1
|
Guo Y, Yao L, Chen X, Xu X, Sang YL, Liu LJ. The transcription factor PagLBD4 represses cell differentiation and secondary cell wall biosynthesis in Populus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108924. [PMID: 38991593 DOI: 10.1016/j.plaphy.2024.108924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/20/2024] [Accepted: 07/07/2024] [Indexed: 07/13/2024]
Abstract
LBD (LATERAL ORGAN BOUNDARIES DOMAIN) transcription factors are key regulators of plant growth and development. In this study, we functionally characterized the PagLBD4 gene in Populus (Populus alba × Populus glandulosa). Overexpression of PagLBD4 (PagLBD4OE) significantly repressed secondary xylem differentiation and secondary cell wall (SCW) deposition, while CRISPR/Cas9-mediated PagLBD4 knockout (PagLBD4KO) significantly increased secondary xylem differentiation and SCW deposition. Consistent with the functional analysis, gene expression analysis revealed that SCW biosynthesis pathways were significantly down-regulated in PagLBD4OE plants but up-regulated in PagLBD4KO plants. We also performed DNA affinity purification followed by sequencing (DAP-seq) to identify genes bound by PagLBD4. Integration of RNA sequencing (RNA-seq) and DAP-seq data identified 263 putative direct target genes (DTGs) of PagLBD4, including important regulatory genes for SCW biosynthesis, such as PagMYB103 and PagIRX12. Together, our results demonstrated that PagLBD4 is a repressor of secondary xylem differentiation and SCW biosynthesis in Populus, which possibly lead to the dramatic growth repression in PagLBD4OE plants.
Collapse
Affiliation(s)
- Ying Guo
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China
| | - Lijuan Yao
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China
| | - Xiaoman Chen
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China
| | - Xiaoqi Xu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China
| | - Ya Lin Sang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China.
| | - Li-Jun Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Taian, 271018, China.
| |
Collapse
|
2
|
Marciniak K, Przedniczek K, Kęsy J, Święcicki W, Kopcewicz J. The development of yellow lupin anthers depends on the relationship between jasmonic acid and indole-3-acetic acid. PHYSIOLOGIA PLANTARUM 2024; 176:e14385. [PMID: 38956782 DOI: 10.1111/ppl.14385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 07/04/2024]
Abstract
The main purpose of this study was to demonstrate that the course of anther development, including post-meiotic maturation, dehiscence and senescence, is ensured by the interdependencies between jasmonic acid (JA) and indole-3-acetic acid (IAA) in yellow lupin (Lupinus luteus L.). The concentration of JA peaked during anther dehiscence when IAA level was low, whereas the inverse relationship was specific to anther senescence. Cellular and tissue localization of JA and IAA, in conjunction with broad expression profile for genes involved in biosynthesis, signalling, response, and homeostasis under different conditions, allowed to complete and define the role of studied phytohormones during late anther development, as well as predict events triggered by them. The development/degeneration of septum and anther wall cells, dehydration of epidermis, and rupture of stomium may involve JA signalling, while the formation of secondary thickening in endothecial cell walls is rather JA independent. The IAA is involved in programmed cell death (PCD)-associated processes during anther senescence but does not exclude its participation in the anther dehiscence processes, mainly related to cell disintegration and degeneration. A detailed understanding of these multistage processes, especially at the level of phytohormonal interplay, can contribute to the effective control of male fertility, potentially revolutionizing the breeding of L. luteus.
Collapse
Affiliation(s)
- Katarzyna Marciniak
- Faculty of Biological and Veterinary Sciences, Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Toruń, Poland
| | - Krzysztof Przedniczek
- Faculty of Biological and Veterinary Sciences, Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Toruń, Poland
| | - Jacek Kęsy
- Faculty of Biological and Veterinary Sciences, Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Toruń, Poland
| | | | - Jan Kopcewicz
- Faculty of Biological and Veterinary Sciences, Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Toruń, Poland
| |
Collapse
|
3
|
Cui Y, Su Y, Bian J, Han X, Guo H, Yang Z, Chen Y, Li L, Li T, Deng XW, Liu X. Single-nucleus RNA and ATAC sequencing analyses provide molecular insights into early pod development of peanut fruit. PLANT COMMUNICATIONS 2024:100979. [PMID: 38794796 DOI: 10.1016/j.xplc.2024.100979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/31/2024] [Accepted: 05/22/2024] [Indexed: 05/26/2024]
Abstract
Peanut (Arachis hypogaea L.) is an important leguminous oil and economic crop that produces flowers aboveground and fruits belowground. Subterranean fruit-pod development, which significantly affects peanut production, involves complex molecular mechanisms that likely require the coordinated regulation of multiple genes in different tissues. To investigate the molecular mechanisms that underlie peanut fruit-pod development, we characterized the anatomical features of early fruit-pod development and integrated single-nucleus RNA-sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) data at the single-cell level. We identified distinct cell types, such as meristem, embryo, vascular tissue, cuticular layer, and stele cells within the shell wall. These specific cell types were used to examine potential molecular changes unique to each cell type during pivotal stages of fruit-pod development. snRNA-seq analyses of differentially expressed genes revealed cell-type-specific insights that were not previously obtainable from transcriptome analyses of bulk RNA. For instance, we identified MADS-box genes that contributes to the formation of parenchyma cells and gravity-related genes that are present in the vascular cells, indicating an essential role for the vascular cells in peg gravitropism. Overall, our single-nucleus analysis provides comprehensive and novel information on specific cell types, gene expression, and chromatin accessibility during the early stages of fruit-pod development. This information will enhance our understanding of the mechanisms that underlie fruit-pod development in peanut and contribute to efforts aimed at improving peanut production.
Collapse
Affiliation(s)
- Yuanyuan Cui
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Yanning Su
- School of Advanced Agricultural Sciences, Peking University, Beijing 100083, China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Xue Han
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Haosong Guo
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences, Peking University, Beijing 100083, China
| | - Zhiyuan Yang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Yijun Chen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Lihui Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Tianyu Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences, Peking University, Beijing 100083, China
| | - Xiaoqin Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Shandong 261325, China.
| |
Collapse
|
4
|
Cong L, Shi YK, Gao XY, Zhao XF, Zhang HQ, Zhou FL, Zhang HJ, Ma BQ, Zhai R, Yang CQ, Wang ZG, Ma FW, Xu LF. Transcription factor PbNAC71 regulates xylem and vessel development to control plant height. PLANT PHYSIOLOGY 2024; 195:395-409. [PMID: 38198215 DOI: 10.1093/plphys/kiae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/13/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
Dwarfism is an important agronomic trait in fruit breeding programs. However, the germplasm resources required to generate dwarf pear (Pyrus spp.) varieties are limited. Moreover, the mechanisms underlying dwarfism remain unclear. In this study, "Yunnan" quince (Cydonia oblonga Mill.) had a dwarfing effect on "Zaosu" pear. Additionally, the dwarfism-related NAC transcription factor gene PbNAC71 was isolated from pear trees comprising "Zaosu" (scion) grafted onto "Yunnan" quince (rootstock). Transgenic Nicotiana benthamiana and pear OHF-333 (Pyrus communis) plants overexpressing PbNAC71 exhibited dwarfism, with a substantially smaller xylem and vessel area relative to the wild-type controls. Yeast one-hybrid, dual-luciferase, chromatin immunoprecipitation-qPCR, and electrophoretic mobility shift assays indicated that PbNAC71 downregulates PbWalls are thin 1 expression by binding to NAC-binding elements in its promoter. Yeast two-hybrid assays showed that PbNAC71 interacts with the E3 ubiquitin ligase PbRING finger protein 217 (PbRNF217). Furthermore, PbRNF217 promotes the ubiquitin-mediated degradation of PbNAC71 by the 26S proteasome, thereby regulating plant height as well as xylem and vessel development. Our findings reveal a mechanism underlying pear dwarfism and expand our understanding of the molecular basis of dwarfism in woody plants.
Collapse
Affiliation(s)
- Liu Cong
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Yi-Ke Shi
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xin-Yi Gao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xiao-Fei Zhao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Hai-Qi Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Feng-Li Zhou
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Hong-Juan Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Bai-Quan Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Rui Zhai
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Cheng-Quan Yang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Zhi-Gang Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Feng-Wang Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Ling-Fei Xu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| |
Collapse
|
5
|
Zhang ZB, Xiong T, Wang XJ, Chen YR, Wang JL, Guo CL, Ye ZY. Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae. PLoS One 2024; 19:e0302292. [PMID: 38626181 PMCID: PMC11020792 DOI: 10.1371/journal.pone.0302292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/01/2024] [Indexed: 04/18/2024] Open
Abstract
Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in Brassicaceae, however, no comprehensive evolutionary analysis of DUF1216 genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in Brassicaceae. Totally 284 DUF1216 genes were identified in 27 Brassicaceae species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that DUF1216 genes within the same subfamily exhibited similar intron/exon patterns and motif composition. The majority members of DUF1216 genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of DUF1216 genes in Brassica oleracea, Brassica juncea, Brassica napus, Lepidium meyneii, and Brassica carinata, while in Arabidopsis thaliana and Capsella rubella, tandem duplication plays a major role in the expansion of the DUF1216 gene family. The analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios for DUF1216 paralogous indicated that most of gene pairs underwent purifying selection. DUF1216 genes displayed a specifically high expression in reproductive tissues in most Brassicaceae species, while its expression in Brassica juncea was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of DUF1216 members in Brassicaceae, which provides a foundation for future functional analysis.
Collapse
Affiliation(s)
- Zai-Bao Zhang
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
| | - Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Xiao-Jia Wang
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Yu-Rui Chen
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Jing-Lei Wang
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Cong-Li Guo
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Zi-Yi Ye
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
| |
Collapse
|
6
|
Carvalho-Madrigal S, Sanín MJ. The role of introgressive hybridization in shaping the geographically isolated gene pools of wax palm populations (genus Ceroxylon). Mol Phylogenet Evol 2024; 193:108013. [PMID: 38195012 DOI: 10.1016/j.ympev.2024.108013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/22/2023] [Accepted: 01/06/2024] [Indexed: 01/11/2024]
Abstract
The speciation continuum is the process by which genetic groups diverge until they reach reproductive isolation. It has become common in the literature to show that this process is gradual and flickering, with possibly many instances of secondary contact and introgression after divergence has started. The level of divergence might vary among genomic regions due to, among others, the different forces and roles of selection played by the shared regions. Through hybrid capture, we sequenced ca. 4,000 nuclear regions in populations of six species of wax palms, five of which form a monophyletic group (genus Ceroxylon, Arecaceae: Ceroxyloideae). We show that in this group, the different populations show varying degrees of introgressive hybridization, and two of them are backcrosses of the other three 'pure' species. This is particularly interesting because these three species are dioecious, have a shared main pollinator, and have slightly overlapping reproductive seasons but highly divergent morphologies. Our work supports shows wax palms diverge under positive and background selection in allopatry, and hybridize due to secondary contact and inefficient reproductive barriers, which sustain genetic diversity. Introgressed regions are generally not under positive selection. Peripheral populations are backcrosses of other species; thus, introgressive hybridization is likely modulated by demographic effects rather than selective pressures. In general, these species might function as an 'evolutionary syngameon' where expanding, peripheral, small, and isolated populations maintain diversity by crossing with available individuals of other wax palms. In the Andean context, species can benefit from gained variation from a second taxon or the enhancement of population sizes by recreating a common genetic pool.
Collapse
Affiliation(s)
| | - María José Sanín
- School of Mathematical and Natural Sciences, Arizona State University, West Valley Campus, Glendale, United States.
| |
Collapse
|
7
|
Yao X, Zhang G, Zhang G, Sun Q, Liu C, Chu J, Jing Y, Niu S, Fu C, Lew TTS, Lin J, Li X. PagARGOS promotes low-lignin wood formation in poplar. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38492213 DOI: 10.1111/pbi.14339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024]
Abstract
Wood formation, which occurs mainly through secondary xylem development, is important not only for supplying raw material for the 'ligno-chemical' industry but also for driving the storage of carbon. However, the complex mechanisms underlying the promotion of xylem formation remain to be elucidated. Here, we found that overexpression of Auxin-Regulated Gene involved in Organ Size (ARGOS) in hybrid poplar 84 K (Populus alba × Populus tremula var. glandulosa) enlarged organ size. In particular, PagARGOS promoted secondary growth of stems with increased xylem formation. To gain further insight into how PagARGOS regulates xylem development, we further carried out yeast two-hybrid screening and identified that the auxin transporter WALLS ARE THIN1 (WAT1) interacts with PagARGOS. Overexpression of PagARGOS up-regulated WAT1, activating a downstream auxin response promoting cambial cell division and xylem differentiation for wood formation. Moreover, overexpressing PagARGOS caused not only higher wood yield but also lower lignin content compared with wild-type controls. PagARGOS is therefore a potential candidate gene for engineering fast-growing and low-lignin trees with improved biomass production.
