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Aufiero G, Fruggiero C, D’Angelo D, D’Agostino N. Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge-A Transcriptomics Perspective. Genes (Basel) 2024; 15:977. [PMID: 39202338 PMCID: PMC11353593 DOI: 10.3390/genes15080977] [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: 07/02/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by elucidating the fate of duplicated genes, revealing evolutionary novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how duplicated genes have evolved to acquire new functions or regulatory roles. This process often leads to the development of novel traits and adaptive strategies that allopolyploid plants leverage to thrive in diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation of the genetic complexity underlying allopolyploidy but also underscores their importance in agriculture and ecosystem resilience. However, transcriptome profiling is challenging due to genomic redundancy, which is further complicated by the presence of multiple chromosomes sets and the variations among homoeologs and allelic genes. Prior to transcriptome analysis, sub-genome phasing and homoeology inference are essential for obtaining a comprehensive view of gene expression. This review aims to clarify the terminology in this field, identify the most challenging aspects of transcriptome analysis, explain their inherent difficulties, and suggest reliable analytic strategies. Furthermore, bulk RNA-seq is highlighted as a primary method for studying allopolyploid gene expression, focusing on critical steps like read mapping and normalization in differential gene expression analysis. This approach effectively captures gene expression from both parental genomes, facilitating a comprehensive analysis of their combined profiles. Its sensitivity in detecting low-abundance transcripts allows for subtle differences between parental genomes to be identified, crucial for understanding regulatory dynamics and gene expression balance in allopolyploids.
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Affiliation(s)
| | | | | | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (G.A.); (C.F.); (D.D.)
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Shao L, Jin S, Chen J, Yang G, Fan R, Zhang Z, Deng Q, Han J, Ma X, Dong Z, Lu H, Hu W, Wang K, Hu L, Shen Z, Huang S, Zhao T, Guan X, Hu Y, Zhang T, Fang L. High-quality genomes of Bombax ceiba and Ceiba pentandra provide insights into the evolution of Malvaceae species and differences in their natural fiber development. PLANT COMMUNICATIONS 2024; 5:100832. [PMID: 38321741 PMCID: PMC11121743 DOI: 10.1016/j.xplc.2024.100832] [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: 08/07/2023] [Revised: 09/15/2023] [Accepted: 02/01/2024] [Indexed: 02/08/2024]
Abstract
Members of the Malvaceae family, including Corchorus spp., Gossypium spp., Bombax spp., and Ceiba spp., are important sources of natural fibers. In the past decade, the genomes of several Malvaceae species have been assembled; however, the evolutionary history of Malvaceae species and the differences in their fiber development remain to be clarified. Here, we report the genome assembly and annotation of two natural fiber plants from the Malvaceae, Bombax ceiba and Ceiba pentandra, whose assembled genome sizes are 783.56 Mb and 1575.47 Mb, respectively. Comparative analysis revealed that whole-genome duplication and Gypsy long terminal repeat retroelements have been the major causes of differences in chromosome number (2n = 14 to 2n = 96) and genome size (234 Mb to 2676 Mb) among Malvaceae species. We also used comparative genomic analyses to reconstruct the ancestral Malvaceae karyotype with 11 proto-chromosomes, providing new insights into the evolutionary trajectories of Malvaceae species. MYB-MIXTA-like 3 is relatively conserved among the Malvaceae and functions in fiber cell-fate determination in the epidermis. It appears to perform this function in any tissue where it is expressed, i.e. in fibers on the endocarp of B. ceiba and in ovule fibers of cotton. We identified a structural variation in a cellulose synthase gene and a higher copy number of cellulose synthase-like genes as possible causes of the finer, less spinnable, weaker fibers of B. ceiba. Our study provides two high-quality genomes of natural fiber plants and offers insights into the evolution of Malvaceae species and differences in their natural fiber formation and development through multi-omics analysis.
