tom Schreiber, Maria Ermakova, Lei Hua, Daniela Vlad, Shuen-Fang Lo, Yi-Shih Chen, Julia Lambret Frotte, Anna S. Hermanns, Benedikt Athmer, Susanne von Caemmerer, Su-May Yu, Julian M. Hibberd, Alain Tissier, Robert T. Furbank, Steven Kelly, Jane A. Langdale
In biological discovery and engineering research there is a need to spatially and/or temporally regulate transgene expression. However, the limited availability of promoter sequences that are uniquely active in specific tissue-types and/or at specific times often precludes co-expression of multiple transgenes in precisely-controlled developmental contexts. Here we developed a system for use in rice
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The upregulated LsKN1 gene transforms pinnately to palmately lobed leaves through auxin, gibberellin, and leaf dorsiventrality pathways in lettuce Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-30 Menglu Wang, Dean Lavelle, Changchun Yu, Weiyi Zhang, Jiongjiong Chen, Xin Wang, Richard W Michelmore, Hanhui Kuang
Leaf shape represents a vital agronomic trait for leafy vegetables such as lettuce. Some lettuce cultivars produce lobed leaves, varying from pinnately to palmately lobed, but the genetic mechanisms remain unclear. In this study, we cloned one major quantitative trait locus (QTL) controlling palmately lobed leaves. The candidate gene, LsKN1, encodes a homeobox transcription factor, and has been shown
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Retrieving a Disrupted Gene Encoding Phospholipase A for Fiber Enhancement in Allotetraploid Cultivated Cotton Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-28 Lei Fang, Zhiyuan Zhang, Ting Zhao, Na Zhou, Huan Mei, Xingqi Huang, Fang Wang, Zhanfeng Si, Zegang Han, Shan Lu, Yan Hu, Xueying Guan, Tianzhen Zhang
After polyploidization originated from one interspecific hybridization event in Gossypium, Gossypium barbadense evolved to produce extra-long staple fibers than Gossypium hirsutum (Upland cotton), which produces a higher fiber yield. The genomic diversity between G. barbadense and G. hirsutum thus provides a genetic basis for fiber trait variation. Recently, rapid accumulation of gene disruption or
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EARLY MORNING FLOWERING 1 (EMF1) regulates the floret opening time by mediating lodicule cell wall formation in rice. Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-30 Peizhou Xu,Tingkai Wu,Asif Ali,Hongyu Zhang,Yongxiang Liao,Xiaoqiong Chen,Yonghang Tian,Wenming Wang,Xiangdong Fu,Yan Li,Jing Fan,He Wang,Yunfeng Tian,Yutong Liu,Qingshan Jiang,Changhui Sun,Hao Zhou,Xianjun Wu
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Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-22 Benedict Coombes, John P. Fellers, Surbhi Grewal, Rachel Rusholme-Pilcher, Stella Hubbart-Edwards, Cai-yun Yang, Ryan Joynson, Ian P. King, Julie King, Anthony Hall
Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat’s wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited
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FLOURY ENDOSPERM20 encoding SHMT4 is required for rice endosperm development Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-20 Mengyuan Yan, Tian Pan, Yun Zhu, Xiaokang Jiang, Mingzhou Yu, Rongqi Wang, Feng Zhang, Sheng Luo, Xiuhao Bao, Yu Chen, Binglei Zhang, Ruonan Jing, Zhijun Cheng, Xin Zhang, Cailin Lei, Qibing Lin, Shanshan Zhu, Xiuping Guo, Yulong Ren, Jianmin Wan
Endosperm stores starch and proteins in cereal crop seeds, providing a major calorie source for human consumption. Rice, given its agricultural importance and rich genetic resources, serves as a model crop for dissecting the molecular basis of endosperm development. Although many genes affecting endosperm development have been functionally characterized, our understanding of storage substance accumulation
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Ubiquitin ligase OsRINGzf1 regulates drought resistance by controlling the turnover of OsPIP2;1 Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-19 Shoujun Chen, Kai Xu, Deyan Kong, Lunying Wu, Qian Chen, Xiaosong Ma, Siqi Ma, Tianfei Li, Qi Xie, Hongyan Liu, Lijun Luo
Water is crucial for plant growth and survival. The transcellular water movement is facilitated by aquaporins (AQPs) that rapidly and reversibly modify water permeability. The abundance of AQPs is regulated by its synthesis, redistribution and degradation. However, the molecular mechanism of proteasomal degradation of AQPs remains unclear. Here, we demonstrate that a novel E3 ligase, OsRINGzf1, mediated
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iSoybean: A database for the mutational fingerprints of soybean Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-17 Mengzhu Zhang, Xiyu Zhang, Xinyu Jiang, Lei Qiu, Guanghong Jia, Longfei Wang, Wenxue Ye, Qingxin Song
Soybean (Glycine max L. Merrill) is one of the most important commercial crops worldwide. However, soybean has undergone severe genetic bottlenecks during domestication (Hyten et al., 2006). It is essential to exploit novel sources of genetic diversity and to expand gene pools for soybean improvement. Plant mutation breeding has been widely used by plant breeders to create novel genetic diversity.