Collapse
Affiliation(s)
- Xiaomin Yao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Guifang Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Geng Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Qian Sun
- Beijing Key Laboratory of Lignocellulosic Chemistry, College of Materials Science and Technology, Beijing Forestry University, Beijing, China
| | - Cuimei Liu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanping Jing
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Shihui Niu
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Tedrick Thomas Salim Lew
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Jinxing Lin
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaojuan Li
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| |
Collapse
|
8
|
Jardim-Messeder D, Cassol D, Souza-Vieira Y, Ehlers Loureiro M, Girke T, Boroni M, Lopes Corrêa R, Coelho A, Sachetto-Martins G. Genome-wide identification of core components of ABA signaling and transcriptome analysis reveals gene circuits involved in castor bean (Ricinus communis L.) response to drought. Gene 2023; 883:147668. [PMID: 37500024 DOI: 10.1016/j.gene.2023.147668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Castor bean (Ricinus communis L.) can withstand long periods of water deficit and high temperatures, and therefore has been recognized as a drought-resistant plant species, allowing the study of gene networks involved in drought response and tolerance. The identification of genes networks related to drought response in this plant may yield important information in the characterization of molecular mechanisms correlating changes in the gene expression with the physiological adaptation processes. In this context, gene families related to abscisic acid (ABA) signaling play a crucial role in developmental and environmental adaptation processes of plants to drought stress. However, the families that function as the core components of ABA signaling, as well as genes networks related to drought response, are not well understood in castor bean. In this study 7 RcPYL, 63 RcPP2C, and 6 RcSnRK2 genes were identified in castor bean genome, which was further supported by chromosomal distribution, gene structure, evolutionary relationships, and conserved motif analyses. The castor bean general expression profile was investigated by RNAseq in root and leaf tissues in response to drought stress. These analyses allowed the identification of genes differentially expressed, including genes from the ABA signaling core, genes related to photosynthesis, cell wall, energy transduction, antioxidant response, and transcription factors. These analyses provide new insights into the core components of ABA signaling in castor bean, allow the identification of several molecular responses associated with the high physiological adaptation of castor bean to drought stress, and contribute to the identification of candidate genes for genetic improvement.
Collapse
Affiliation(s)
- Douglas Jardim-Messeder
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Daniela Cassol
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Institute for Integrative Genome Biology, Genomics Building, University of California, Riverside, CA 92521, USA
| | - Ygor Souza-Vieira
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Thomas Girke
- Institute for Integrative Genome Biology, Genomics Building, University of California, Riverside, CA 92521, USA
| | - Mariana Boroni
- Bioinformatics and Computational Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro, Brazil
| | - Régis Lopes Corrêa
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Coelho
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | | |
Collapse
|
9
|
Sheng Y, Yao X, Liu L, Yu C, Wang K, Wang K, Chang J, Chen J, Cao Y. Transcriptomic Time-Course Sequencing: Insights into the Cell Wall Macromolecule-Mediated Fruit Dehiscence during Ripening in Camellia oleifera. PLANTS (BASEL, SWITZERLAND) 2023; 12:3314. [PMID: 37765478 PMCID: PMC10535178 DOI: 10.3390/plants12183314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/27/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023]
Abstract
Camellia oleifera (C. oleifera), one of the world's four major edible woody oil crops, has been widely planted in southern China's subtropical region for the extremely high nutritional and health benefits of its seed oil. Timing and synchronization of fruit dehiscence are critical factors influencing the oil output and quality, as well as the efficiency and cost of harvesting C. oleifera, yet they extremely lack attention. To gain an understanding of the molecular basis underlying the dehiscence of C. oleifera fruit, we sampled pericarp-replum tissues containing dehiscence zones from fruits at different developmental stages and performed time-series transcriptomic sequencing and analysis for the first time. Statistical and GO enrichment analysis of differentially expressed genes revealed that drastic transcriptional changes occurred over the last short sampling interval (4 days, 18th-22nd October), which directed functional classifications link to cell wall and cell wall macromolecule activity. WGCNA further showed that factors controlling cell wall modification, including endo-1,3;1,4-beta-D-glucanase, WAT1-like protein 37, LRR receptor-like serine/threonine-protein kinase, and cellulose synthase A catalytic subunit, were identified as core members of the co-expression network of the last stage highly related modules. Furthermore, in these modules, we also noted genes that were annotated as coding for polygalacturonase and pectinesterase, two pectinases that were expected to be major players in cell separation during dehiscence. qRT-PCR further confirmed the expression profiles of these cell wall modification relating factors, which possessed a special high transcriptional abundance at the final stage. These results suggested the cell wall associated cell separation, one of the essential processes downstream of fruit dehiscence, happened in dehiscing fruit of C. oleifera during ripening. Hydrolases acting on cell wall components are good candidates for signal mediating dehiscence of C. oleifera fruit. In conclusion, our analysis provided insights into the cell wall macromolecule-mediated fruit dehiscence during ripening in C. oleifera.
Collapse
Affiliation(s)
- Yu Sheng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.S.); (L.L.)
- Quzhou Doctoral Innovation Workstation, Changshan Country Oil Tea Industry Development Center, Quzhou 323900, China; (C.Y.); (K.W.)
| | - Xiaohua Yao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.S.); (L.L.)
| | - Linxiu Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.S.); (L.L.)
- Faculty of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Chunlian Yu
- Quzhou Doctoral Innovation Workstation, Changshan Country Oil Tea Industry Development Center, Quzhou 323900, China; (C.Y.); (K.W.)
| | - Kunxi Wang
- Quzhou Doctoral Innovation Workstation, Changshan Country Oil Tea Industry Development Center, Quzhou 323900, China; (C.Y.); (K.W.)
| | - Kailiang Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.S.); (L.L.)
| | - Jun Chang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.S.); (L.L.)
| | - Juanjuan Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.S.); (L.L.)
- Faculty of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yongqing Cao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (Y.S.); (L.L.)
| |
Collapse
|
10
|
Liang X, Li Q, Cao L, Du X, Qiang J, Hou J, Li X, Zhu H, Yang S, Liu D, Zhu L, Yang L, Wang P, Hu J. Natural allelic variation in the EamA-like transporter, CmSN, is associated with fruit skin netting in melon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:192. [PMID: 37603118 DOI: 10.1007/s00122-023-04443-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
KEY MESSAGE A SNP mutation in CmSN, encoding an EamA-like transporter, is responsible for fruit skin netting in melon. In maturing melon (Cucumis melo L.), the rind becomes reticulated or netted, a unique characteristic that dramatically changes the appearance of the fruit. However, little is known about the molecular basis of fruit skin netting formation in this important cucurbit crop. Here, we conducted map-based cloning of a skin netting (CmSN) locus using segregating populations derived from the cross between the smooth-fruit line H906 and the netted-fruit line H581. The results showed that CmSN was controlled by a single dominant gene and was primarily positioned on melon chromosome 2, within a physical interval of ~ 351 kb. Further fine mapping in a large F2 population narrowed this region to a 71-kb region harboring 5 genes. MELO3C010288, which encodes a protein in the EamA-like transporter family, is the best possible candidate gene for the netted phenotype. Two nonsynonymous single nucleotide polymorphisms (SNPs) were identified in the third and sixth exons of the CmSN gene and co-segregated with the skin netting (SN) phenotype among the genetic population. A genome-wide association study (GWAS) determined that CmSN is probably a domestication gene under selective pressure during the subspecies C. melo subsp. melo differentiation. The SNP in the third exon of CmSN (the leading SNP in GWAS) revealed a bi-allelic diversity in natural accessions with SN traits. Our results lay a foundation for deciphering the molecular mechanism underlying the formation of fruit skin netting in melon, as well as provide a strategy for genetic improvement of netted fruit using a marker-assisted selection approach.
Collapse
Affiliation(s)
- Xiaoxue Liang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiong Li
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lei Cao
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuanyu Du
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Junhao Qiang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Juan Hou
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Xiang Li
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Huayu Zhu
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Sen Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Dongming Liu
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Lei Zhu
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Panqiao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China.
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China.
| | - Jianbin Hu
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China.
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China.
| |
Collapse
|
11
|
Castro C, Massonnet M, Her N, DiSalvo B, Jablonska B, Jeske DR, Cantu D, Roper MC. Priming grapevine with lipopolysaccharide confers systemic resistance to Pierce's disease and identifies a peroxidase linked to defense priming. THE NEW PHYTOLOGIST 2023; 239:687-704. [PMID: 37149885 DOI: 10.1111/nph.18945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 04/05/2023] [Indexed: 05/09/2023]
Abstract
Priming is an adaptive mechanism that fortifies plant defense by enhancing activation of induced defense responses following pathogen challenge. Microorganisms have signature microbe-associated molecular patterns (MAMPs) that induce the primed state. The lipopolysaccharide (LPS) MAMP isolated from the xylem-limited pathogenic bacterium, Xylella fastidiosa, acts as a priming stimulus in Vitis vinifera grapevines. Grapevines primed with LPS developed significantly less internal tyloses and external disease symptoms than naive vines. Differential gene expression analysis indicated major transcriptomic reprogramming during the priming and postpathogen challenge phases. Furthermore, the number of differentially expressed genes increased temporally and spatially in primed vines, but not in naive vines during the postpathogen challenge phase. Using a weighted gene co-expression analysis, we determined that primed vines have more genes that are co-expressed in both local and systemic petioles than naive vines indicating an inherent synchronicity that underlies the systemic response to this vascular pathogen specific to primed plants. We identified a cationic peroxidase, VviCP1, that was upregulated during the priming and postpathogen challenge phases in an LPS-dependent manner. Transgenic expression of VviCP1 conferred significant disease resistance, thus, demonstrating that grapevine is a robust model for mining and expressing genes linked to defense priming and disease resistance.
Collapse
Affiliation(s)
- Claudia Castro
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA
| | - Nancy Her
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Biagio DiSalvo
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Barbara Jablonska
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Daniel R Jeske
- Department of Statistics, University of California, Riverside, CA, 92521, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| |
Collapse
|
12
|
Koseoglou E, Hanika K, Mohd Nadzir MM, Kohlen W, van der Wolf JM, Visser RGF, Bai Y. Inactivation of tomato WAT1 leads to reduced susceptibility to Clavibacter michiganensis through downregulation of bacterial virulence factors. FRONTIERS IN PLANT SCIENCE 2023; 14:1082094. [PMID: 37324660 PMCID: PMC10264788 DOI: 10.3389/fpls.2023.1082094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
Tomato bacterial canker caused by Clavibacter michiganensis (Cm) is considered to be one of the most destructive bacterial diseases of tomato. To date, no resistance to the pathogen has been identified. While several molecular studies have identified (Cm) bacterial factors involved in disease development, the plant genes and mechanisms associated with susceptibility of tomato to the bacterium remain largely unknown. Here, we show for the first time that tomato gene SlWAT1 is a susceptibility gene to Cm. We inactivated the gene SlWAT1 through RNAi and CRISPR/Cas9 to study changes in tomato susceptibility to Cm. Furthermore, we analysed the role of the gene in the molecular interaction with the pathogen. Our findings demonstrate that SlWAT1 functions as an S gene to genetically diverse Cm strains. Inactivation of SlWAT1 reduced free auxin contents and ethylene synthesis in tomato stems and suppressed the expression of specific bacterial virulence factors. However, CRISPR/Cas9 slwat1 mutants exhibited severe growth defects. The observed reduced susceptibility is possibly a result of downregulation of bacterial virulence factors and reduced auxin contents in transgenic plants. This shows that inactivation of an S gene may affect the expression of bacterial virulence factors.