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Affiliation(s)
- Lei Shao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Shangkun Jin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guangsui Yang
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Rui Fan
- Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Zhiyuan Zhang
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Qian Deng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jin Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaowei Ma
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zeyu Dong
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hejun Lu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wanying Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Lisong Hu
- Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Zhen Shen
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Surong Huang
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
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Genome wide identification and evolutionary analysis of vat like NBS-LRR genes potentially associated with resistance to aphids in cotton. Genetica 2023; 151:119-131. [PMID: 36717534 DOI: 10.1007/s10709-023-00181-1] [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: 09/05/2022] [Accepted: 01/24/2023] [Indexed: 02/01/2023]
Abstract
Nucleotide Binding Site - Leucine Rich Repeat (NBS-LRR) genes play a significant role in plant defense against biotic stresses and are an integral part of signal transduction pathways. Vat gene has been well reported for their role in resistance to Aphis gossypii and viruses transmitted by them. Despite their importance, Vat like NBS-LRR resistance genes have not yet been identified and studied in cotton species. This study report hundreds of orthologous Vat like NBS-LRR genes from the genomes of 18 cotton species through homology searches and the distribution of those identified genes were tend to be clustered on different chromosome. Especially, in a majority of the cases, Vat like genes were located on chromosome number 13 and they all shared two conserved NBS-LRR domains, one disease resistant domain and several repeats of LRR on the investigated cotton Vat like proteins. Gene ontology study on Vat like NBS-LRR genes revealed the molecular functions viz., ADP and protein binding. Phylogenetic analysis also revealed that Vat like sequences of two diploid species, viz., G. arboreum and G. anomalum, were closely related to the sequences of the tetraploids than all other diploids. The Vat like genes of G. aridum and G. schwendimanii were distantly related among diploids and tetraploids species. Various hormones and defense related cis-acting regulatory elements were identified from the 2 kb upstream sequences of the Vat like genes implying their defensive response towards the biotic stresses. Interestingly, G. arboreum and G. trilobum were found to have more regulatory elements than larger genomes of tetraploid cotton species. Thus, the present study provides the evidence for the evolution of Vat like genes in defense mechanisms against aphids infestation in cotton genomes and allows further characterization of candidate genes for developing aphid and aphid transmitted viruses resistant crops through cotton breeding.
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Wang H, Umer MJ, Liu F, Cai X, Zheng J, Xu Y, Hou Y, Zhou Z. Genome-Wide Identification and Characterization of CPR5 Genes in Gossypium Reveals Their Potential Role in Trichome Development. Front Genet 2022; 13:921096. [PMID: 35754813 PMCID: PMC9213653 DOI: 10.3389/fgene.2022.921096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/10/2022] [Indexed: 01/18/2023] Open
Abstract
Trichomes protect plants against insects, microbes, herbivores, and abiotic damages and assist seed dispersal. The function of CPR5 genes have been found to be involved in the trichome development but the research on the underlying genetic and molecular mechanisms are extremely limited. Herein, genome wide identification and characterization of CPR5 genes was performed. In total, 26 CPR5 family members were identified in Gossypium species. Phylogenetic analysis, structural characteristics, and synteny analysis of CPR5s showed the conserved evolution relationships of CPR5. The promoter analysis of CPR5 genes revealed hormone, stress, and development-related cis-elements. Gene ontology (GO) enrichment analysis showed that the CPR5 genes were largely related to biological regulation, developmental process, multicellular organismal process. Protein-protein interaction analysis predicted several trichome development related proteins (SIM, LGO, and GRL) directly interacting with CPR5 genes. Further, nine putative Gossypium-miRNAs were also identified, targeting Gossypium CPR5 genes. RNA-Seq data of G. arboreum (with trichomes) and G. herbaceum (with no trichomes) was used to perform the co-expression network analysis. GheCPR5.1 was identified as a hub gene in a co-expression network analysis. RT-qPCR of GheCPR5.1 gene in different tissues suggests that this gene has higher expressions in the petiole and might be a key candidate involved in the trichome development. Virus induced gene silencing of GheCPR5.1 (Ghe02G17590) confirms its role in trichome development and elongation. Current results provide proofs of the possible role of CPR5 genes and provide preliminary information for further studies of GheCPR5.1 functions in trichome development.