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Du13 encodes a C2H2 zinc-finger protein that regulates Wxb pre-mRNA splicing and microRNA biogenesis in rice endosperm Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-13 Yue Cai, Wenwei Zhang, Yushuang Fu, Zhuangzhuang Shan, Jiahuan Xu, Peng Wang, Fei Kong, Jie Jin, Haigang Yan, Xinyuan Ge, Yongxiang Wang, Xiaoman You, Jie Chen, Xin Li, Weiwei Chen, Xingang Chen, Jing Ma, Xiaojie Tang, Jie Zhang, Yiqun Bao, Ling Jiang, Haiyang Wang, Jianmin Wan
Amylose content is a crucial physicochemical property responsible for the eating and cooking quality of rice (Oryza sativa L.) grain and is mainly controlled by the Waxy (Wx) gene. Previous studies have identified several Dull genes that modulate the expression of the Wxb allele in japonica rice by affecting the splicing efficiency of the Wxb pre-mRNA. Here, we uncover dual roles for a novel Dull gene
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A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-13 Sandip M. Kale, Albert W. Schulthess, Sudharsan Padmarasu, Philipp H. G. Boeven, Johannes Schacht, Axel Himmelbach, Burkhard Steuernagel, Brande B. H. Wulff, Jochen C. Reif, Nils Stein, Martin Mascher
A resistance gene atlas is an integral component of the breeder’s arsenal in the fight against evolving pathogens. Thanks to high-throughput sequencing, catalogues of resistance genes can be assembled even in crop species with large and polyploid genomes. Here, we report on capture sequencing and assembly of resistance gene homologs in a diversity panel of 907 winter wheat genotypes comprising ex situ
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CRISPR/Cas9-mediated tetra-allelic mutation of the ‘Green Revolution’ SEMIDWARF-1 (SD-1) gene confers lodging resistance in tef (Eragrostis tef) Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-12 Getu Beyene, Raj Deepika Chauhan, Justin Villmer, Nada Husic, Ning Wang, Endale Gebre, Dejene Girma, Solomon Chanyalew, Kebebew Assefa, Girma Tabor, Malia Gehan, Michael McGrone, Meizhu Yang, Brian Lenderts, Chris Schwartz, Huirong Gao, William Gordon-Kamm, Nigel J. Taylor, Donald J. MacKenzie
Tef is a staple food and a valuable cash crop for millions of people in Ethiopia. Lodging is a major limitation to tef production, and for decades, the development of lodging resistant varieties proved difficult with conventional breeding approaches. We used CRISPR/Cas9 to introduce knockout mutations in the tef orthologue of the rice SEMIDWARF-1 (SD-1) gene to confer semidwarfism and ultimately lodging
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Efficient C-to-G editing in rice using an optimized base editor Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-09 Yifu Tian, Rundong Shen, Zuren Li, Qi Yao, Xuening Zhang, Dating Zhong, Xinhang Tan, Minglei Song, Han Han, Jian-Kang Zhu, Yuming Lu
Cytosine and adenosine base editors (CBE and ABE) have been vigorously developed in plants, but the base conversion types are limited (Ren et al., 2018, 2021; Xu et al., 2021). A new base editor CGBE with a uracil DNA N-glycosylase (UNG) has recently been reported that enables efficient C-to-G editing in mammalian cells (Kurt et al., 2021). In plants, generating more base substitution types can expand
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Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-09 Rutwik Barmukh, Manish Roorkiwal, Vanika Garg, Aamir W. Khan, Liam German, Deepa Jaganathan, Annapurna Chitikineni, Jana Kholova, Himabindu Kudapa, Kaliamoorthy Sivasakthi, Srinivasan Samineni, Sandip M. Kale, Pooran M. Gaur, Someswar Rao Sagurthi, Yoselin Benitez-Alfonso, Rajeev K. Varshney
