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Sun W, Xia L, Deng J, Sun S, Yue D, You J, Wang M, Jin S, Zhu L, Lindsey K, Zhang X, Yang X. Evolution and subfunctionalization of CIPK6 homologous genes in regulating cotton drought resistance. Nat Commun 2024; 15:5733. [PMID: 38977687 PMCID: PMC11231324 DOI: 10.1038/s41467-024-50097-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 06/28/2024] [Indexed: 07/10/2024] Open
Abstract
The occurrence of whole-genome duplication or polyploidy may promote plant adaptability to harsh environments. Here, we clarify the evolutionary relationship of eight GhCIPK6 homologous genes in upland cotton (Gossypium hirsutum). Gene expression and interaction analyses indicate that GhCIPK6 homologous genes show significant functional changes after polyploidy. Among these, GhCIPK6D1 and GhCIPK6D3 are significantly up-regulated by drought stress. Functional studies reveal that high GhCIPK6D1 expression promotes cotton drought sensitivity, while GhCIPK6D3 expression promotes drought tolerance, indicating clear functional differentiation. Genetic and biochemical analyses confirm the synergistic negative and positive regulation of cotton drought resistance through GhCBL1A1-GhCIPK6D1 and GhCBL2A1-GhCIPK6D3, respectively, to regulate stomatal movement by controlling the directional flow of K+ in guard cells. These results reveal differentiated roles of GhCIPK6 homologous genes in response to drought stress in upland cotton following polyploidy. The work provides a different perspective for exploring the functionalization and subfunctionalization of duplicated genes in response to polyploidization.
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Affiliation(s)
- Weinan Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
| | - Linjie Xia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
| | - Jinwu Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
| | - Simin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
| | - Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China.
- Hubei Hongshan Laboratory, Wuhan, China.
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Almeida-Silva F, Prost-Boxoen L, Van de Peer Y. hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors. THE NEW PHYTOLOGIST 2024; 243:811-819. [PMID: 38798271 PMCID: PMC7616114 DOI: 10.1111/nph.19862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).
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Affiliation(s)
- Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Lucas Prost-Boxoen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Biology, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
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3
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Sun R, Wu Y, Zhang X, Lv M, Yu D, Sun Y. Chromosome-level genome assembly and annotation of a potential model organism Gossypium arboreum ZB-1. Sci Data 2024; 11:620. [PMID: 38866802 PMCID: PMC11169495 DOI: 10.1038/s41597-024-03481-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Recent advancements in plant regeneration and synthetic polyploid creation have been documented in Gossypium arboreum ZB-1. These developments make ZB-1 a potential model within the Gossypium genus for investigating gene function and polyploidy. This work generated the sequence and annotation of the ZB-1 genome. The contig-level genome was constructed using the PacBio high-fidelity reads, encompassing 81 contigs with an N50 length of 112.12 Mb. The Hi-C data assisted the construction of the chromosome-level genome, which consists of 13 pseudo-chromosomes and 39 un-anchored contigs, with a total length of about 1.67 Gb. Repetitive sequences accounted for about 69.7% of the genome in length. Based on ab initio and evidence-based prediction, we have identified 48,021 protein-coding genes in the ZB-1 genome. Comparative genomics analysis revealed conserved gene content and arrangement between ZB-1 and G. arboreum SXY1. The single nucleotide polymorphism occurrence rate between ZB-1 and SXY1 was about 0.54 per 1,000 nucleotides. This study enriched the genomic resources for further exploration into cotton regeneration and polyploidy mechanisms.
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Affiliation(s)
- Rongnan Sun
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Yuqing Wu
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Xinyu Zhang
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Minghua Lv
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Dongliang Yu
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China.
| | - Yuqiang Sun
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China.
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Wu Y, Sun R, Huan T, Zhao Y, Yu D, Sun Y. An insight into the gene expression evolution in Gossypium species based on the leaf transcriptomes. BMC Genomics 2024; 25:179. [PMID: 38355396 PMCID: PMC10868065 DOI: 10.1186/s12864-024-10091-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/05/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Gene expression pattern is associated with biological phenotype and is widely used in exploring gene functions. Its evolution is also crucial in understanding species speciation and divergence. The genus Gossypium is a bona fide model for studying plant evolution and polyploidization. However, the evolution of gene expression during cotton species divergence has yet to be extensively discussed. RESULTS Based on the seedling leaf transcriptomes, this work analyzed the transcriptomic content and expression patterns across eight cotton species, including six diploids and two natural tetraploids. Our findings indicate that, while the biological function of these cotton transcriptomes remains largely conserved, there has been significant variation in transcriptomic content during species divergence. Furthermore, we conducted a comprehensive analysis of expression distances across cotton species. This analysis lends further support to the use of G. arboreum as a substitute for the A-genome donor of natural cotton polyploids. Moreover, our research highlights the evolution of stress-responsive pathways, including hormone signaling, fatty acid degradation, and flavonoid biosynthesis. These processes appear to have evolved under lower selection pressures, presumably reflecting their critical role in the adaptations of the studied cotton species to diverse environments. CONCLUSIONS In summary, this study provided insights into the gene expression variation within the genus Gossypium and identified essential genes/pathways whose expression evolution was closely associated with the evolution of cotton species. Furthermore, the method of characterizing genes and pathways under unexpected high or slow selection pressure can also serve as a new strategy for gene function exploration.