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Affiliation(s)
- Heng Wang
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Jie Zheng
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China.,Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
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Han G, Li Y, Yang Z, Wang C, Zhang Y, Wang B. Molecular Mechanisms of Plant Trichome Development. FRONTIERS IN PLANT SCIENCE 2022; 13:910228. [PMID: 35720574 PMCID: PMC9198495 DOI: 10.3389/fpls.2022.910228] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
Plant trichomes, protrusions formed from specialized aboveground epidermal cells, provide protection against various biotic and abiotic stresses. Trichomes can be unicellular, bicellular or multicellular, with multiple branches or no branches at all. Unicellular trichomes are generally not secretory, whereas multicellular trichomes include both secretory and non-secretory hairs. The secretory trichomes release secondary metabolites such as artemisinin, which is valuable as an antimalarial agent. Cotton trichomes, also known as cotton fibers, are an important natural product for the textile industry. In recent years, much progress has been made in unraveling the molecular mechanisms of trichome formation in Arabidopsis thaliana, Gossypium hirsutum, Oryza sativa, Cucumis sativus, Solanum lycopersicum, Nicotiana tabacum, and Artemisia annua. Here, we review current knowledge of the molecular mechanisms underlying fate determination and initiation, elongation, and maturation of unicellular, bicellular and multicellular trichomes in several representative plants. We emphasize the regulatory roles of plant hormones, transcription factors, the cell cycle and epigenetic modifications in different stages of trichome development. Finally, we identify the obstacles and key points for future research on plant trichome development, and speculated the development relationship between the salt glands of halophytes and the trichomes of non-halophytes, which provides a reference for future studying the development of plant epidermal cells.
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Affiliation(s)
- Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
- Dongying Institute, Shandong Normal University, Dongying, China
| | - Yuxia Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zongran Yang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Chengfeng Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yuanyuan Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
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6
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Wang Y, Zhou Q, Meng Z, Abid MA, Wang Y, Wei Y, Guo S, Zhang R, Liang C. Multi-Dimensional Molecular Regulation of Trichome Development in Arabidopsis and Cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:892381. [PMID: 35463426 PMCID: PMC9021843 DOI: 10.3389/fpls.2022.892381] [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: 03/09/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Plant trichomes are specialized epidermal cells that are widely distributed on plant aerial tissues. The initiation and progression of trichomes are controlled in a coordinated sequence of multiple molecular events. During the past decade, major breakthroughs in the molecular understanding of trichome development were achieved through the characterization of various trichomes defective mutants and trichome-associated genes, which revealed a highly complex molecular regulatory network underlying plant trichome development. This review focuses on the recent millstone in plant trichomes research obtained using genetic and molecular studies, as well as 'omics' analyses in model plant Arabidopsis and fiber crop cotton. In particular, we discuss the latest understanding and insights into the underlying molecular mechanisms of trichomes formation at multiple dimensions, including at the chromatin, transcriptional, post-transcriptional, and post-translational levels. We summarize that the integration of multi-dimensional trichome-associated genes will enable us to systematically understand the molecular regulation network that landscapes the development of the plant trichomes. These advances will enable us to address the unresolved questions regarding the molecular crosstalk that coordinate concurrent and ordered the changes in cotton fiber initiation and progression, together with their possible implications for genetic improvement of cotton fiber.