Collapse
Affiliation(s)
- Eleni Koseoglou
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
- Graduate School Experimental Plant Sciences Wageningen University & Research, Wageningen, Netherlands
| | - Katharina Hanika
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Mas M. Mohd Nadzir
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Wouter Kohlen
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Jan M. van der Wolf
- Biointeractions & Plant Health, Wageningen University & Research, Wageningen, Netherlands
| | | | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| |
Collapse
|
13
|
Yao X, Li H, Nie J, Liu H, Guo Y, Lv L, Yang Z, Sui X. Disruption of the amino acid transporter CsAAP2 inhibits auxin-mediated root development in cucumber. THE NEW PHYTOLOGIST 2023. [PMID: 37129077 DOI: 10.1111/nph.18947] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/06/2023] [Indexed: 05/03/2023]
Abstract
Amino acid transporters are the principal mediators of organic nitrogen distribution within plants and are essential for plant growth and development. Despite this importance, relatively few amino acid transporter genes have been explored and elucidated in cucumber (Cucumis sativus). Here, a total of 86 amino acid transporter genes were identified in the cucumber genome. We further identified Amino Acid Permease (AAP) subfamily members that exhibited distinct expression patterns in different tissues. We found that the CsAAP2 as a candidate gene encoding a functional amino acid transporter is highly expressed in cucumber root vascular cells. CsAAP2 knockout lines exhibited arrested development of root meristem, which then caused the delayed initiation of lateral root and the inhibition of root elongation. What is more, the shoot growth of aap2 mutants was strongly retarded due to defects in cucumber root development. Moreover, aap2 mutants exhibited higher concentrations of amino acids and lignin in roots. We found that the mutant roots had a stronger ability to acidize medium. Furthermore, in the aap2 mutants, polar auxin transport was disrupted in the root tip, leading to high auxin levels in roots. Interestingly, slightly alkaline media rescued their severely reduced root growth by stimulating auxin pathway.
Collapse
Affiliation(s)
- Xuehui Yao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Hujian Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jing Nie
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Huan Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yicong Guo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Lijun Lv
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhen Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xiaolei Sui
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
14
|
Mazuecos-Aguilera I, Suárez-Santiago VN. Identification of Candidate Genes Involved in the Determinism of Pollen Grain Aperture Morphology by Comparative Transcriptome Analysis in Papaveraceae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1570. [PMID: 37050196 PMCID: PMC10096813 DOI: 10.3390/plants12071570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 06/19/2023]
Abstract
In the last decade, certain genes involved in pollen aperture formation have been discovered. However, those involved in pollen aperture shape remain largely unknown. In Arabidopsis, the interaction during the tetrad development stage of one member of the ELMOD protein family, ELMOD_E, with two others, MCR/ELMOD_B and ELMOD_A, can change the morphology of apertures from colpus (elongated) to pore (round). Here, comparative transcriptome analysis is used to identify candidate genes involved in the determination of pollen aperture morphology in Papaveraceae (order Ranunculales). Furthermore, the role of ELMOD genes in the genetic determinism of aperture shape was tested by comparative analysis of their expression levels using RNA-seq data and RT-qPCR. Two pairs of species belonging to two different subfamilies were used. Within each pair, one species has colpate pollen and the other porate (Fumarioideae-Dactylicapnos torulosa, 6-colpate, and Fumaria bracteosa, pantoporate; Papaveroideae-Eschsholzia californica, 5-7 colpate, and Roemeria refracta, 6-porate). The transcriptomes were obtained at the tetrad stage of pollen development. A total of 531 DEGs were found between the colpate and porate pollen species groups. The results from RNA-seq and RT-qPCR indicate that pollen aperture shape is not determined by the relative expression levels of ELMOD family genes in Papaveraceae. However, genes related to callose wall formation or cytoskeleton organisation were found, these processes being involved in pollen aperture formation. In addition, transcriptomes from anthers with pollen during the tetrad stage of three species (D. torulosa, R. refracta, and F. bracteosa) were obtained for the first time. These data will be available for further studies in the field of floral evolution and development.
Collapse
|
15
|
Zhang L, He C, Lai Y, Wang Y, Kang L, Liu A, Lan C, Su H, Gao Y, Li Z, Yang F, Li Q, Mao H, Chen D, Chen W, Kaufmann K, Yan W. Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis. Genome Biol 2023; 24:65. [PMID: 37016448 PMCID: PMC10074895 DOI: 10.1186/s13059-023-02908-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/23/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types. RESULTS Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process. CONCLUSIONS Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.
Collapse
Affiliation(s)
- Lihua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuting Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yating Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu Kang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuwen Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zeqing Li
- Wuhan Igenebook Biotechnology Co., Ltd, Wuhan, 430014, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
16
|
Reim S, Emeriewen OF, Peil A, Flachowsky H. Deciphering the Mechanism of Tolerance to Apple Replant Disease Using a Genetic Mapping Approach in a Malling 9 × M. × robusta 5 Population Identifies SNP Markers Linked to Candidate Genes. Int J Mol Sci 2023; 24:ijms24076307. [PMID: 37047278 PMCID: PMC10094387 DOI: 10.3390/ijms24076307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Apple replant disease (ARD) is a worldwide economic risk in apple production. Although several studies have shown that the wild apple accession Malus × robusta 5 (Mr5) is ARD-tolerant, the genetics of this tolerance have not yet been elucidated. A genetic mapping approach with a biparental population derived from contrasting parents involving molecular markers provides a means for marker-assisted selection of genetically complex traits and for determining candidate genes. In this study, we crossed the ARD-tolerant wild apple accession Mr5 and the ARD-susceptible rootstock ‘M9’ and analyzed the resultant progeny for ARD tolerance. Hence, a high-density genetic map using a tunable genotyping-by-sequencing (tGBS) approach was established. A total of 4804 SNPs together with 77 SSR markers were included in the parental maps comprising 17 linkage groups. The phenotypic responses to ARD were evaluated for 106 offspring and classified by an ARD-susceptibility index (ASI). A Kruskal–Wallis test identified SNP markers and one SSR marker on linkage groups (LG) 6 and 2 that correlated with ARD tolerance. We found nine candidate genes linked with these markers, which may be associated with plant response to ARD. These candidate genes provide some insight into the defense mechanisms against ARD and should be studied in more detail.
Collapse
|
17
|
Liu H, Zhou C, Nisa ZU, El-Kassaby YA, Li W. Exogenous 6-BA inhibited hypocotyl elongation under darkness in Picea crassifolia Kom revealed by transcriptome profiling. FRONTIERS IN PLANT SCIENCE 2023; 14:1086879. [PMID: 36923127 PMCID: PMC10009258 DOI: 10.3389/fpls.2023.1086879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Hypocotyl elongation is an important process in plant growth and development, and is under hormonal regulatory signaling pathways. In our study, exogenous 6-BA significantly inhibited Picea crassifolia hypocotyl elongation more than ethylene in the dark, indicating the existence of different regulatory strategies in conifers, therefore, the P. crassifolia transcriptome was studied to explore the responsive genes and their regulatory pathways for exogenous N6-benzyladenine (6-BA) inhibition of hypocotyl elongation using RNA-Sequencing approach. We present the first transcriptome assembly of P. crassifolia obtained from 24.38 Gb clean data. With lowly-expressed and short contigs excluded, the assembly contains roughly 130,612 unigenes with an N50 length of 1,278 bp. Differential expression analysis found 3,629 differentially expressed genes (DEGs) and found that the differential expression fold of genes was mainly concentrated between 2 and 8 (1 ≤ log2FoldChange ≤ 3). Functional annotation showed that the GO term with the highest number of enriched genes (83 unigenes) was the shoot system development (GO: 0048367) and the KEGG category, plant hormone signal transduction (ko04075), was enriched 30 unigenes. Further analysis revealed that several cytokinin dehydrogenase genes (PcCTD1, PcCTD3 and PcCTD6) catabolized cytokinins, while xyloglucan endotransglucosylase hydrolase gene (PcXTH31), WALLS ARE THIN 1-like gene (PcWAT1-1) and Small auxin-induced gene (PcSAUR15) were strongly repressed thus synergistically completing the inhibition of hypocotyl elongation in P. crassifolia. Besides, PcbHLH149, PcMYB44 and PcERF14 were predicted to be potential core TFs that may form a multi-layered regulatory network with the above proteins for the regulation of hypocotyl growth.
Collapse
Affiliation(s)
- Hongmei Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Chengcheng Zhou
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zaib Un Nisa
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Cotton Research Institute, Multan, Punjab, Pakistan
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| |
Collapse
|
18
|
Lv P, Wan J, Zhang C, Hina A, Al Amin GM, Begum N, Zhao T. Unraveling the Diverse Roles of Neglected Genes Containing Domains of Unknown Function (DUFs): Progress and Perspective. Int J Mol Sci 2023; 24:ijms24044187. [PMID: 36835600 PMCID: PMC9966272 DOI: 10.3390/ijms24044187] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Domain of unknown function (DUF) is a general term for many uncharacterized domains with two distinct features: relatively conservative amino acid sequence and unknown function of the domain. In the Pfam 35.0 database, 4795 (24%) gene families belong to the DUF type, yet, their functions remain to be explored. This review summarizes the characteristics of the DUF protein families and their functions in regulating plant growth and development, generating responses to biotic and abiotic stress, and other regulatory roles in plant life. Though very limited information is available about these proteins yet, by taking advantage of emerging omics and bioinformatic tools, functional studies of DUF proteins could be utilized in future molecular studies.
Collapse
Affiliation(s)
- Peiyun Lv
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinlu Wan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunting Zhang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiman Hina
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - G M Al Amin
- Department of Botany, Jagannath University, Dhaka 1100, Bangladesh
| | - Naheeda Begum
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (N.B.); (T.Z.)
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (N.B.); (T.Z.)
| |
Collapse
|
19
|
Zeng D, Si C, Teixeira da Silva JA, Shi H, Chen J, Huang L, Duan J, He C. Uncovering the involvement of DoDELLA1-interacting proteins in development by characterizing the DoDELLA gene family in Dendrobium officinale. BMC PLANT BIOLOGY 2023; 23:93. [PMID: 36782128 PMCID: PMC9926750 DOI: 10.1186/s12870-023-04099-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gibberellins (GAs) are widely involved in plant growth and development. DELLA proteins are key regulators of plant development and a negative regulatory factor of GA. Dendrobium officinale is a valuable traditional Chinese medicine, but little is known about D. officinale DELLA proteins. Assessing the function of D. officinale DELLA proteins would provide an understanding of their roles in this orchid's development. RESULTS In this study, the D. officinale DELLA gene family was identified. The function of DoDELLA1 was analyzed in detail. qRT-PCR analysis showed that the expression levels of all DoDELLA genes were significantly up-regulated in multiple shoots and GA3-treated leaves. DoDELLA1 and DoDELLA3 were significantly up-regulated in response to salt stress but were significantly down-regulated under drought stress. DoDELLA1 was localized in the nucleus. A strong interaction was observed between DoDELLA1 and DoMYB39 or DoMYB308, but a weak interaction with DoWAT1. CONCLUSIONS In D. officinale, a developmental regulatory network involves a close link between DELLA and other key proteins in this orchid's life cycle. DELLA plays a crucial role in D. officinale development.
Collapse
Affiliation(s)
- Danqi Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | | | - Hongyu Shi
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
| |
Collapse
|
20
|
Garcia K, Cloghessy K, Cooney DR, Shelley B, Chakraborty S, Kafle A, Busidan A, Sonawala U, Collier R, Jayaraman D, Ané JM, Pilot G. The putative transporter MtUMAMIT14 participates in nodule formation in Medicago truncatula. Sci Rep 2023; 13:804. [PMID: 36646812 PMCID: PMC9842706 DOI: 10.1038/s41598-023-28160-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/13/2023] [Indexed: 01/17/2023] Open
Abstract
Transport systems are crucial in many plant processes, including plant-microbe interactions. Nodule formation and function in legumes involve the expression and regulation of multiple transport proteins, and many are still uncharacterized, particularly for nitrogen transport. Amino acids originating from the nitrogen-fixing process are an essential form of nitrogen for legumes. This work evaluates the role of MtN21 (henceforth MtUMAMIT14), a putative transport system from the MtN21/EamA-like/UMAMIT family, in nodule formation and nitrogen fixation in Medicago truncatula. To dissect this transporter's role, we assessed the expression of MtUMAMIT14 using GUS staining, localized the corresponding protein in M. truncatula root and tobacco leaf cells, and investigated two independent MtUMAMIT14 mutant lines. Our results indicate that MtUMAMIT14 is localized in endosomal structures and is expressed in both the infection zone and interzone of nodules. Comparison of mutant and wild-type M. truncatula indicates MtUMAMIT14, the expression of which is dependent on the presence of NIN, DNF1, and DNF2, plays a role in nodule formation and nitrogen-fixation. While the function of the transporter is still unclear, our results connect root nodule nitrogen fixation in legumes with the UMAMIT family.