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Affiliation(s)
- Yuqing Wu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Rongnan Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Tong Huan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yanyan Zhao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Dongliang Yu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Yuqiang Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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You J, Liu Z, Qi Z, Ma Y, Sun M, Su L, Niu H, Peng Y, Luo X, Zhu M, Huang Y, Chang X, Hu X, Zhang Y, Pi R, Liu Y, Meng Q, Li J, Zhang Q, Zhu L, Lin Z, Min L, Yuan D, Grover CE, Fang DD, Lindsey K, Wendel JF, Tu L, Zhang X, Wang M. Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton. Nat Genet 2023; 55:1987-1997. [PMID: 37845354 PMCID: PMC10632151 DOI: 10.1038/s41588-023-01530-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 09/14/2023] [Indexed: 10/18/2023]
Abstract
Polyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic regulation of gene expression between coresident subgenomes in polyploids remains to be understood. Here we document the genetic regulation of fiber development in allotetraploid cotton Gossypium hirsutum by sequencing 376 genomes and 2,215 time-series transcriptomes. We characterize 1,258 genes comprising 36 genetic modules that control staged fiber development and uncover genetic components governing their partitioned expression relative to subgenomic duplicated genes (homoeologs). Only about 30% of fiber quality-related homoeologs show phenotypically favorable allele aggregation in cultivars, highlighting the potential for subgenome additivity in fiber improvement. We envision a genome-enabled breeding strategy, with particular attention to 48 favorable alleles related to fiber phenotypes that have been subjected to purifying selection during domestication. Our work delineates the dynamics of gene regulation during fiber development and highlights the potential of subgenomic coordination underpinning phenotypes in polyploid plants.
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Affiliation(s)
- Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhengyang Qi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Mengling Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ling Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Hao Niu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yabing Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuanxuan Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Mengmeng Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuefan Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xing Chang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiubao Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuqi Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ruizhen Pi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuqi Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qingying Meng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, USA
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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Nazir MF, Chen B, Umer MJ, Sarfraz Z, Peng Z, He S, Iqbal MS, Wang J, Li H, Pan Z, Hu D, Song M, Du X. Transcriptomic analysis reveals the beneficial effects of salt priming on enhancing defense responses in upland cotton under successive salt stress. PHYSIOLOGIA PLANTARUM 2023; 175:e14074. [PMID: 38148226 DOI: 10.1111/ppl.14074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/11/2023] [Accepted: 10/24/2023] [Indexed: 12/28/2023]
Abstract
Priming-mediated stress tolerance in plants stimulates defense mechanisms and enables plants to cope with future stresses. Seed priming has been proven effective for tolerance against abiotic stresses; however, underlying genetic mechanisms are still unknown. We aimed to assess upland cotton genotypes and their transcriptional behaviors under salt priming and successive induced salt stress. We pre-selected 16 genotypes based on previous studies and performed morpho-physiological characterization, from which we selected three genotypes, representing different tolerance levels, for transcriptomic analysis. We subjected these genotypes to four different treatments: salt priming (P0), salt priming with salinity dose at 3-true-leaf stage (PD), salinity dose at 3-true-leaf stage without salt priming (0D), and control (CK). Although the three genotypes displayed distinct expression patterns, we identified common differentially expressed genes (DEGs) under PD enriched in pathways related to transferase activity, terpene synthase activity, lipid biosynthesis, and regulation of acquired resistance, indicating the beneficial role of salt priming in enhancing salt stress resistance. Moreover, the number of unique DEGs associated with G. hirsutum purpurascens was significantly higher compared to other genotypes. Coexpression network analysis identified 16 hub genes involved in cell wall biogenesis, glucan metabolic processes, and ribosomal RNA binding. Functional characterization of XTH6 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE) using virus-induced gene silencing revealed that suppressing its expression improves plant growth under salt stress. Overall, findings provide insights into the regulation of candidate genes in response to salt stress and the beneficial effects of salt priming on enhancing defense responses in upland cotton.