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Prasad P, Khatoon U, Verma RK, Aalam S, Kumar A, Mohapatra D, Bhattacharya P, Bag SK, Sawant SV. Transcriptional Landscape of Cotton Fiber Development and Its Alliance With Fiber-Associated Traits. FRONTIERS IN PLANT SCIENCE 2022; 13:811655. [PMID: 35283936 PMCID: PMC8908376 DOI: 10.3389/fpls.2022.811655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Cotton fiber development is still an intriguing question to understand fiber commitment and development. At different fiber developmental stages, many genes change their expression pattern and have a pivotal role in fiber quality and yield. Recently, numerous studies have been conducted for transcriptional regulation of fiber, and raw data were deposited to the public repository for comprehensive integrative analysis. Here, we remapped > 380 cotton RNAseq data with uniform mapping strategies that span ∼400 fold coverage to the genome. We identified stage-specific features related to fiber cell commitment, initiation, elongation, and Secondary Cell Wall (SCW) synthesis and their putative cis-regulatory elements for the specific regulation in fiber development. We also mined Exclusively Expressed Transcripts (EETs) that were positively selected during cotton fiber evolution and domestication. Furthermore, the expression of EETs was validated in 100 cotton genotypes through the nCounter assay and correlated with different fiber-related traits. Thus, our data mining study reveals several important features related to cotton fiber development and improvement, which were consolidated in the "CottonExpress-omics" database.
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Affiliation(s)
- Priti Prasad
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Uzma Khatoon
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Rishi Kumar Verma
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shahre Aalam
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
| | - Ajay Kumar
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
| | | | | | - Sumit K. Bag
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Samir V. Sawant
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Sun J, Cui H, Wu B, Wang W, Yang Q, Zhang Y, Yang S, Zhao Y, Xu D, Liu G, Qin T. Genome-Wide Identification of Cotton ( Gossypium spp.) Glycerol-3-Phosphate Dehydrogenase (GPDH) Family Members and the Role of GhGPDH5 in Response to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:592. [PMID: 35270062 PMCID: PMC8912411 DOI: 10.3390/plants11050592] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Glycerol-3-phosphate dehydrogenase (GPDH) is a key enzyme in plant glycerol synthesis and metabolism, and plays an important role in plant resistance to abiotic stress. Here, we identified 6, 7, 14 and 14 GPDH genes derived from Gossypium arboreum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum, respectively. Phylogenetic analysis assigned these genes into three classes, and most of the genes within the family were expanded by whole-genome duplication (WGD) and segmental duplications. Moreover, determination of the nonsynonymous substitution rate/synonymous substitution rate (Ka/Ks) ratio showed that the GPDH had an evolutionary preference for purifying selection. Transcriptome data revealed that GPDH genes were more active in the early stages of fiber development. Additionally, numerous stress-related cis-elements were identified in the potential promoter region. Then, a protein-protein-interaction (PPI) network of GPDH5 in G. hirsutum was constructed. In addition, we predicted 30 underlying miRNAs in G. hirsutum. Functional validation results indicated that silencing GhGPDH5 diminished drought tolerance in the upland cotton TM-1 line. In summary, this study provides a fundamental understanding of the GPDH gene family in cotton, GhGPDH5 exerts a positive effect during drought stress and is potentially involved in stomatal closure movements.
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Affiliation(s)
- Jialiang Sun
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266100, China;
- College of Agriculture, Liaocheng University, Liaocheng 252059, China; (B.W.); (W.W.); (Q.Y.); (Y.Z.); (S.Y.); (Y.Z.)
| | - Hua Cui
- Key Laboratory of Cell and Gene Circuit Design, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
| | - Bingjie Wu
- College of Agriculture, Liaocheng University, Liaocheng 252059, China; (B.W.); (W.W.); (Q.Y.); (Y.Z.); (S.Y.); (Y.Z.)
| | - Weipeng Wang
- College of Agriculture, Liaocheng University, Liaocheng 252059, China; (B.W.); (W.W.); (Q.Y.); (Y.Z.); (S.Y.); (Y.Z.)
| | - Qiuyue Yang
- College of Agriculture, Liaocheng University, Liaocheng 252059, China; (B.W.); (W.W.); (Q.Y.); (Y.Z.); (S.Y.); (Y.Z.)
| | - Yaxin Zhang
- College of Agriculture, Liaocheng University, Liaocheng 252059, China; (B.W.); (W.W.); (Q.Y.); (Y.Z.); (S.Y.); (Y.Z.)