Chickpea production is vulnerable to drought stress. Identifying the genetic components underlying drought adaptation is crucial for enhancing chickpea productivity. Here, we present the fine mapping and characterization of ‘QTL-hotspot’, a genomic region controlling chickpea growth with positive consequences on crop production under drought. We report that a non-synonymous substitution in the transcription
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The MdBBX22–miR858–MdMYB9/11/12 module regulates proanthocyanidin biosynthesis in apple peel Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-08 Bo Zhang, Hui-Juan Yang, Dong Qu, Zhen-Zhen Zhu, Ya-Zhou Yang, Zheng-Yang Zhao
Proanthocyanidins (PAs) have antioxidant properties and are beneficial to human health. The fruit of apple (Malus × domestica Borkh.), especially the peel, is rich in various flavonoids, such as PAs, and thus is an important source of dietary antioxidants. Previous research on the regulation of PAs in apple has mainly focussed on the transcription level, whereas studies conducted at the post-transcriptional
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Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-06 Yuechao Wu, Qiurong Ren, Zhaohui Zhong, Guanqing Liu, Yangshuo Han, Yu Bao, Li Liu, Shuyue Xiang, Shuo Liu, Xu Tang, Jianping Zhou, Xuelian Zheng, Simon Sretenovic, Tao Zhang, Yiping Qi, Yong Zhang
PAM-relaxed Cas9 nucleases, cytosine base editors and adenine base editors are promising tools for precise genome editing in plants. However, their genome-wide off-target effects are largely unexplored. Here, we conduct whole-genome sequencing (WGS) analyses of transgenic plants edited by xCas9, Cas9-NGv1, Cas9-NG, SpRY, nCas9-NG-PmCDA1, nSpRY-PmCDA1 and nSpRY-ABE8e in rice. Our results reveal that
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Application of developmental regulators to improve in planta or in vitro transformation in plants Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-06 Zhaoyuan Lian, Chi Dinh Nguyen, Li Liu, Guiluan Wang, Jianjun Chen, Songhu Wang, Ganjun Yi, Sandra Wilson, Peggy Ozias-Akins, Haijun Gong, Heqiang Huo
Plant genetic transformation is a crucial step for applying biotechnology such as genome editing to basic and applied plant science research. Its success primarily relies on the efficiency of gene delivery into plant cells and the ability to regenerate transgenic plants. In this study, we have examined the effect of several developmental regulators (DRs), including PLETHORA (PLT5), WOUND INDUCED DEDIFFERENTIATION
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Natural variation of HTH5 from wild rice, Oryza rufipogon Griff., is involved in conferring high-temperature tolerance at the heading stage Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-05 Zhibin Cao, Huiwu Tang, Yaohui Cai, Bohong Zeng, Jialiang Zhao, Xiuying Tang, Ming Lu, Huimin Wang, Xuejing Zhu, Xiaofeng Wu, Linfeng Yuan, Jianlin Wan
Global warming is a major abiotic stress factor, which limit rice production. Exploiting the genetic basis of the natural variation in heat resistance at different reproductive stages among diverse exotic Oryza germplasms can help breeding heat-resistant rice cultivars. Here, we identified a stable quantitative trait locus (QTL) for heat tolerance at the heading stage on chromosome 5 (qHTH5) in O.