Collapse
Affiliation(s)
- Kevin Garcia
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695-7619, USA.
| | - Kaylee Cloghessy
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Biological Sciences, The University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Danielle R Cooney
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695-7619, USA
| | - Brett Shelley
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Arjun Kafle
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695-7619, USA
| | - Aymeric Busidan
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Unnati Sonawala
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Ray Collier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Molecular Technologies Department, Wisconsin Crop Innovation Center, University of Wisconsin-Madison, Madison, WI, 53562, USA
| | | | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Guillaume Pilot
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24060, USA
| |
Collapse
|
21
|
Mokshina N, Panina A, Galinousky D, Sautkina O, Mikshina P. Transcriptome profiling of celery petiole tissues reveals peculiarities of the collenchyma cell wall formation. PLANTA 2022; 257:18. [PMID: 36538078 DOI: 10.1007/s00425-022-04042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Transcriptome and biochemical analyses are applied to individual plant cell types to reveal potential players involved in the molecular machinery of cell wall formation in specialized cells such as collenchyma. Plant collenchyma is a mechanical tissue characterized by an irregular, thickened cell wall and the ability to support cell elongation. The composition of the collenchyma cell wall resembles that of the primary cell wall and includes cellulose, xyloglucan, and pectin; lignin is absent. Thus, the processes associated with the formation of the primary cell wall in the collenchyma can be more pronounced compared to other tissues due to its thickening. Primary cell walls intrinsic to different tissues may differ in structure and composition, which should be reflected at the transcriptomic level. For the first time, we conducted transcriptome profiling of collenchyma strands isolated from young celery petioles and compared them with other tissues, such as parenchyma and vascular bundles. Genes encoding proteins involved in the primary cell wall formation during cell elongation, such as xyloglucan endotransglucosylase/hydrolases, expansins, and leucine-rich repeat proteins, were significantly activated in the collenchyma. As the key players in the transcriptome orchestra of collenchyma, xyloglucan endotransglucosylase/hydrolase transcripts were characterized in more detail, including phylogeny and expression patterns. The comprehensive approach that included transcriptome and biochemical analyses allowed us to reveal peculiarities of collenchyma cell wall formation and modification, matching the abundance of upregulated transcripts and their potential substrates for revealed gene products. As a result, specific isoforms of multigene families were determined for further functional investigation.
Collapse
Affiliation(s)
- Natalia Mokshina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia.
| | - Anastasia Panina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
| | - Dmitry Galinousky
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576, CNRS, Université de Lille, 59655, Villeneuve d'Ascq, France
| | - Olga Sautkina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
| | - Polina Mikshina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
| |
Collapse
|
22
|
Liu Y, Wu Q, Qin Z, Huang J. Transcription factor OsNAC055 regulates GA-mediated lignin biosynthesis in rice straw. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111455. [PMID: 36152809 DOI: 10.1016/j.plantsci.2022.111455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/04/2022] [Indexed: 06/16/2023]
Abstract
Crop straws represent enormous biomass resource that mainly contain secondary cell walls (SCWs) consisting of cellulose, hemicelluloses and lignin. Nevertheless, the regulatory mechanism of SCW biosynthesis still needs to be well understood. In this study, we identified a rice NAC (NAM, ATAF1/2, CUC2) transcription factor OsNAC055 that regulates GA-mediated lignin biosynthesis. As a nucleus-localized transcription factor, OsNAC055 exhibits the transcriptional activation activity. Overexpression of OsNAC055 increases the lignin content in rice straw. Transcriptomic analyses showed that the expression of multiple lignin biosynthetic genes was increased in OsNAC055-overexpressing plants. Further ChIP-qPCR analysis and transient transactivation assays indicated that OsNAC055 directly activates rice lignin biosynthetic genes CINNAMOYL-CoA REDUCTASE 10 (OsCCR10) and CINNAMYL ALCOHOL DEHYDROGENASE 2 (OsCAD2) by binding to their promoters. On the other hand, phytohormone measurement showed that OsNAC055 overexpression significantly increased exogenous GA3 levels in rice plants by regulating GA biosynthetic gene OsGA20ox2. Moreover, yeast two-hybrid and bimolecular fluorescence complement (BiFC) assays indicated that OsNAC055 interacts with SLENDER RICE1 (SLR1), the repressor in GA signaling. More importantly, exogenous GA treatment markedly enhanced the transcription of OsCCR10 and OsCAD2, suggesting the role of GA in lignin biosynthesis. Together, our results provide the evidence that OsNAC055 functions as an essential transcription factor to regulate the GA-mediated lignin biosynthesis, which provides a strategy for manipulating lignin production.
Collapse
Affiliation(s)
- Yingfan Liu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Qi Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Zhongliang Qin
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Junli Huang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China.
| |
Collapse
|
23
|
Zhao CX, Su XX, Xu MR, An XL, Su JQ. Uncovering the diversity and contents of gene cassettes in class 1 integrons from the endophytes of raw vegetables. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114282. [PMID: 36371907 DOI: 10.1016/j.ecoenv.2022.114282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/22/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables represents a pathway for human exposure to environmental ARGs. However, few studies have focused on integron-associated ARGs in the endophytes of raw vegetables. Here, based on the approach of qPCR and clone library, we quantified the abundance of integrase genes and analyzed the diversity and contents of resistance gene cassettes in class 1 integrons from the endophytes of six common raw vegetables. The results revealed that integrase genes for class 1 integron were most prevalent compared with class 2 and class 3 integron integrase genes (1-2 order magnitude, P < 0.05). The cucumber endophytes harbored a higher absolute abundance of integrase genes than other vegetables, while the highest bacterial abundance was detected in cabbage and cucumber endophytes. Thirty-two unique resistance gene cassettes were detected, the majority of which were associated with the genes encoding resistance to beta-lactam and aminoglycoside. Antibiotic resistance gene cassettes accounted for 52.5 % of the functionally annotated gene cassettes, and blaTEM-157 and aadA2 were the most frequently detected resistance cassettes. Additionally, carrot endophytes harbored the highest proportion of antibiotic resistance gene cassettes in the class 1 integrons. Collectively, these results provide an in-depth view of acquired resistance genes by integrons in the raw vegetable endophytes and highlight the potential health risk of the transmission of ARGs via the food chain.
Collapse
Affiliation(s)
- Cai-Xia Zhao
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Xuan Su
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, 400715 Chongqing, China
| | - Mei-Rong Xu
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Li An
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jian-Qiang Su
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
24
|
Kanapin A, Rozhmina T, Bankin M, Surkova S, Duk M, Osyagina E, Samsonova M. Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration. Int J Mol Sci 2022; 23:ijms232314536. [PMID: 36498863 PMCID: PMC9738745 DOI: 10.3390/ijms232314536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
In this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in the course of 3 successive years. A genome-wide association study was performed for each phenotype independently using six different single-locus models implemented in the GAPIT3 R package. Moreover, we applied a multivariate linear mixed model implemented in the GEMMA package to account for trait correlations and potential pleiotropic effects of polymorphisms. The analyses revealed a number of genomic variants associated with different fiber traits, implying the complex and polygenic control. All stable variants demonstrate a statistically significant allelic effect across all 3 years of the experiment. We tested the validity of the predicted variants using gene expression data available for the flax fiber studies. The results shed new light on the processes and pathways associated with the complex fiber traits, while the pinpointed candidate genes may be further used for marker-assisted selection.
Collapse
Affiliation(s)
- Alexander Kanapin
- Centre for Computational Biology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Tatyana Rozhmina
- Laboratory of Breeding Technologies, Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
| | - Mikhail Bankin
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Svetlana Surkova
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Maria Duk
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia
| | - Ekaterina Osyagina
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Maria Samsonova
- Mathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-812-290-9645
| |
Collapse
|
25
|
Wang Q, Wu Y, Peng A, Cui J, Zhao M, Pan Y, Zhang M, Tian K, Schwab W, Song C. Single-cell transcriptome atlas reveals developmental trajectories and a novel metabolic pathway of catechin esters in tea leaves. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2089-2106. [PMID: 35810348 PMCID: PMC9616531 DOI: 10.1111/pbi.13891] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 05/26/2023]
Abstract
The tea plant is an economically important woody beverage crop. The unique taste of tea is evoked by certain metabolites, especially catechin esters, whereas their precise formation mechanism in different cell types remains unclear. Here, a fast protoplast isolation method was established and the transcriptional profiles of 16 977 single cells from 1st and 3rd leaves were investigated. We first identified 79 marker genes based on six isolated tissues and constructed a transcriptome atlas, mapped developmental trajectories and further delineated the distribution of different cell types during leaf differentiation and genes associated with cell fate transformation. Interestingly, eight differently expressed genes were found to co-exist at four branch points. Genes involved in the biosynthesis of certain metabolites showed cell- and development-specific characteristics. An unexpected catechin ester glycosyltransferase was characterized for the first time in plants by a gene co-expression network in mesophyll cells. Thus, the first single-cell transcriptional landscape in woody crop leave was reported and a novel metabolism pathway of catechin esters in plants was discovered.
Collapse
Affiliation(s)
- Qiang Wang
- State Key Laboratory of Tea Plant Biology and UtilizationInternational Joint Laboratory on Tea Chemistry and Health EffectsAnhui Agricultural UniversityHefei, AnhuiChina
| | - Yi Wu
- State Key Laboratory of Tea Plant Biology and UtilizationInternational Joint Laboratory on Tea Chemistry and Health EffectsAnhui Agricultural UniversityHefei, AnhuiChina
| | - Anqi Peng
- State Key Laboratory of Tea Plant Biology and UtilizationInternational Joint Laboratory on Tea Chemistry and Health EffectsAnhui Agricultural UniversityHefei, AnhuiChina
| | - Jilai Cui
- State Key Laboratory of Tea Plant Biology and UtilizationInternational Joint Laboratory on Tea Chemistry and Health EffectsAnhui Agricultural UniversityHefei, AnhuiChina
- Key Laboratory of Tea Plant Biology of Henan ProvinceCollege of Life ScienceXinyang Normal UniversityXinyang, HenanChina
| | - Mingyue Zhao
- State Key Laboratory of Tea Plant Biology and UtilizationInternational Joint Laboratory on Tea Chemistry and Health EffectsAnhui Agricultural UniversityHefei, AnhuiChina
| | - Yuting Pan
- State Key Laboratory of Tea Plant Biology and UtilizationInternational Joint Laboratory on Tea Chemistry and Health EffectsAnhui Agricultural UniversityHefei, AnhuiChina
| | - Mengting Zhang
- State Key Laboratory of Tea Plant Biology and UtilizationInternational Joint Laboratory on Tea Chemistry and Health EffectsAnhui Agricultural UniversityHefei, AnhuiChina
| | - Kai Tian
- Key Laboratory of Ecological Security for Water Source Region of Mid‐Line Project of South‐To‐North Diversion Project of Henan ProvinceSchool of Life Sciences and Agricultural EngineeringNanyang Normal UniversityNanyangChina
| | - Wilfried Schwab
- State Key Laboratory of Tea Plant Biology and UtilizationInternational Joint Laboratory on Tea Chemistry and Health EffectsAnhui Agricultural UniversityHefei, AnhuiChina
- Biotechnology of Natural ProductsTechnische Universität MünchenFreisingGermany
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and UtilizationInternational Joint Laboratory on Tea Chemistry and Health EffectsAnhui Agricultural UniversityHefei, AnhuiChina
| |
Collapse
|
26
|
Bashyal BM, Rawat K, Parmar P, Gupta AK, Gupta S, Krishnan SG, Choudhary R, Ercisli S, Kovacevic A, Aggarwal R. Transcriptomic analysis of bakanae disease resistant and susceptible rice genotypes in response to infection by Fusarium fujikuroi. Mol Biol Rep 2022; 49:11959-11972. [PMID: 36271308 DOI: 10.1007/s11033-022-07877-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/21/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Fusarium fujikuroi causing bakanae is one of the most significant pathogens of rice and much responsible for yield losses thereby emerging as a major risk to food security. METHODS In the present study transcriptomic analysis was conducted between two contrasting resistant (C101A51) and susceptible (Rasi) genotypes of rice with the combinations of C101A51 control (CC) vs. C101A51 inoculated (CI); Rasi control (RC) vs. Rasi inoculated (RI) and C101A51 inoculated (CI) vs. Rasi inoculated (RI). RESULTS In CC vs. CI commonly expressed genes were 12,764. Out of them 567 (4%) were significantly upregulated and 1399 (9%) genes were downregulated. For the RC vs. RI 14, 333 (79%) genes were commonly expressed. For CI vs. RI 13,662 (72%) genes were commonly expressed. Genes related to cysteine proteinase inhibitor 10, disease resistance protein TAO1-like, oleosin 16 kDa-like, pathogenesis-related protein (PR1), (PR4), BTB/POZ and MATH domain-containing protein 5-like, alpha-amylase isozyme were upregulated in resistant genotype C101A51. Whereas, genes related to GDSL esterase/lipase, serine glyoxylate aminotransferase, CASP-like protein 2C1, WAT1-related protein, Cytoplasmic linker associated proteins, xyloglucan endotransglucosylase/hydrolase protein and β-D xylosidase 7 were upregulated in susceptible genotype Rasi. Gene ontology analysis showed functions related to defence response (GO:0006952), regulation of plant hypersensitive type response (GO:0010363), Potassium ion transmembrane activity (GO:0015079), chloroplast (GO:0009507), response to wounding (GO:0009611), xylan biosynthetic process (GO:0045492) were upregulated in resistant genotype C101A51 under inoculated conditions. CONCLUSION Real time PCR based validation of the selected DEGs showed that the qRT-PCR was consistent with the RNA-Seq results. This is the first transcriptomic study against bakanae disease of rice in Indian genotypes. Further, functional studies on identified genes and their utilization through different methodology will be helpful for the development of bakanae disease management strategies.