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Affiliation(s)
- Mian Faisal Nazir
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Baojun Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Muhammad Jawad Umer
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Zareen Sarfraz
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Zhen Peng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Shoupu He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Muhammad Shahid Iqbal
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Jingjing Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Hongge Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Zhaoe Pan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Daowu Hu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Meizhen Song
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
| | - Xiongming Du
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
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7
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Zhang Z, Lv R, Wang B, Xun H, Liu B, Xu C. Effects of Allopolyploidization and Homoeologous Chromosomal Segment Exchange on Homoeolog Expression in a Synthetic Allotetraploid Wheat under Variable Environmental Conditions. PLANTS (BASEL, SWITZERLAND) 2023; 12:3111. [PMID: 37687357 PMCID: PMC10490264 DOI: 10.3390/plants12173111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023]
Abstract
Allopolyploidy through the combination of divergent genomes into a common nucleus at doubled dosage is known as a potent genetic and evolutionary force. As a macromutation, a striking feature of allopolyploidy in comparison with other mutational processes is that 'genome shock' can be evoked, thereby generating rapid and saltational biological consequences. A major manifestation of genome shock is genome-wide gene expression rewiring, which previously remained to be fully elucidated. Here, using a large set of RNAseq-based transcriptomic data of a synthetic allotetraploid wheat (genome AADD) and its parental species, we performed in-depth analyses of changes in the genome-wide gene expression under diverse environmental conditions at the subgenome (homoeolog) level and investigated the additional effects of homoeologous chromosomal segment exchanges (abbreviated HEs). We show that allopolyploidy caused large-scale changes in gene expression that were variable across the conditions and exacerbated by both stresses and HEs. Moreover, although both subgenomes (A and D) showed clear commonality in the changes, they responded differentially under variable conditions. The subgenome- and condition-dependent differentially expressed genes were enriched for different gene ontology terms implicating different biological functions. Our results provide new insights into the direct impacts of allopolyploidy on condition-dependent changes in subgenome expression and the additional effects of HEs in nascent allopolyploidy.
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Affiliation(s)
- Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences (CAS), Changchun 130102, China
| | - Hongwei Xun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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8
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Zhang Q, Ye Z, Wang Y, Zhang X, Kong W. Haplotype-Resolution Transcriptome Analysis Reveals Important Responsive Gene Modules and Allele-Specific Expression Contributions under Continuous Salt and Drought in Camellia sinensis. Genes (Basel) 2023; 14:1417. [PMID: 37510320 PMCID: PMC10379978 DOI: 10.3390/genes14071417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/29/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The tea plant, Camellia sinensis (L.) O. Kuntze, is one of the most important beverage crops with significant economic and cultural value. Global climate change and population growth have led to increased salt and drought stress, negatively affecting tea yield and quality. The response mechanism of tea plants to these stresses remains poorly understood due to the lack of reference genome-based transcriptional descriptions. This study presents a high-quality genome-based transcriptome dynamic analysis of C. sinensis' response to salt and drought stress. A total of 2244 upregulated and 2164 downregulated genes were identified under salt and drought stress compared to the control sample. Most of the differentially expression genes (DEGs) were found to involve divergent regulation processes at different time points under stress. Some shared up- and downregulated DEGs related to secondary metabolic and photosynthetic processes, respectively. Weighted gene co-expression network analysis (WGCNA) revealed six co-expression modules significantly positively correlated with C. sinensis' response to salt or drought stress. The MEpurple module indicated crosstalk between the two stresses related to ubiquitination and the phenylpropanoid metabolic regulation process. We identified 1969 salt-responsive and 1887 drought-responsive allele-specific expression (ASE) genes in C. sinensis. Further comparison between these ASE genes and tea plant heterosis-related genes suggests that heterosis likely contributes to the adversity and stress resistance of C. sinensis. This work offers new insight into the underlying mechanisms of C. sinensis' response to salt and drought stress and supports the improved breeding of tea plants with enhanced salt and drought tolerance.