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Two high hierarchical regulators, PuMYB40 and PuWRKY75, control the low phosphorus driven adventitious root formation in Populus ussuriensis Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-05 Hanzeng Wang, Solme Pak, Jia Yang, Ye Wu, Wenlong Li, He Feng, Jingli Yang, Hairong Wei, Chenghao Li
Adventitious rooting is an essential biological process in the vegetative propagation of economically important horticultural and forest tree species. It enables utilization of the elite genotypes in breeding programmes and production. Promotion of adventitious root (AR) formation has been associated with starvation of inorganic phosphate and some factors involved in low phosphorus (LP) signalling
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GmTDN1 improves wheat yields by inducing dual tolerance to both drought and low-N stress Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-05 Yongbin Zhou, Jun Liu, Jinkao Guo, Yanxia Wang, Hutai Ji, Xiusheng Chu, Kai Xiao, Xueli Qi, Lin Hu, Hui Li, Mengyun Hu, Wensi Tang, Jiji Yan, Huishu Yan, Xinxuan Bai, Linhao Ge, Mingjie Lyu, Jun Chen, Zhaoshi Xu, Ming Chen, Youzhi Ma
Genetically enhancing drought tolerance and nutrient use efficacy enables sustainable and stable wheat production in drought-prone areas exposed to water shortages and low soil fertility, due to global warming and declining natural resources. In this study, wheat plants, exhibiting improved drought tolerance and N-use efficacy, were developed by introducing GmTDN1, a gene encoding a DREB-like transcription
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Custom-made design of metabolite composition in N. benthamiana leaves using CRISPR activators Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-05 Sara Selma, Neus Sanmartín, Ana Espinosa-Ruiz, Silvia Gianoglio, Maria Pilar Lopez-Gresa, Marta Vázquez-Vilar, Victor Flors, Antonio Granell, Diego Orzaez
Transcriptional regulators based on CRISPR architecture expand our ability to reprogramme endogenous gene expression in plants. One of their potential applications is the customization of plant metabolome through the activation of selected enzymes in a given metabolic pathway. Using the previously described multiplexable CRISPR activator dCasEV2.1, we assayed the selective enrichment in Nicotiana benthamiana
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Function deficiency of GhOMT1 causes anthocyanidins over-accumulation and diversifies fibre colours in cotton (Gossypium hirsutum) Plant Biotech. J. (IF 9.803) Pub Date : 2022-05-03 Liping Ke, Dongliang Yu, Hongli Zheng, Yihan Xu, Yuqing Wu, Junye Jiao, Xiaoli Wang, Jun Mei, Fangfang Cai, Yanyan Zhao, Jie Sun, Xianlong Zhang, Yuqiang Sun
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JULGI-mediated increment in phloem transport capacity relates to fruit yield in tomato Plant Biotech. J. (IF 9.803) Pub Date : 2022-04-28 Hoyoung Nam, Aarti Gupta, Heejae Nam, Seungchul Lee, Hyun Seob Cho, Chanyoung Park, Soyoung Park, Soon Ju Park, Ildoo Hwang
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Overexpression of cytoplasmic C4 Flaveria bidentis carbonic anhydrase in C3 Arabidopsis thaliana increases amino acids, photosynthetic potential, and biomass Plant Biotech. J. (IF 9.803) Pub Date : 2022-04-25 Deepika Kandoi, Kamal Ruhil, Govindjee Govindjee, Baishnab C. Tripathy
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Time-resolved fluorescent microsphere lateral flow biosensors for rapid detection of Candidatus Liberibacter asiaticus Plant Biotech. J. (IF 9.803) Pub Date : 2022-04-21 Cong Su, Fang Ding, Wenjing Wang, Zhiyong Song, Qurban Ali, Mubassir Ali, Ni Hong, Guoping Wang, Heyou Han
Citrus Huanglongbing (HLB) is one of the most devastating diseases causing unprecedented global economic losses and constituting a major hindrance to the development of the citrus industry. ‘Ca. Liberibacter asiaticus’ (CLas) is the most prevalent strain. Almost all commercial citrus cultivars are sensitive to it, and no curable method is available. Accurate plant disease diagnoses and rapid detection