Collapse
Affiliation(s)
- Bishnu Maya Bashyal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India.
| | - Kirti Rawat
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India
| | - Pooja Parmar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India
| | - Ashish Kumar Gupta
- ICAR-National Institute of Plant Biotechnology, 110012, New Delhi, India
| | - Sangeeta Gupta
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India
| | - Ravish Choudhary
- Division of Seed Science and Technology, Indian Agricultural Research Institute, 110012, New Delhi, India
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, 25240, Erzurum, Turkey
| | - Antonija Kovacevic
- BIOTECH - Center for Biotechnological Research and Development, Ivana Cankara 76, 35 000, Slavonski Brod, Croatia
| | - Rashmi Aggarwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, 110012, New Delhi, India
| |
Collapse
|
27
|
Li Y, Yang Z, Zhang Y, Guo J, Liu L, Wang C, Wang B, Han G. The roles of HD-ZIP proteins in plant abiotic stress tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1027071. [PMID: 36311122 PMCID: PMC9598875 DOI: 10.3389/fpls.2022.1027071] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/26/2022] [Indexed: 05/31/2023]
Abstract
Homeodomain leucine zipper (HD-ZIP) proteins are plant-specific transcription factors that contain a homeodomain (HD) and a leucine zipper (LZ) domain. The highly conserved HD binds specifically to DNA and the LZ mediates homodimer or heterodimer formation. HD-ZIP transcription factors control plant growth, development, and responses to abiotic stress by regulating downstream target genes and hormone regulatory pathways. HD-ZIP proteins are divided into four subclasses (I-IV) according to their sequence conservation and function. The genome-wide identification and expression profile analysis of HD-ZIP proteins in model plants such as Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have improved our understanding of the functions of the different subclasses. In this review, we mainly summarize and discuss the roles of HD-ZIP proteins in plant response to abiotic stresses such as drought, salinity, low temperature, and harmful metals. HD-ZIP proteins mainly mediate plant stress tolerance by regulating the expression of downstream stress-related genes through abscisic acid (ABA) mediated signaling pathways, and also by regulating plant growth and development. This review provides a basis for understanding the roles of HD-ZIP proteins and potential targets for breeding abiotic stress tolerance in plants.
Collapse
|
28
|
Shrestha HK, Fichman Y, Engle NL, Tschaplinski TJ, Mittler R, Dixon RA, Hettich RL, Barros J, Abraham PE. Multi-omic characterization of bifunctional peroxidase 4-coumarate 3-hydroxylase knockdown in Brachypodium distachyon provides insights into lignin modification-associated pleiotropic effects. FRONTIERS IN PLANT SCIENCE 2022; 13:908649. [PMID: 36247563 PMCID: PMC9554711 DOI: 10.3389/fpls.2022.908649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
A bifunctional peroxidase enzyme, 4-coumarate 3-hydroxylase (C3H/APX), provides a parallel route to the shikimate shunt pathway for the conversion of 4-coumarate to caffeate in the early steps of lignin biosynthesis. Knockdown of C3H/APX (C3H/APX-KD) expression has been shown to reduce the lignin content in Brachypodium distachyon. However, like many other lignin-modified plants, C3H/APX-KDs show unpredictable pleiotropic phenotypes, including stunted growth, delayed senescence, and reduced seed yield. A system-wide level understanding of altered biological processes in lignin-modified plants can help pinpoint the lignin-modification associated growth defects to benefit future studies aiming to negate the yield penalty. Here, a multi-omic approach was used to characterize molecular changes resulting from C3H/APX-KD associated lignin modification and negative growth phenotype in Brachypodium distachyon. Our findings demonstrate that C3H/APX knockdown in Brachypodium stems substantially alters the abundance of enzymes implicated in the phenylpropanoid biosynthetic pathway and disrupt cellular redox homeostasis. Moreover, it elicits plant defense responses associated with intracellular kinases and phytohormone-based signaling to facilitate growth-defense trade-offs. A deeper understanding along with potential targets to mitigate the pleiotropic phenotypes identified in this study could aid to increase the economic feasibility of lignocellulosic biofuel production.
Collapse
Affiliation(s)
- Him K. Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, United States
| | - Yosef Fichman
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Ron Mittler
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jaime Barros
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| |
Collapse
|
29
|
Du K, Zhao W, Mao Y, Lv Z, Khattak WA, Ali S, Zhou Z, Wang Y. Maize ear growth is stimulated at the fourth day after pollination by cell wall remodeling and changes in lipid and hormone signaling. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:5429-5439. [PMID: 35338493 DOI: 10.1002/jsfa.11896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Stimulating maize ear development is an effective way of improving yield. However, limited information is available regarding the regulation of sink strength change from weak to strong at the same position of maize plants. Here, a novel method for stimulating development combined with physiological assays and proteomics was applied to explore the regulation of ear strengthened development. RESULTS By blocking pollination of the upper ear of maize hybrid Suyu 41, the adjacent lower ear was dramatically stimulated at 4 days after pollination (DAP). Tandem mass tag (TMT)-based proteomics identified 173 differentially expressed proteins (fold change >1.2 or <0.83, P < 0.05) from 7793 total proteins. Gene ontology annotations indicated that several pathways showed noticeable changes, with a preferential distribution to cell wall remodeling, hormone signals and lipid metabolism in the stimulated kernels. Cell wall remodeling was highly mediated by chitinase, exhydrolase II and xyloglucan enotransglucosylase/hydrolase, and accompanied by increased sucrose and glucose content. A series of lipoxygenase proteins were significantly upregulated, causing a significant alteration in lipid metabolism. Hormone signals were influenced by the expression of the proteins involved in indole-3-acetic acid (IAA) transport, zeatin (ZT) biosynthesis and abscisic acid (ABA) signal response, and increased IAA, ZT and ABA content. CONCLUSION The critical time for understanding the mechanism by which ear growth is stimulated is 4 DAP. Comparative proteomics and physiological analysis revealed that lipid metabolism enhancement, cell wall remodeling and changes in hormone signaling (IAA, ZT and ABA) were all important in stimulating early ear development. Proper regulation of these pathways may improve ear development, resulting in increased maize yield. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Kang Du
- College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, P. R. China
| | - Wenqing Zhao
- College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, P. R. China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC- MCP), Nanjing Agricultural University, 210095, Nanjing, P. R. China
| | - Yu Mao
- College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, P. R. China
| | - Zhiwei Lv
- College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, P. R. China
| | - Wajid Ali Khattak
- College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, P. R. China
| | - Saif Ali
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Zhiguo Zhou
- College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, P. R. China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC- MCP), Nanjing Agricultural University, 210095, Nanjing, P. R. China
| | - Youhua Wang
- College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, P. R. China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC- MCP), Nanjing Agricultural University, 210095, Nanjing, P. R. China
| |
Collapse
|
30
|
Liu H, Liu X, Zhao Y, Nie J, Yao X, Lv L, Yang J, Ma N, Guo Y, Li Y, Yang X, Lin T, Sui X. Alkaline α-galactosidase 2 (CsAGA2) plays a pivotal role in mediating source-sink communication in cucumber. PLANT PHYSIOLOGY 2022; 189:1501-1518. [PMID: 35357489 PMCID: PMC9237694 DOI: 10.1093/plphys/kiac152] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/07/2022] [Indexed: 05/27/2023]
Abstract
Sugars are necessary for plant growth and fruit development. Cucumber (Cucumis sativus L.) transports sugars, mainly raffinose family oligosaccharides (RFOs), in the vascular bundle. As the dominant sugars in cucumber fruit, glucose and fructose are derived from sucrose, which is the product of RFO hydrolysis by α-galactosidase (α-Gal). Here, we characterized the cucumber alkaline α-galactosidase 2 (CsAGA2) gene and found that CsAGA2 has undergone human selection during cucumber domestication. Further experiments showed that the expression of CsAGA2 increases gradually during fruit development, especially in fruit vasculature. In CsAGA2-RNA interference (RNAi) lines, fruit growth was delayed because of lower hexose production in the peduncle and fruit main vascular bundle (MVB). In contrast, CsAGA2-overexpressing (OE) plants displayed bigger fruits. Functional enrichment analysis of transcriptional data indicated that genes related to sugar metabolism, cell wall metabolism, and hormone signaling were significantly downregulated in the peduncle and fruit MVBs of CsAGA2-RNAi plants. Moreover, downregulation of CsAGA2 also caused negative feedback regulation on source leaves, which was shown by reduced photosynthetic efficiency, fewer plasmodesmata at the surface between mesophyll cell and intermediary cell (IC) or between IC and sieve element, and downregulated gene expression and enzyme activities related to phloem loading, as well as decreased sugar production and exportation from leaves and petioles. The opposite trend was observed in CsAGA2-OE lines. Overall, we conclude that CsAGA2 is essential for cucumber fruit set and development through mediation of sugar communication between sink strength and source activity.
Collapse
Affiliation(s)
| | | | - Yalong Zhao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Jing Nie
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xuehui Yao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Lijun Lv
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Junwei Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ning Ma
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yicong Guo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yaxin Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xueyong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tao Lin
- Authors for correspondence: (T.L.); (X.S.)
| | | |
Collapse
|
31
|
Lyu X, Shi L, Zhao M, Li Z, Liao N, Meng Y, Ma Y, Zhou Y, Xue Q, Hu Z, Yang J, Zhang M. A natural mutation of the NST1 gene arrests secondary cell wall biosynthesis in the seed coat of a hull-less pumpkin accession. HORTICULTURE RESEARCH 2022; 9:uhac136. [PMID: 36072840 PMCID: PMC9437724 DOI: 10.1093/hr/uhac136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/07/2022] [Indexed: 05/31/2023]
Abstract
Hull-less pumpkins (Cucurbita pepo L.) are naturally occurring novel variants known as oilseed or naked-seeded pumpkins, and are characterized by the absence of a normal lignified seed coat. Due to a specialized seed coat structure, these variants serve as a good model for studying seed coat formation and simplify the processing of pumpkin seeds. However, causal genes for this hull-less trait still remain unknown. Here, by bulked segregant analysis and fine mapping, we found that mutation of a single gene, NAC SECONDARY WALL THICKENING PROMOTING FACTOR 1 (NST1), accounts for the hull-less trait. A 14-bp sequence insertion in the CpNST1 gene causes premature termination of CpNST1 translation, leading to lack of secondary cell wall (SCW) biosynthesis in hull-less seed coats. In situ hybridization analysis provided further evidence for the role of CpNST1 in pumpkin seed coat SCW biosynthesis. Interestingly, through secondary cell wall compositional analysis, we found that the main SCW components differed among cell layers in the seed coat. RNA-seq analysis indicated an upstream role of CpNST1 in the SCW biosynthesis network. Collectively, our findings provide mechanistic insight into seed coat SCW biosynthesis, and a target gene for breeders to introduce this hull-less trait for commercial exploitation.