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Affiliation(s)
- Qing Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ziqi Ye
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yinghao Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weilong Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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9
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Vasudevan A, Lévesque-Lemay M, Edwards T, Cloutier S. Global transcriptome analysis of allopolyploidization reveals large-scale repression of the D-subgenome in synthetic hexaploid wheat. Commun Biol 2023; 6:426. [PMID: 37069312 PMCID: PMC10110605 DOI: 10.1038/s42003-023-04781-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
Synthetic hexaploid wheat (SHW) lines are created as pre-breeding germplasm to diversify the D subgenome of hexaploid wheat and capitalize upon the untapped genetic diversity of the Aegilops tauschii gene pool. However, the phenotypes observed in the Ae. tauschii parents are not always recovered in the SHW lines, possibly due to inter-subgenome interactions. To elucidate this post-polyploidization genome reprogramming phenomenon, we performed RNA-seq of four SHW lines and their corresponding tetraploid and diploid parents, across ten tissues and three biological replicates. Homoeologue expression bias (HEB) analysis using more than 18,000 triads suggests massive suppression of homoeoalleles of the D subgenome in SHWs. Comparative transcriptome analysis of the whole-genome gene set further corroborated this finding. Alternative splicing analysis of the high-confidence genes indicates an additional layer of complexity where all five splice events are identified, and retained intron is predominant. Homoeologue expression upon resynthesis of hexaploid wheat has implications to the usage and handling of this germplasm in breeding as it relates to capturing the effects of epistatic interaction across subgenomes upon polyploidization. Special considerations must be given to this germplasm in pre-breeding activities to consider the extent of the inter-subgenome interactions on gene expression and their impact on traits for crop improvement.
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Affiliation(s)
- Akshaya Vasudevan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | | | - Tara Edwards
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada.
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.
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Li X, Wang X, Ma Q, Zhong Y, Zhang Y, Zhang P, Li Y, He R, Zhou Y, Li Y, Cheng M, Yan X, Li Y, He J, Iqbal MZ, Rong T, Tang Q. Integrated single-molecule real-time sequencing and RNA sequencing reveal the molecular mechanisms of salt tolerance in a novel synthesized polyploid genetic bridge between maize and its wild relatives. BMC Genomics 2023; 24:55. [PMID: 36717785 PMCID: PMC9887930 DOI: 10.1186/s12864-023-09148-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/23/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Tripsacum dactyloides (2n = 4x = 72) and Zea perennis (2n = 4x = 40) are tertiary gene pools of Zea mays L. and exhibit many abiotic adaptations absent in modern maize, especially salt tolerance. A previously reported allopolyploid (hereafter referred to as MTP, 2n = 74) synthesized using Zea mays, Tripsacum dactyloides, and Zea perennis has even stronger salt tolerance than Z. perennis and T. dactyloides. This allopolyploid will be a powerful genetic bridge for the genetic improvement of maize. However, the molecular mechanisms underlying its salt tolerance, as well as the key genes involved in regulating its salt tolerance, remain unclear. RESULTS Single-molecule real-time sequencing and RNA sequencing were used to identify the genes involved in salt tolerance and reveal the underlying molecular mechanisms. Based on the SMRT-seq results, we obtained 227,375 reference unigenes with an average length of 2300 bp; most of the unigenes were annotated to Z. mays sequences (76.5%) in the NR database. Moreover, a total of 484 and 1053 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Functional enrichment analysis of DEGs revealed that multiple pathways responded to salt stress, including "Flavonoid biosynthesis," "Oxidoreductase activity," and "Plant hormone signal transduction" in the leaves and roots, and "Iron ion binding," "Acetyl-CoA carboxylase activity," and "Serine-type carboxypeptidase activity" in the roots. Transcription factors, such as those in the WRKY, B3-ARF, and bHLH families, and cytokinin negatively regulators negatively regulated the salt stress response. According to the results of the short time series-expression miner analysis, proteins involved in "Spliceosome" and "MAPK signal pathway" dynamically responded to salt stress as salinity changed. Protein-protein interaction analysis revealed that heat shock proteins play a role in the large interaction network regulating salt tolerance. CONCLUSIONS Our results reveal the molecular mechanism underlying the regulation of MTP in the response to salt stress and abundant salt-tolerance-related unigenes. These findings will aid the retrieval of lost alleles in modern maize and provide a new approach for using T. dactyloides and Z. perennis to improve maize.
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Affiliation(s)
- Xiaofeng Li
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Xingyu Wang
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Qiangqiang Ma
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yunfeng Zhong
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yibo Zhang
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Ping Zhang
- grid.452857.9Chengdu Research Base of Giant Panda Breeding, Chengdu, 61130 China
| | - Yingzheng Li
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Ruyu He
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yang Zhou
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yang Li
- Mianyang Teachers’ College School of Urban and Rural Construction and Planning, Mianyany, 621000 China
| | - Mingjun Cheng
- grid.412723.10000 0004 0604 889XInstitute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610041 China
| | - Xu Yan
- grid.465230.60000 0004 1777 7721Sericulture Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, 637000 China
| | - Yan Li
- grid.465230.60000 0004 1777 7721Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611041 China
| | - Jianmei He
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Muhammad Zafar Iqbal
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Tingzhao Rong
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Qilin Tang
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
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