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R gene triplication confers European fodder turnip with improved clubroot resistance Plant Biotech. J. (IF 9.803) Pub Date : 2022-04-21 Zhiquan Yang, Yingfen Jiang, Jianfang Gong, Qian Li, Bicheng Dun, Dongxu Liu, Feifan Yin, Lei Yuan, Xueqing Zhou, Huiying Wang, Jing Wang, Zongxiang Zhan, Nadil Shah, Chinedu Charles Nwafor, Yuanwei Zhou, Peng Chen, Li Zhu, Shisheng Li, Bingrui Wang, Jun Xiang, Yongming Zhou, Zaiyun Li, Zhongyun Piao, Qingyong Yang, Chunyu Zhang
Clubroot is one of the most important diseases for many important cruciferous vegetables and oilseed crops worldwide. Different clubroot resistance (CR) loci have been identified from only limited species in Brassica, making it difficult to compare and utilize these loci. European fodder turnip ECD04 is considered one of the most valuable resources for CR breeding. To explore the genetic and evolutionary
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The plant epitranscriptome: revisiting pseudouridine and 2′-O-methyl RNA modifications Plant Biotech. J. (IF 9.803) Pub Date : 2022-04-21 Muthusamy Ramakrishnan, K. Shanmugha Rajan, Sileesh Mullasseri, Sarin Palakkal, Krishnan Kalpana, Anket Sharma, Mingbing Zhou, Kunnummal Kurungara Vinod, Subbiah Ramasamy, Qiang Wei
There is growing evidence that post-transcriptional RNA modifications are highly dynamic and can be used to improve crop production. Although more than 172 unique types of RNA modifications have been identified throughout the kingdom of life, we are yet to leverage upon the understanding to optimize RNA modifications in crops to improve productivity. The contributions of internal mRNA modifications
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Riboflavin integrates cellular energetics and cell cycle to regulate maize seed development Plant Biotech. J. (IF 9.803) Pub Date : 2022-04-14 Qiuzhen Tian, Gang Wang, Xuexia Ma, Qingwen Shen, Mengli Ding, Xueyi Yang, Xiaoli Luo, Rongrong Li, Zhenghui Wang, Xiangyang Wang, Zhiyuan Fu, Qinghua Yang, Jihua Tang, Guifeng Wang
Riboflavin is the precursor of essential cofactors for diverse metabolic processes. Unlike animals, plants can de novo produce riboflavin through an ancestrally conserved pathway, like bacteria and fungi. However, the mechanism by which riboflavin regulates seed development is poorly understood. Here, we report a novel maize (Zea mays L.) opaque mutant o18, which displays an increase in lysine accumulation
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The OsEIL1-OsERF115-target gene regulatory module controls grain size and weight in rice Plant Biotech. J. (IF 9.803) Pub Date : 2022-04-11 Chang Liu, Tian Ma, Dingyang Yuan, Yang Zhou, Yan Long, Ziwen Li, Zhenying Dong, Meijuan Duan, Dong Yu, Yizhi Jing, Xiaoyue Bai, Yanbo Wang, Quancan Hou, Shuangshuang Liu, Jin-Song Zhang, Shou-Yi Chen, Dayong Li, Xue Liu, Zhikang Li, Wensheng Wang, Jinping Li, Xun Wei, Biao Ma, Xiangyuan Wan
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SlMIR164A regulates fruit ripening and quality by controlling SlNAM2 and SlNAM3 in tomato Plant Biotech. J. (IF 9.803) Pub Date : 2022-04-11 Dongbo Lin, Xiaoen Zhu, Binglin Qi, Zhong Gao, Peng Tian, Ziwei Li, Zeteng Lin, Yongxia Zhang, Tengbo Huang
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PPVED: A machine learning tool for predicting the effect of single amino acid substitution on protein function in plants Plant Biotech. J. (IF 9.803) Pub Date : 2022-04-10 Xiangjian Gou, Xuanjun Feng, Haoran Shi, Tingting Guo, Rongqian Xie, Yaxi Liu, Qi Wang, Hongxiang Li, Banglie Yang, Lixue Chen, Yanli Lu
Single amino acid substitution (SAAS) produces the most common variant of protein function change under physiological conditions. As the number of SAAS events in plants has increased exponentially, an effective prediction tool is required to help identify and distinguish functional SAASs from the whole genome as either potentially causal traits or as variants. Here, we constructed a plant SAAS database
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Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non-polyadenylated flower lncRNAs in chickpea Plant Biotech. J. (IF 9.803) Pub Date : 2022-04-08 Mayank Kaashyap, Sukhjiwan Kaur, Rebecca Ford, David Edwards, Kadambot H.M. Siddique, Rajeev K. Varshney, Nitin Mantri