Collapse
Affiliation(s)
- Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lu Shi
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Meng Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhangping Li
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Nanqiao Liao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yiqing Meng
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuyuan Ma
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yulan Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qin Xue
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | | |
Collapse
|
32
|
Echeverría A, Petrone‐Mendoza E, Segovia‐Rivas A, Figueroa‐Abundiz VA, Olson ME. The vessel wall thickness-vessel diameter relationship across woody angiosperms. AMERICAN JOURNAL OF BOTANY 2022; 109:856-873. [PMID: 35435252 PMCID: PMC9328290 DOI: 10.1002/ajb2.1854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 05/26/2023]
Abstract
PREMISE Comparative anatomy is necessary to identify the extremes of combinations of functionally relevant structural traits, to ensure that physiological data cover xylem anatomical diversity adequately, and thus achieve a global understanding of xylem structure-function relations. A key trait relationship is that between xylem vessel diameter and wall thickness of both the single vessel and the double vessel+adjacent imperforate tracheary element (ITE). METHODS We compiled a comparative data set with 1093 samples, 858 species, 350 genera, 86 families, and 33 orders. We used broken linear regression and an algorithm to explore changes in parameter values from linear regressions using subsets of the data set to identify a threshold, at 90-µm vessel diameter, in the wall thickness-diameter relationship. RESULTS Below 90 µm diameter for vessels, virtually any wall thickness could be associated with virtually any diameter. Below this threshold, selection is free to favor a very wide array of combinations, such as very thick walls and narrow vessels in ITE-free herbs, or very thin-walled, wide vessels in evergreen dryland pioneers. Above 90 µm, there was a moderate positive relationship. CONCLUSIONS Our analysis shows that the space of vessel wall thickness-diameter combinations is very wide, with selection apparently eliminating individuals with vessel walls "too thin" for their diameter. Most importantly, our survey revealed poorly studied plant hydraulic syndromes (functionally significant trait combinations). These data suggest that the full span of trait combinations, and thus the minimal set of hydraulic syndromes requiring study to span woody plant functional diversity adequately, remains to be documented.
Collapse
Affiliation(s)
- Alberto Echeverría
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n de Ciudad Universitaria, Ciudad de México, 04510México
| | - Emilio Petrone‐Mendoza
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n de Ciudad Universitaria, Ciudad de México, 04510México
| | - Alí Segovia‐Rivas
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n de Ciudad Universitaria, Ciudad de México, 04510México
| | - Víctor A. Figueroa‐Abundiz
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n de Ciudad Universitaria, Ciudad de México, 04510México
| | - Mark E. Olson
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n de Ciudad Universitaria, Ciudad de México, 04510México
| |
Collapse
|
33
|
Dong M, Xue S, Bartholomew ES, Zhai X, Sun L, Xu S, Zhang Y, Yin S, Ma W, Chen S, Feng Z, Geng C, Li X, Liu X, Ren H. Transcriptomic and functional analysis provides molecular insights into multicellular trichome development. PLANT PHYSIOLOGY 2022; 189:301-314. [PMID: 35171294 PMCID: PMC9070826 DOI: 10.1093/plphys/kiac050] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/13/2022] [Indexed: 05/31/2023]
Abstract
Trichomes, the hair-like structures located on aerial parts of most vascular plants, are associated with a wide array of biological processes and affect the economic value of certain species. The processes involved in unicellular trichome formation have been well-studied in Arabidopsis (Arabidopsis thaliana). However, our understanding of the morphological changes and the underlying molecular processes involved in multicellular trichome development is limited. Here, we studied the dynamic developmental processes involved in glandular and nonglandular multicellular trichome formation in cucumber (Cucumis sativus L.) and divided these processes into five sequential stages. To gain insights into the underlying mechanisms of multicellular trichome formation, we performed a time-course transcriptome analysis using RNA-sequencing analysis. A total of 711 multicellular trichome-related genes were screened and a model for multicellular trichome formation was developed. The transcriptome and co-expression datasets were validated by reverse transcription-quantitative PCR and in situ hybridization. In addition, virus-induced gene silencing analysis revealed that CsHOMEOBOX3 (CsHOX3) and CsbHLH1 are involved in nonglandular trichome elongation and glandular trichome formation, respectively, which corresponds with the transcriptome data. This study presents a transcriptome atlas that provides insights into the molecular processes involved in multicellular trichome formation in cucumber and can be an important resource for future functional studies.
Collapse
Affiliation(s)
- Mingming Dong
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shudan Xue
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ezra S Bartholomew
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xuling Zhai
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Lei Sun
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shuo Xu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yaqi Zhang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shuai Yin
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Wenyue Ma
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shuying Chen
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhongxuan Feng
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Chao Geng
- Department of Plant Pathology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
| | - Xiangdong Li
- Department of Plant Pathology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
| | | | | |
Collapse
|
34
|
Ollivier R, Glory I, Cloteau R, Le Gallic JF, Denis G, Morlière S, Miteul H, Rivière JP, Lesné A, Klein A, Aubert G, Kreplak J, Burstin J, Pilet-Nayel ML, Simon JC, Sugio A. A major-effect genetic locus, ApRVII, controlling resistance against both adapted and non-adapted aphid biotypes in pea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1511-1528. [PMID: 35192006 DOI: 10.1007/s00122-022-04050-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE A genome-wide association study for pea resistance against a pea-adapted biotype and a non-adapted biotype of the aphid, Acyrthosiphon pisum, identified a genomic region conferring resistance to both biotypes. In a context of reduced insecticide use, the development of cultivars resistant to insect pests is crucial for an integrated pest management. Pea (Pisum sativum) is a crop of major importance among cultivated legumes, for the supply of dietary proteins and nitrogen in low-input cropping systems. However, yields of the pea crop have become unstable due to plant parasites. The pea aphid (Acyrthosiphon pisum) is an insect pest species forming a complex of biotypes, each one adapted to feed on one or a few related legume species. This study aimed to identify resistance to A. pisum and the underlying genetic determinism by examining a collection of 240 pea genotypes. The collection was screened against a pea-adapted biotype and a non-adapted biotype of A. pisum to characterize their resistant phenotype. Partial resistance was observed in some pea genotypes exposed to the pea-adapted biotype. Many pea genotypes were completely resistant to non-adapted biotype, but some exhibited partial susceptibility. A genome-wide association study, using pea exome-capture sequencing data, enabled the identification of the major-effect quantitative trait locus ApRVII on the chromosome 7. ApRVII includes linkage disequilibrium blocks significantly associated with resistance to one or both of the two aphid biotypes studied. Finally, we identified candidate genes underlying ApRVII that are potentially involved in plant-aphid interactions and marker haplotypes linked with aphid resistance. This study sets the ground for the functional characterization of molecular pathways involved in pea defence to the aphids but also is a step forward for breeding aphid-resistant cultivars.
Collapse
Affiliation(s)
- Rémi Ollivier
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Isabelle Glory
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Romuald Cloteau
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | | | - Gaëtan Denis
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | | | - Henri Miteul
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | | | - Angélique Lesné
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Anthony Klein
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | - Grégoire Aubert
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | - Jonathan Kreplak
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | - Judith Burstin
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | | | | | - Akiko Sugio
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France.
| |
Collapse
|
35
|
Liang C, Wei C, Wang L, Guan Z, Shi T, Huang J, Li B, Lu Y, Liu H, Wang Y. Characterization of a Novel Creeping Tartary Buckwheat ( Fagopyrum tataricum) Mutant lazy1. FRONTIERS IN PLANT SCIENCE 2022; 13:815131. [PMID: 35574111 PMCID: PMC9094088 DOI: 10.3389/fpls.2022.815131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/02/2022] [Indexed: 06/15/2023]
Abstract
Gravity is known as an important environmental factor involved in the regulation of plant architecture. To identify genes related to the gravitropism of Tartary buckwheat, a creeping line was obtained and designated as lazy1 from the mutant bank by 60Co-γ ray radiation. Genetic analysis indicated that the creeping phenotype of lazy1 was attributed to a single recessive locus. As revealed by the horizontal and inverted suspension tests, lazy1 was completely lacking in shoot negative gravitropism. The creeping growth of lazy1 occurred at the early seedling stage, which could not be recovered by exogenous heteroauxin, hormodin, α-rhodofix, or gibberellin. Different from the well-organized and equivalent cell elongation of wild type (WT), lazy1 exhibited dilated, distorted, and abnormally arranged cells in the bending stem. However, no statistical difference of indole-3-acetic acid (IAA) levels was found between the far- and near-ground bending sides in lazy1, which suggests that the asymmetric cell elongation of lazy1 was not induced by auxin gradient. Whereas, lazy1 showed up-expressed gibberellin-regulated genes by quantitative real-time PCR (qRT-PCR) as well as significantly higher levels of gibberellin, suggesting that gibberellin might be partly involved in the regulation of creeping growth in lazy1. RNA sequencing (RNA-seq) identified a number of differentially expressed genes (DEGs) related to gravitropism at stages I (before bending), II (bending), and III (after bending) between WT and lazy1. Venn diagram indicated that only Pectate lyase 5 was down-expressed at stages I [Log2 fold change (Log2FC): -3.20], II (Log2FC: -4.97), and III (Log2FC: -1.23) in lazy1, compared with WT. Gene sequencing revealed that a fragment deletion occurred in the coding region of Pectate lyase 5, which induced the destruction of a pbH domain in Pectate lyase 5 of lazy1. qRT-PCR indicated that Pectate lyase 5 was extremely down-expressed in lazy1 at stage II (0.02-fold of WT). Meanwhile, lazy1 showed the affected expression of lignin- and cellulose-related genes and cumulatively abnormal levels of pectin, lignin, and cellulose. These results demonstrate the possibility that Pectate lyase 5 functions as the key gene that could mediate primary cell wall metabolism and get involved in the asymmetric cell elongation regulation of lazy1.
Collapse
Affiliation(s)
- Chenggang Liang
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Chunyu Wei
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Li Wang
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Zhixiu Guan
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Taoxiong Shi
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Juan Huang
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Bin Li
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yang Lu
- Guizhou Biotechnology Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, China
| | - Hui Liu
- Guizhou Biotechnology Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, China
| | - Yan Wang
- Research Center of Buckwheat Industry Technology, School of Life Sciences, Guizhou Normal University, Guiyang, China
| |
Collapse
|
36
|
Achom M, Roy P, Lagunas B, Picot E, Richards L, Bonyadi-Pour R, Pardal AJ, Baxter L, Richmond BL, Aschauer N, Fletcher EM, Rowson M, Blackwell J, Rich-Griffin C, Mysore KS, Wen J, Ott S, Carré IA, Gifford ML. Plant circadian clock control of Medicago truncatula nodulation via regulation of nodule cysteine-rich peptides. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2142-2156. [PMID: 34850882 PMCID: PMC8982390 DOI: 10.1093/jxb/erab526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules, we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcription factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset of nodule-specific cysteine-rich peptides (NCRs) that have the LHY-bound conserved evening element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis.
Collapse
Affiliation(s)
- Mingkee Achom
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Proyash Roy
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Beatriz Lagunas
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Emma Picot
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Luke Richards
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Roxanna Bonyadi-Pour
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Alonso J Pardal
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Laura Baxter
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Bethany L Richmond
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Nadine Aschauer
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Eleanor M Fletcher
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Monique Rowson
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Joseph Blackwell
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Charlotte Rich-Griffin
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kirankumar S Mysore
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Sascha Ott
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Isabelle A Carré
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
| | - Miriam L Gifford
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| |
Collapse
|
37
|
Natukunda MI, Mantilla-Perez MB, Graham MA, Liu P, Salas-Fernandez MG. Dissection of canopy layer-specific genetic control of leaf angle in Sorghum bicolor by RNA sequencing. BMC Genomics 2022; 23:95. [PMID: 35114939 PMCID: PMC8812014 DOI: 10.1186/s12864-021-08251-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/10/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Leaf angle is an important plant architecture trait, affecting plant density, light interception efficiency, photosynthetic rate, and yield. The "smart canopy" model proposes more vertical leaves in the top plant layers and more horizontal leaves in the lower canopy, maximizing conversion efficiency and photosynthesis. Sorghum leaf arrangement is opposite to that proposed in the "smart canopy" model, indicating the need for improvement. Although leaf angle quantitative trait loci (QTL) have been previously reported, only the Dwarf3 (Dw3) auxin transporter gene, colocalizing with a major-effect QTL on chromosome 7, has been validated. Additionally, the genetic architecture of leaf angle across canopy layers remains to be elucidated. RESULTS This study characterized the canopy-layer specific transcriptome of five sorghum genotypes using RNA sequencing. A set of 284 differentially expressed genes for at least one layer comparison (FDR < 0.05) co-localized with 69 leaf angle QTL and were consistently identified across genotypes. These genes are involved in transmembrane transport, hormone regulation, oxidation-reduction process, response to stimuli, lipid metabolism, and photosynthesis. The most relevant eleven candidate genes for layer-specific angle modification include those homologous to genes controlling leaf angle in rice and maize or genes associated with cell size/expansion, shape, and cell number. CONCLUSIONS Considering the predicted functions of candidate genes, their potential undesirable pleiotropic effects should be further investigated across tissues and developmental stages. Future validation of proposed candidates and exploitation through genetic engineering or gene editing strategies targeted to collar cells will bring researchers closer to the realization of a "smart canopy" sorghum.