| | - Song Yang
- College of Agriculture, Liaocheng University, Liaocheng 252059, China; (B.W.); (W.W.); (Q.Y.); (Y.Z.); (S.Y.); (Y.Z.)
| | - Yuping Zhao
- College of Agriculture, Liaocheng University, Liaocheng 252059, China; (B.W.); (W.W.); (Q.Y.); (Y.Z.); (S.Y.); (Y.Z.)
| | - Dongbei Xu
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoxiang Liu
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266100, China;
| | - Tengfei Qin
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266100, China;
- College of Agriculture, Liaocheng University, Liaocheng 252059, China; (B.W.); (W.W.); (Q.Y.); (Y.Z.); (S.Y.); (Y.Z.)
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9
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Westermann J. Two Is Company, but Four Is a Party-Challenges of Tetraploidization for Cell Wall Dynamics and Efficient Tip-Growth in Pollen. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112382. [PMID: 34834745 PMCID: PMC8623246 DOI: 10.3390/plants10112382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 05/27/2023]
Abstract
Some cells grow by an intricately coordinated process called tip-growth, which allows the formation of long tubular structures by a remarkable increase in cell surface-to-volume ratio and cell expansion across vast distances. On a broad evolutionary scale, tip-growth has been extraordinarily successful, as indicated by its recurrent 're-discovery' throughout evolutionary time in all major land plant taxa which allowed for the functional diversification of tip-growing cell types across gametophytic and sporophytic life-phases. All major land plant lineages have experienced (recurrent) polyploidization events and subsequent re-diploidization that may have positively contributed to plant adaptive evolutionary processes. How individual cells respond to genome-doubling on a shorter evolutionary scale has not been addressed as elaborately. Nevertheless, it is clear that when polyploids first form, they face numerous important challenges that must be overcome for lineages to persist. Evidence in the literature suggests that tip-growth is one of those processes. Here, I discuss the literature to present hypotheses about how polyploidization events may challenge efficient tip-growth and strategies which may overcome them: I first review the complex and multi-layered processes by which tip-growing cells maintain their cell wall integrity and steady growth. I will then discuss how they may be affected by the cellular changes that accompany genome-doubling. Finally, I will depict possible mechanisms polyploid plants may evolve to compensate for the effects caused by genome-doubling to regain diploid-like growth, particularly focusing on cell wall dynamics and the subcellular machinery they are controlled by.
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Affiliation(s)
- Jens Westermann
- Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, Universitätsstrasse 2, 8092 Zürich, Switzerland
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10
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Qiu T, Du K, Jing Y, Zeng Q, Liu Z, Li Y, Ren Y, Yang J, Kang X. Integrated transcriptome and miRNA sequencing approaches provide insights into salt tolerance in allotriploid Populus cathayana. PLANTA 2021; 254:25. [PMID: 34226949 DOI: 10.1007/s00425-021-03600-9] [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: 01/05/2021] [Accepted: 03/18/2021] [Indexed: 06/13/2023]
Abstract
Some salt-stress responsive DEGs, mainly involved in ion transmembrane transport, hormone regulation, antioxidant system, osmotic regulation, and some miRNA jointly regulated the salt response process in allotriploid Populus cathayana. The molecular mechanism of plant polyploid stress resistance has been a hot topic in biological research. In this study, Populus diploids and first division restitution (FDR) and second division restitution (SDR) triploids were selected as research materials. All materials were treated with 70 mM NaCl solutions for 30 days in the same pot environment. We observed the growth state of triploids and diploids and determined the ratio of potassium and sodium ions, peroxidase (POD) activity, proline content, and ABA and jasmonic acid (JA) hormone content in leaves in the same culture environment with the same concentration of NaCl solution treatment. In addition, RNA-seq technology was used to study the differential expression of mRNA and miRNA. The results showed that triploid Populus grew well and the K+ content and the K+/Na+ ratio in the salt treatment were significantly lower than those in the control. The contents of ABA, JA, POD, and proline were increased compared with contents in diploid under salt stress. The salt-stress responsive DEGs were mainly involved in ion transport, cell homeostasis, the MAPK signaling pathway, peroxisome, citric acid cycle, and other salt response and growth pathways. The transcription factors mainly included NAC, MYB, MYB_related and AP2/ERF. Moreover, the differentially expressed miRNAs involved 32 families, including 743 miRNAs related to predicted target genes, among which 22 miRNAs were significantly correlated with salt-stress response genes and related to the regulation of hormones, ion transport, reactive oxygen species (ROS) and other biological processes. Our results provided insights into the physiological and molecular aspects for further research into the response mechanisms of allotriploid Populus cathayana to salt stress. This study provided valuable information for the salt tolerance mechanism of allopolyploids.