Salinity severely affects the yield of chickpea. Understanding the role of lncRNAs can shed light on chickpea salt tolerance mechanisms. However, because lncRNAs are encoded by multiple sites within the genome, their classification to reveal functional versatility at the transcriptional and the post-transcriptional levels is challenging. To address this, we deep sequenced 24 salt-challenged flower
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Genomes of single- and double-petal jasmines (Jasminum sambac) provide insights into their divergence time and structural variations Plant Biotech. J. (IF 9.803) Pub Date : 2022-04-03 Pengjie Wang, Jingping Fang, Hongzheng Lin, Wenwen Yang, Jiaxin Yu, Yaping Hong, Mengwei Jiang, Mengya Gu, Qinchang Chen, Yucheng Zheng, ZhenYang Liao, Guixin Chen, Jiangfan Yang, Shan Jin, Xingtan Zhang, Naixing Ye
Jasmine Jasminum sambac (L.) Aiton belongs to the genus Jasminum of the Oleaceae family. It is commercially cultivated worldwide for its sweetly fragrant flowers, and it is widely used in the fields of food, medicine and industry. Jasmine flowers are used to extract essential oils on a commercial scale and make jasmine tea, a well-known Chinese tea produced from tea leaves and fresh jasmine flowers
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Development and optimization of a Barley stripe mosaic virus-mediated gene editing system to improve Fusarium head blight resistance in wheat Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-29 Hui Chen, Zhenqi Su, Bin Tian, Yang Liu, Yuhui Pang, Volodymyr Kavetskyi, Harold N. Trick, Guihua Bai
Fusarium head blight (FHB) caused by Fusarium graminearum is a destructive wheat (Triticum aestivum) disease worldwide (Bai et al., 2018). Previously, we cloned Fhb1 (TaHRC) encoding a histidine-rich calcium-binding protein and demonstrated that a large deletion near the start codon of TaHRC reduced FHB susceptibility (Su et al., 2019), which indicates that wheat carries susceptibility genes (S-genes)
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Chromosome-scale reference genome provides insights into the genetic origin and grafting-mediated stress tolerance of Malus prunifolia Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-29 Zhongxing Li, Lun Wang, Jieqiang He, Xuewei Li, Nan Hou, Junxing Guo, Chundong Niu, Chaoshuo Li, Shengjun Liu, Jidi Xu, Yinpeng Xie, Dehui Zhang, Xiaoxia Shen, Liyuan Lu, Dali Geng, Pengxiang Chen, Lijuan Jiang, Liping Wang, Haiyan Li, Mickael Malnoy, Cecilia Deng, Yangjun Zou, Cuiying Li, Xiangqiang Zhan, Yang Dong, Michitaka Notaguchi, Fengwang Ma, Qiang Xu, Qingmei Guan
Grafting, an ancient horticultural cultivation technique, is essential for commercial apple (Malus × domestica Borkh.) production. M. prunifolia ‘Fupingqiuzi’ is used as a common apple rootstock due to its known tolerances to abiotic and biotic stresses. However, the genetic origin and evolutionary history of M. prunifolia are largely unknown, as are the molecular bases underlying its innate stress
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Brassica napus genes Rlm4 and Rlm7, conferring resistance to Leptosphaeria maculans, are alleles of the Rlm9 wall-associated kinase-like resistance locus Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-25 Parham Haddadi, Nicholas J. Larkan, Angela Van deWouw, Yueqi Zhang, Ting Xiang Neik, Elena Beynon, Philipp Bayer, Dave Edwards, Jacqueline Batley, Mohammad Hossein Borhan
Plant cell surface receptors are at the forefront of defence against pathogens, involved in pathogen sensing through the detection of conserved molecules named pathogen-associated molecular patterns (PAMP) and highly variable pathogen virulence (effector) proteins. The recently reported Brassica napus (canola, oilseed rape) disease resistance gene Rlm9 encodes a wall-associated kinase-like (WAKL) receptor
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Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-25 Pavla Navrátilová, Helena Toegelová, Zuzana Tulpová, Yi-Tzu Kuo, Nils Stein, Jaroslav Doležel, Andreas Houben, Hana Šimková, Martin Mascher