Collapse
Affiliation(s)
| | - Maria B Mantilla-Perez
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Present address: Bayer Crop Science, Chesterfield, MO, USA
| | - Michelle A Graham
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Corn Insects and Crop Genetics Research, USDA-ARS, Ames, IA, 50011, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA, 50011, USA
| | | |
Collapse
|
38
|
He W, Xie R, Wang Y, Chen Q, Wang H, Yang S, Luo Y, Zhang Y, Tang H, Gmitter FG, Wang X. Comparative transcriptomic analysis on compatible/incompatible grafts in citrus. HORTICULTURE RESEARCH 2022; 9:uhab072. [PMID: 35043167 PMCID: PMC8931943 DOI: 10.1093/hr/uhab072] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Grafting is a useful cultivation technology to resist abiotic and biotic stresses and is an integral part of citrus production. However, some widely utilized rootstocks may still exhibit graft incompatibility in the orchard. "Hongmian miyou" (Citrus maxima (Burm.) Merrill) is mutated from "Guanxi miyou", but these two scions showed different compatibility with available Poncirus trifoliata rootstock. Foliage etiolation is an observed symptom of graft incompatibility, but its mechanism remains poorly understood. This study is the first to investigate the morphological, physiological, and anatomical differences between the compatible/incompatible grafts, and perform transcriptome profiling at crucial stages of the foliage etiolation process. Based on the comprehensive analyses, hormonal balance was disordered, and two rate-limiting genes, NCED3 (9-cis-epoxycarotenoid dioxygenases 3) and NCED5, being responsible for ABA (abscisic acid) accumulation, were highlighted. Further correlation analysis indicated that IAA (indole-3-acetic acid) and ABA were the most likely inducers of the expression of stresses-related genes. In addition, excessive starch accumulation was observed in lamina and midribs of incompatible grafts leaves. These results provided a new insight into the role of the hormonal balance and abscisic acid biosynthesis genes in regulation and contribution to the graft incompatibility, and will further define and deploy candidate genes to explore the mechanisms underlying citrus rootstock- scion interactions.
Collapse
Affiliation(s)
- Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Rui Xie
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Shaofeng Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Frederick G Gmitter
- Citrus Research and Education Center, University of Florida, Lake Alfred 33850, FL, USA
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| |
Collapse
|
39
|
Zhang M, Zhong X, Li M, Yang X, Abou Elwafa SF, Albaqami M, Tian H. Genome-wide analyses of the Nodulin-like gene family in bread wheat revealed its potential roles during arbuscular mycorrhizal symbiosis. Int J Biol Macromol 2022; 201:424-436. [PMID: 35041884 DOI: 10.1016/j.ijbiomac.2022.01.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 11/05/2022]
Abstract
Nodulin-like (NL) genes are involved in transporting of various substances and may play key roles during the establishment of symbiosis in legumes plants. However, basic biological information of NL genes in the wheat genome is still largely unknown. Here, we identified and characterized NL genes in wheat via integrating genomic information, collinearity analysis, co-expression network analysis (WGCNA) and transcriptome analysis. In addition, we analyzed the polymorphisms and the roles of NL genes during arbuscular mycorrhizal (AM) symbiosis using a large wheat panel consists of 259 wheat genotypes. We identified 181 NL genes in the wheat genome, which were classified into SWEET, Early Nodulin-Like (ENODL), Major Facilitator Superfamily-Nodulin (MFS), Vacuolar Iron Transporter (VIT) and Early nodulin 93 (ENOD93) subfamily. The expansion of NL genes was mainly driven by segmental duplication. The bHLH genes are potential unrecognized transcription factors regulating NL genes. Moreover, two NL genes were more sensitive than other NL genes to AM colonization. The polymorphisms of NL genes are mainly due to random drift, and the natural mutation of NL genes led to significant differences in the mycorrhizal dependence of wheat in phosphorus uptake. The results concluded that NL genes potentially play important roles during AM symbiosis with wheat.
Collapse
Affiliation(s)
- Mingming Zhang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiong Zhong
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengjiao Li
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiuming Yang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Salah F Abou Elwafa
- Agronomy department, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt
| | - Mohammed Albaqami
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Hui Tian
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
40
|
Swetha C, Narjala A, Pandit A, Tirumalai V, Shivaprasad PV. Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs. BMC Genomics 2022; 23:53. [PMID: 35031003 PMCID: PMC8759253 DOI: 10.1186/s12864-021-08288-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/23/2021] [Indexed: 11/14/2022] Open
Abstract
Background Small non-coding (s)RNAs are involved in the negative regulation of gene expression, playing critical roles in genome integrity, development and metabolic pathways. Targeting of RNAs by ribonucleoprotein complexes of sRNAs bound to Argonaute (AGO) proteins results in cleaved RNAs having precise and predictable 5` ends. While tools to study sliced bits of RNAs to confirm the efficiency of sRNA-mediated regulation are available, they are sub-optimal. In this study, we provide an improvised version of a tool with better efficiency to accurately validate sRNA targets. Results Here, we improvised the CleaveLand tool to identify additional micro (mi)RNA targets that belong to the same family and also other targets within a specified free energy cut-off. These additional targets were otherwise excluded during the default run. We employed these tools to understand the sRNA targeting efficiency in wild and cultivated rice, sequenced degradome from two rice lines, O. nivara and O. sativa indica Pusa Basmati-1 and analyzed variations in sRNA targeting. Our results indicate the existence of multiple miRNA-mediated targeting differences between domesticated and wild species. For example, Os5NG4 was targeted only in wild rice that might be responsible for the poor secondary wall formation when compared to cultivated rice. We also identified differential mRNA targets of secondary sRNAs that were generated after miRNA-mediated cleavage of primary targets. Conclusions We identified many differentially targeted mRNAs between wild and domesticated rice lines. In addition to providing a step-wise guide to generate and analyze degradome datasets, we showed how domestication altered sRNA-mediated cascade silencing during the evolution of indica rice. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08288-5.
Collapse
Affiliation(s)
- Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India.,SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Anushree Narjala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India.,SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Varsha Tirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India.,SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India.
| |
Collapse
|
41
|
Fang ZT, Kapoor R, Datta A, Okumoto S. Tissue specific expression of UMAMIT amino acid transporters in wheat. Sci Rep 2022; 12:348. [PMID: 35013480 PMCID: PMC8748447 DOI: 10.1038/s41598-021-04284-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/20/2021] [Indexed: 11/09/2022] Open
Abstract
Wheat grain protein content and composition are important for its end-use quality. Protein synthesis during the grain filling phase is supported by the amino acids remobilized from the vegetative tissue, the process in which both amino acid importers and exporters are expected to be involved. Previous studies identified amino acid importers that might function in the amino acid remobilization in wheat. However, the amino acid exporters involved in this process have been unexplored so far. In this study, we have curated the Usually Multiple Amino acids Move In and out Transporter (UMAMIT) family of transporters in wheat. As expected, the majority of UMAMITs were found as triads in the A, B, and D genomes of wheat. Expression analysis using publicly available data sets identified groups of TaUMAMITs expressed in root, leaf, spike, stem and grain tissues, many of which were temporarily regulated. Strong expression of TaUMAMITs was detected in the late senescing leaves and transfer cells in grains, both of which are the expected site of apoplastic amino acid transport during grain filling. Biochemical characterization of selected TaUMAMITs revealed that TaUMAMIT17 shows a strong amino acid export activity and might play a role in amino acid transfer to the grains.
Collapse
Affiliation(s)
- Ze Tian Fang
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, TX, USA
| | - Rajan Kapoor
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Aniruddha Datta
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Sakiko Okumoto
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, TX, USA.
| |
Collapse
|
42
|
Uchendu K, Njoku DN, Paterne A, Rabbi IY, Dzidzienyo D, Tongoona P, Offei S, Egesi C. Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava. FRONTIERS IN PLANT SCIENCE 2021; 12:770434. [PMID: 34975953 PMCID: PMC8719520 DOI: 10.3389/fpls.2021.770434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.
Collapse
Affiliation(s)
- Kelechi Uchendu
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | | | - Agre Paterne
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Daniel Dzidzienyo
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Samuel Offei
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| |
Collapse
|
43
|
Hosaka GK, Correr FH, da Silva CC, Sforça DA, Barreto FZ, Balsalobre TWA, Pasha A, de Souza AP, Provart NJ, Carneiro MS, Margarido GRA. Temporal Gene Expression in Apical Culms Shows Early Changes in Cell Wall Biosynthesis Genes in Sugarcane. FRONTIERS IN PLANT SCIENCE 2021; 12:736797. [PMID: 34966397 PMCID: PMC8710541 DOI: 10.3389/fpls.2021.736797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Multiple genes in sugarcane control sucrose accumulation and the biosynthesis of cell wall components; however, it is unclear how these genes are expressed in its apical culms. To better understand this process, we sequenced mRNA from +1 stem internodes collected from four genotypes with different concentrations of soluble solids. Culms were collected at four different time points, ranging from six to 12-month-old plants. Here we show differentially expressed genes related to sucrose metabolism and cell wall biosynthesis, including genes encoding invertases, sucrose synthase and cellulose synthase. Our results showed increased expression of invertases in IN84-58, the genotype with lower sugar and higher fiber content, as well as delayed expression of secondary cell wall-related cellulose synthase for the other genotypes. Interestingly, genes involved with hormone metabolism were differentially expressed across time points in the three genotypes with higher soluble solids content. A similar result was observed for genes controlling maturation and transition to reproductive stages, possibly a result of selection against flowering in sugarcane breeding programs. These results indicate that carbon partitioning in apical culms of contrasting genotypes is mainly associated with differential cell wall biosynthesis, and may include early modifications for subsequent sucrose accumulation. Co-expression network analysis identified transcription factors related to growth and development, showing a probable time shift for carbon partitioning occurred in 10-month-old plants.
Collapse
Affiliation(s)
- Guilherme Kenichi Hosaka
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Fernando Henrique Correr
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Fernanda Zatti Barreto
- Plant Biotechnology Laboratory, Centre for Agricultural Sciences, Federal University of São Carlos (CCA-UFSCar), Araras, Brazil
| | | | - Asher Pasha
- Department of Cell and Systems Biology, Centre for the Analysis of the Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Nicholas James Provart
- Department of Cell and Systems Biology, Centre for the Analysis of the Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Monalisa Sampaio Carneiro
- Plant Biotechnology Laboratory, Centre for Agricultural Sciences, Federal University of São Carlos (CCA-UFSCar), Araras, Brazil
| | | |
Collapse
|
44
|
Kim JY, Loo EPI, Pang TY, Lercher M, Frommer WB, Wudick MM. Cellular export of sugars and amino acids: role in feeding other cells and organisms. PLANT PHYSIOLOGY 2021; 187:1893-1914. [PMID: 34015139 PMCID: PMC8644676 DOI: 10.1093/plphys/kiab228] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/29/2021] [Indexed: 05/20/2023]
Abstract
Sucrose, hexoses, and raffinose play key roles in the plant metabolism. Sucrose and raffinose, produced by photosynthesis, are translocated from leaves to flowers, developing seeds and roots. Translocation occurs in the sieve elements or sieve tubes of angiosperms. But how is sucrose loaded into and unloaded from the sieve elements? There seem to be two principal routes: one through plasmodesmata and one via the apoplasm. The best-studied transporters are the H+/SUCROSE TRANSPORTERs (SUTs) in the sieve element-companion cell complex. Sucrose is delivered to SUTs by SWEET sugar uniporters that release these key metabolites into the apoplasmic space. The H+/amino acid permeases and the UmamiT amino acid transporters are hypothesized to play analogous roles as the SUT-SWEET pair to transport amino acids. SWEETs and UmamiTs also act in many other important processes-for example, seed filling, nectar secretion, and pollen nutrition. We present information on cell type-specific enrichment of SWEET and UmamiT family members and propose several members to play redundant roles in the efflux of sucrose and amino acids across different cell types in the leaf. Pathogens hijack SWEETs and thus represent a major susceptibility of the plant. Here, we provide an update on the status of research on intercellular and long-distance translocation of key metabolites such as sucrose and amino acids, communication of the plants with the root microbiota via root exudates, discuss the existence of transporters for other important metabolites and provide potential perspectives that may direct future research activities.