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Affiliation(s)
- Tong Qiu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Kang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yanchun Jing
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Qingqing Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhao Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yun Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yongyu Ren
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jun Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiangyang Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- National Engineering Laboratory for Tree Breeding, Ministry of Education, Beijing Forestry University, Beijing, 100083, China.
- Beijing Laboratory of Urban and Rural Ecological Environment, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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11
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Wan K, Lu K, Gao M, Zhao T, He Y, Yang DL, Tao X, Xiong G, Guan X. Functional analysis of the cotton CLE polypeptide signaling gene family in plant growth and development. Sci Rep 2021; 11:5060. [PMID: 33658526 PMCID: PMC7930028 DOI: 10.1038/s41598-021-84312-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 02/10/2021] [Indexed: 11/23/2022] Open
Abstract
The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)–RELATED (CLE) gene family encodes a large number of polypeptide signaling molecules involved in the regulation of shoot apical meristem division and root and vascular bundle development in a variety of plants. CLE family genes encode important short peptide hormones; however, the functions of these signaling polypeptides in cotton remain largely unknown. In the current work, we studied the effects of the CLE family genes on growth and development in cotton. Based on the presence of a conserved CLE motif of 13 amino acids, 93 genes were characterized as GhCLE gene family members, and these were subcategorized into 7 groups. A preliminary analysis of the cotton CLE gene family indicated that the activity of its members tends to be conserved in terms of both the 13-residue conserved domain at the C-terminus and their subcellular localization pattern. Among the 14 tested genes, the ectopic overexpression of GhCLE5::GFP partially mimicked the phenotype of the clv3 mutant in Arabidopsis. GhCLE5 could affect the endogenous CLV3 in binding to the receptor complex, comprised of CLV1, CLV2, and CRN, in the yeast two-hybrid assay and split-luciferase assay. Silencing GhCLE5 in cotton caused a short seedling phenotype. Therefore, we concluded that the cotton GhCLE gene family is functionally conserved in apical shoot development regulation. These results indicate that CLE also plays roles in cotton development as a short peptide hormone.
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Affiliation(s)
- Ke Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Kening Lu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Mengtao Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ting Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.,College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 210058, Zhejiang, China
| | - Yuxin He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Dong-Lei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 210058, Zhejiang, China
| | - Guosheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 210058, Zhejiang, China.