The first gapless, telomere-to-telomere (T2T) sequence assemblies of plant chromosomes were reported recently. However, sequence assemblies of most plant genomes remain fragmented. Only recent breakthroughs in accurate long-read sequencing have made it possible to achieve highly contiguous sequence assemblies with a few tens of contigs per chromosome, that is a number small enough to allow for a systematic
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De novo phasing resolves haplotype sequences in complex plant genomes Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-25 Ji-Yoon Guk, Min-Jeong Jang, Jin-Wook Choi, Yeon Mi Lee, Seungill Kim
Genome phasing is a recently developed assembly method that separates heterozygous eukaryotic genomic regions and builds haplotype-resolved assemblies. Because differences between haplotypes are ignored in most published de novo genomes, assemblies are available as consensus genomes consisting of haplotype mixtures, thus increasing the need for genome phasing. Here, we review the operating principles
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CsMYB184 regulates caffeine biosynthesis in tea plants Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-25 Penghui Li, Zhili Ye, Jiamin Fu, Yujie Xu, Yihua Shen, Yanrui Zhang, Dingkun Tang, Ping Li, Hao Zuo, Wei Tong, Shucai Wang, Alisdair R. Fernie, Jian Zhao
As the most well-known and globally consumed central nervous system stimulant, caffeine is a purine alkaloid natural product usually derived from tea and coffee. Caffeine has a wide range of health benefits on the human body, and plays crucial roles in pollination, resistance to herbivore attacks, and pathogen infections in plants (Zhao et al., 2020). While caffeine biosynthetic pathways have been
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Plant-based expression and characterization of SARS-CoV-2 virus-like particles presenting a native spike protein Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-24 Jae-Wan Jung, Gergana Zahmanova, Ivan Minkov, George P. Lomonossoff
We have investigated the use of transient expression to produce virus-like particles (VLPs) of severe acute respiratory syndrome coronavirus 2, the causative agent of COVID-19, in Nicotiana benthamiana. Expression of a native form of the spike (S) protein, either alone or in combination with the envelope (E) and membrane (M) proteins, all of which were directed to the plant membranes via their native
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The PGS1 basic helix-loop-helix protein regulates Fl3 to impact seed growth and grain yield in cereals Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-22 Xiaojiang Guo, Yuxin Fu, Yuh-Ru Julie Lee, Mawsheng Chern, Maolian Li, Mengping Cheng, Huixue Dong, Zhongwei Yuan, Lixuan Gui, Junjie Yin, Hai Qing, Chengbi Zhang, Zhien Pu, Yujiao Liu, Weitao Li, Wei Li, Pengfei Qi, Guoyue Chen, Qiantao Jiang, Jian Ma, Xuewei Chen, Yuming Wei, Youliang Zheng, Yongrui Wu, Bo Liu, Jirui Wang
Plant transcription factors (TFs), such as basic helix-loop-helix (bHLH) and AT-rich zinc-binding proteins (PLATZ), play critical roles in regulating the expression of developmental genes in cereals. We identified the bHLH protein TaPGS1 (T. aestivum Positive Regulator of Grain Size 1) specifically expressed in the seeds at 5–20 days post-anthesis in wheat. TaPGS1 was ectopically overexpressed (OE)
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OsHIPL1, a hedgehog-interacting protein-like 1 protein, increases seed vigour in rice Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-22 Ying He, Shanshan Chen, Kexin Liu, Yongji Chen, Yanhao Cheng, Peng Zeng, Peiwen Zhu, Ting Xie, Sunlu Chen, Hongsheng Zhang, Jinping Cheng
The cultivation of rice varieties with high seed vigour is vital for the direct seeding of rice, and the molecular basis of regulation of seed vigour remains elusive. Here, we cloned a new gene OsHIPL1, which encodes hedgehog-interacting protein-like 1 protein as a causal gene of the major QTL qSV3 for rice seed vigour. OsHIPL1 was mainly localized in the plasma membrane and nucleus. RNA sequencing