Collapse
Affiliation(s)
- Ji-Yun Kim
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Eliza P -I Loo
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Tin Yau Pang
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Martin Lercher
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Michael M Wudick
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Author for communication:
| |
Collapse
|
45
|
Dhatterwal P, Mehrotra S, Miller AJ, Mehrotra R. Promoter profiling of Arabidopsis amino acid transporters: clues for improving crops. PLANT MOLECULAR BIOLOGY 2021; 107:451-475. [PMID: 34674117 DOI: 10.1007/s11103-021-01193-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
The review describes the importance of amino acid transporters in plant growth, development, stress tolerance, and productivity. The promoter analysis provides valuable insights into their functionality leading to agricultural benefits. Arabidopsis thaliana genome is speculated to possess more than 100 amino acid transporter genes. This large number suggests the functional significance of amino acid transporters in plant growth and development. The current article summarizes the substrate specificity, cellular localization, tissue-specific expression, and expression of the amino acid transporter genes in response to environmental cues. However, till date functionality of a majority of amino acid transporter genes in plant development and stress tolerance is unexplored. Considering, that gene expression is mainly regulated by the regulatory motifs localized in their promoter regions at the transcriptional levels. The promoter regions ( ~ 1-kbp) of these amino acid transporter genes were analysed for the presence of cis-regulatory motifs responsive to developmental and external cues. This analysis can help predict the functionality of known and unexplored amino acid transporters in different tissues, organs, and various growth and development stages and responses to external stimuli. Furthermore, based on the promoter analysis and utilizing the microarray expression data we have attempted to identify plausible candidates (listed below) that might be targeted for agricultural benefits.
Collapse
Affiliation(s)
- Pinky Dhatterwal
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K.K. Birla Goa Campus, Goa, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K.K. Birla Goa Campus, Goa, India
| | - Anthony J Miller
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, K.K. Birla Goa Campus, Goa, India.
| |
Collapse
|
46
|
Adaptive divergence in shoot gravitropism creates hybrid sterility in an Australian wildflower. Proc Natl Acad Sci U S A 2021; 118:2004901118. [PMID: 34789571 PMCID: PMC8617494 DOI: 10.1073/pnas.2004901118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2021] [Indexed: 11/18/2022] Open
Abstract
New species originate as populations become reproductively isolated from one another. Despite recent progress in uncovering the genetic basis of reproductive isolation, it remains unclear whether intrinsic reproductive barriers, such as hybrid sterility, can evolve as a by-product of local adaptation to contrasting environments. Here, we show that differences in a plant’s response to the pull of gravity have repeatedly evolved amongst coastal populations of an Australian wildflower, thus implicating a role of natural selection in their evolution. We found a strong genetic association between variation in this adaptive trait and hybrid sterility, suggesting that intrinsic reproductive barriers contribute to the origin of new species as populations adapt to heterogeneous environments. Natural selection is responsible for much of the diversity we see in nature. Just as it drives the evolution of new traits, it can also lead to new species. However, it is unclear whether natural selection conferring adaptation to local environments can drive speciation through the evolution of hybrid sterility between populations. Here, we show that adaptive divergence in shoot gravitropism, the ability of a plant’s shoot to bend upwards in response to the downward pull of gravity, contributes to the evolution of hybrid sterility in an Australian wildflower, Senecio lautus. We find that shoot gravitropism has evolved multiple times in association with plant height between adjacent populations inhabiting contrasting environments, suggesting that these traits have evolved by natural selection. We directly tested this prediction using a hybrid population subjected to eight rounds of recombination and three rounds of selection in the field. Our experiments revealed that shoot gravitropism responds to natural selection in the expected direction of the locally adapted population. Using the advanced hybrid population, we discovered that individuals with extreme differences in gravitropism had more sterile crosses than individuals with similar gravitropic responses, which were largely fertile, indicating that this adaptive trait is genetically correlated with hybrid sterility. Our results suggest that natural selection can drive the evolution of locally adaptive traits that also create hybrid sterility, thus revealing an evolutionary connection between local adaptation and the origin of new species.
Collapse
|
47
|
Takata N, Tsuyama T, Nagano S, Baba K, Yasuda Y, Sakamoto S, Mitsuda N, Taniguchi T. Prior secondary cell wall formation is required for gelatinous layer deposition and posture control in gravi-stimulated aspen. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:725-736. [PMID: 34396622 DOI: 10.1111/tpj.15466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/19/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
Cell walls, especially secondary cell walls (SCWs), maintain cell shape and reinforce wood, but their structure and shape can be altered in response to gravity. In hardwood trees, tension wood is formed along the upper side of a bending stem and contains wood fiber cells that have a gelatinous layer (G-layer) inside the SCW. In a previous study, we generated nst/snd quadruple-knockout aspens (Populus tremula × Populus tremuloides), in which SCW formation was impaired in 99% of the wood fiber cells. In the present study, we produced nst/snd triple-knockout aspens, in which a large number of wood fibers had thinner SCWs than the wild type (WT) and some had no SCW. Because SCW layers are always formed prior to G-layer deposition, the nst/snd mutants raise interesting questions of whether the mutants can form G-layers without SCW and whether they can control their postures in response to changes in gravitational direction. The nst/snd mutants and the WT plants showed growth eccentricity and vessel frequency reduction when grown on an incline, but the triple mutants recovered their upright growth only slightly, and the quadruple mutants were unable to maintain their postures. The mutants clearly showed that the G-layers were formed in SCW-containing wood fibers but not in those lacking the SCW. Our results indicate that SCWs are essential for G-layer formation and posture control. Furthermore, each wood fiber cell may be able to recognize its cell wall developmental stage to initiate the formation of the G-layer as a response to gravistimulation.
Collapse
Affiliation(s)
- Naoki Takata
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, 319-1301, Japan
| | - Taku Tsuyama
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, 889-2192, Japan
| | - Soichiro Nagano
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, 319-1301, Japan
| | - Kei'ichi Baba
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Yuko Yasuda
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, 319-1301, Japan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
- Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
- Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Toru Taniguchi
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, 319-1301, Japan
| |
Collapse
|
48
|
Zhai N, Xu L. Pluripotency acquisition in the middle cell layer of callus is required for organ regeneration. NATURE PLANTS 2021; 7:1453-1460. [PMID: 34782770 DOI: 10.1038/s41477-021-01015-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/05/2021] [Indexed: 05/12/2023]
Abstract
In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.
Collapse
Affiliation(s)
- Ning Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
49
|
Ying S. Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family. Int J Mol Sci 2021; 22:11442. [PMID: 34768874 PMCID: PMC8583954 DOI: 10.3390/ijms222111442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
The Domain of unknown function 506 (DUF506) family, which belongs to the PD-(D/E)XK nuclease superfamily, has not been functionally characterized. In this study, 266 DUF506 domain-containing genes were identified from algae, mosses, and land plants showing their wide occurrence in photosynthetic organisms. Bioinformatics analysis identified 211 high-confidence DUF506 genes across 17 representative land plant species. Phylogenetic modeling classified three groups of plant DUF506 genes that suggested functional preservation among the groups based on conserved gene structure and motifs. Gene duplication and Ka/Ks evolutionary rates revealed that DUF506 genes are under purifying positive selection pressure. Subcellular protein localization analysis revealed that DUF506 proteins were present in different organelles. Transcript analyses showed that 13 of the Arabidopsis DUF506 genes are ubiquitously expressed in various tissues and respond to different abiotic stresses and ABA treatment. Protein-protein interaction network analysis using the STRING-DB, AtPIN (Arabidopsis thaliana Protein Interaction Network), and AI-1 (Arabidopsis Interactome-1) tools indicated that AtDUF506s potentially interact with iron-deficiency response proteins, salt-inducible transcription factors, or calcium sensors (calmodulins), implying that DUF506 genes have distinct biological functions including responses to environmental stimuli, nutrient-deficiencies, and participate in Ca(2+) signaling. Current results provide insightful information regarding the molecular features of the DUF506 family in plants, to support further functional characterizations.
Collapse
Affiliation(s)
- Sheng Ying
- Noble Research Institute LLC, Ardmore, OK 73401, USA
| |
Collapse
|
50
|
Chopra D, Hasan MS, Matera C, Chitambo O, Mendy B, Mahlitz SV, Naz AA, Szumski S, Janakowski S, Sobczak M, Mithöfer A, Kyndt T, Grundler FMW, Siddique S. Plant parasitic cyst nematodes redirect host indole metabolism via NADPH oxidase-mediated ROS to promote infection. THE NEW PHYTOLOGIST 2021; 232:318-331. [PMID: 34133755 DOI: 10.1111/nph.17559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/11/2021] [Indexed: 06/12/2023]
Abstract
Reactive oxygen species (ROS) generated in response to infections often activate immune responses in eukaryotes including plants. In plants, ROS are primarily produced by plasma membrane-bound NADPH oxidases called respiratory burst oxidase homologue (Rboh). Surprisingly, Rbohs can also promote the infection of plants by certain pathogens, including plant parasitic cyst nematodes. The Arabidopsis genome contains 10 Rboh genes (RbohA-RbohJ). Previously, we showed that cyst nematode infection causes a localised ROS burst in roots, mediated primarily by RbohD and RbohF. We also found that plants deficient in RbohD and RbohF (rbohD/F) exhibit strongly decreased susceptibility to cyst nematodes, suggesting that Rboh-mediated ROS plays a role in promoting infection. However, little information is known of the mechanism by which Rbohs promote cyst nematode infection. Here, using detailed genetic and biochemical analyses, we identified WALLS ARE THIN1 (WAT1), an auxin transporter, as a downstream target of Rboh-mediated ROS during parasitic infections. We found that WAT1 is required to modulate the host's indole metabolism, including indole-3-acetic acid levels, in infected cells and that this reprogramming is necessary for successful establishment of the parasite. In conclusion, this work clarifies a unique mechanism that enables cyst nematodes to use the host's ROS for their own benefit.
Collapse
Affiliation(s)
- Divykriti Chopra
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, Bonn, D-53115, Germany
| | - M Shamim Hasan
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, Bonn, D-53115, Germany
- Department of Plant Pathology, Faculty of Agriculture, Hajee Mohammad Danesh Science and Technology University, Dinajpur, 5200, Bangladesh
| | - Christiane Matera
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, Bonn, D-53115, Germany
| | - Oliver Chitambo
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, Bonn, D-53115, Germany
| | - Badou Mendy
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, Bonn, D-53115, Germany
| | - Sina-Valerie Mahlitz
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, Bonn, D-53115, Germany
| | - Ali Ahmad Naz
- Department of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, D-53115, Germany
| | - Shelly Szumski
- Department of Entomology and Nematology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Slawomir Janakowski
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences (SGGW), Warsaw, PL-02-787, Poland
| | - Miroslaw Sobczak
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences (SGGW), Warsaw, PL-02-787, Poland
| | - Axel Mithöfer
- Research Group Plant Defense Physiology, Max Plank Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena, D-07745, Germany
| | - Tina Kyndt
- Department Biotechnology, Research Group Epigenetics & Defence, Coupure links 653, Gent, B-9000, Belgium
| | - Florian M W Grundler
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, Bonn, D-53115, Germany
| | - Shahid Siddique
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES - Molecular Phytomedicine, Karlrobert-Kreiten-Straße 13, Bonn, D-53115, Germany
- Department of Entomology and Nematology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| |
Collapse
|