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Pore-C simultaneously captures genome-wide multi-way chromatin interaction and associated DNA methylation status in Arabidopsis Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-21 Zhuowen Li, Yanping Long, Yiming Yu, Fei Zhang, Hong Zhang, Zhijian Liu, Jinbu Jia, Weipeng Mo, Simon Zhongyuan Tian, Meizhen Zheng, Jixian Zhai
Dear editor, In the past decade, genome-wide characterization of the three-dimensional chromatin structure using high-throughput methods has greatly advanced our knowledge in plant genome architecture (Liu and Weigel, 2015; Ouyang et al., 2020). However, due to the limitation of Illumina paired-end short read, most contacts obtained by Hi-C/ChIA-PET are pairwise, and interactions among three or more
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Expression of AtWRI1 and AtDGAT1 during soybean embryo development influences oil and carbohydrate metabolism Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-20 Cintia Lucía Arias, Truyen Quach, Tu Huynh, Hanh Nguyen, Ademar Moretti, Yu Shi, Ming Guo, Amira Rasoul, Kyujung Van, Leah McHale, Tom Elmo Clemente, Ana Paula Alonso, Chi Zhang
Soybean oil is one of the most consumed vegetable oils worldwide. Genetic improvement of its concentration in seeds has been historically pursued due to its direct association with its market value. Engineering attempts aiming to increase soybean seed oil presented different degrees of success that varied with the genetic design and the specific variety considered. Understanding the embryo’s responses
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Host-induced silencing of a nematode chitin synthase gene enhances resistance of soybeans to both pathogenic Heterodera glycines and Fusarium oxysporum Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-17 Lingan Kong, Xue Shi, Deng Chen, Nan Yang, Changfa Yin, Jun Yang, Gaofeng Wang, Wenkun Huang, Huan Peng, Deliang Peng, Shiming Liu
Soybean cyst nematode (SCN), Heterodera glycines, is a devastating pathogen in soybean worldwide, causing huge yield losses annually. Host-induced gene silencing (HIGS) has shown potentials to control plant parasitic nematodes by generating transgenic plants carrying hairpin constructs against nematode target genes (Chaudhary et al., 2019; Li et al., 2010; Mani et al., 2020; Shivakumara et al., 2017;
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Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-12 Xu Cai, Runmao Lin, Jianli Liang, Graham J. King, Jian Wu, Xiaowu Wang
Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan-genome analysis combined with population-scale resequencing, and we adopt
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CRISPR/Cas9-mediated P-CR domain-specific engineering of CESA4 heterodimerization capacity alters cell wall architecture and improves saccharification efficiency in poplar Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-09 Shahnoush Nayeri, Bahram Baghban Kohnehrouz, Asadollah Ahmadikhah, Nasser Mahna
Cellulose is the most abundant unique biopolymer in nature with widespread applications in bioenergy and high-value bioproducts. The large transmembrane-localized cellulose synthase (CESA) complexes (CSCs) play a pivotal role in the biosynthesis and orientation of the para-crystalline cellulose microfibrils during secondary cell wall (SCW) deposition. However, the hub CESA subunit with high potential
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Increasing floral visitation and hybrid seed production mediated by beauty mark in Gossypium hirsutum Plant Biotech. J. (IF 9.803) Pub Date : 2022-03-09 Muhammad Ali Abid, Yunxiao Wei, Zhigang Meng, Yuan Wang, Yulu Ye, Yanan Wang, Haiyan He, Qi Zhou, Yanyan Li, Peilin Wang, Xianggan Li, Liuhua Yan, Waqas Malik, Sandui Guo, Chengcai Chu, Rui Zhang, Chengzhen Liang
Hybrid crop varieties have been repeatedly demonstrated to produce significantly higher yields than their parental lines; however, the low efficiency and high cost of hybrid seed production has limited the broad exploitation of heterosis for cotton production. One option for increasing the yield of hybrid seed is to improve pollination efficiency by insect pollinators. Here, we report the molecular