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12
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He P, Zhang Y, Li H, Fu X, Shang H, Zou C, Friml J, Xiao G. GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:548-562. [PMID: 32981232 PMCID: PMC7955886 DOI: 10.1111/pbi.13484] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/31/2020] [Accepted: 09/13/2020] [Indexed: 05/04/2023]
Abstract
The leaf is a crucial organ evolved with remarkable morphological diversity to maximize plant photosynthesis. The leaf shape is a key trait that affects photosynthesis, flowering rates, disease resistance and yield. Although many genes regulating leaf development have been identified in the past years, the precise regulatory architecture underlying the generation of diverse leaf shapes remains to be elucidated. We used cotton as a reference model to probe the genetic framework underlying divergent leaf forms. Comparative transcriptome analysis revealed that the GhARF16-1 and GhKNOX2-1 genes might be potential regulators of leaf shape. We functionally characterized the auxin-responsive factor ARF16-1 acting upstream of GhKNOX2-1 to determine leaf morphology in cotton. The transcription of GhARF16-1 was significantly higher in lobed-leaved cotton than in smooth-leaved cotton. Furthermore, the overexpression of GhARF16-1 led to the up-regulation of GhKNOX2-1 and resulted in more and deeper serrations in cotton leaves, similar to the leaf shape of cotton plants overexpressing GhKNOX2-1. We found that GhARF16-1 specifically bound to the promoter of GhKNOX2-1 to induce its expression. The heterologous expression of GhARF16-1 and GhKNOX2-1 in Arabidopsis led to lobed and curly leaves, and a genetic analysis revealed that GhKNOX2-1 is epistatic to GhARF16-1 in Arabidopsis, suggesting that the GhARF16-1 and GhKNOX2-1 interaction paradigm also functions to regulate leaf shape in Arabidopsis. To our knowledge, our results uncover a novel mechanism by which auxin, through the key component ARF16-1 and its downstream-activated gene KNOX2-1, determines leaf morphology in eudicots.
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Affiliation(s)
- Peng He
- College of Life SciencesShaanxi Normal UniversityXi’anChina
| | - Yuzhou Zhang
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Hongbin Li
- College of Life SciencesKey Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of EducationShihezi UniversityShiheziChina
| | - Xuan Fu
- College of Life SciencesShaanxi Normal UniversityXi’anChina
| | - Haihong Shang
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
- Key Laboratory of Biological and Genetic Breeding of CottonThe Ministry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Changsong Zou
- Key Laboratory of Plant Stress BiologyState Key Laboratory of Cotton BiologySchool of Life SciencesHenan UniversityKaifengChina
| | - Jiří Friml
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Guanghui Xiao
- College of Life SciencesShaanxi Normal UniversityXi’anChina
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13
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He P, Zhang Y, Xiao G. Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species. MOLECULAR PLANT 2020; 13:1238-1240. [PMID: 32688032 DOI: 10.1016/j.molp.2020.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/19/2020] [Accepted: 07/14/2020] [Indexed: 05/28/2023]
Affiliation(s)
- Peng He
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yuzhou Zhang
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Guanghui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
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14
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Cao JF, Zhao B, Huang CC, Chen ZW, Zhao T, Liu HR, Hu GJ, Shangguan XX, Shan CM, Wang LJ, Zhang TZ, Wendel JF, Guan XY, Chen XY. The miR319-Targeted GhTCP4 Promotes the Transition from Cell Elongation to Wall Thickening in Cotton Fiber. MOLECULAR PLANT 2020; 13:1063-1077. [PMID: 32422188 DOI: 10.1016/j.molp.2020.05.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 05/03/2020] [Accepted: 05/12/2020] [Indexed: 05/08/2023]
Abstract
Plant cell growth involves a complex interplay among cell-wall expansion, biosynthesis, and, in specific tissues, secondary cell wall (SCW) deposition, yet the coordination of these processes remains elusive. Cotton fiber cells are developmentally synchronous, highly elongated, and contain nearly pure cellulose when mature. Here, we report that the transcription factor GhTCP4 plays an important role in balancing cotton fiber cell elongation and wall synthesis. During fiber development the expression of miR319 declines while GhTCP4 transcript levels increase, with high levels of the latter promoting SCW deposition. GhTCP4 interacts with a homeobox-containing factor, GhHOX3, and repressing its transcriptional activity. GhTCP4 and GhHOX3 function antagonistically to regulate cell elongation, thereby establishing temporal control of fiber cell transition to the SCW stage. We found that overexpression of GhTCP4A upregulated and accelerated activation of the SCW biosynthetic pathway in fiber cells, as revealed by transcriptome and promoter activity analyses, resulting in shorter fibers with varied lengths and thicker walls. In contrast, GhTCP4 downregulation led to slightly longer fibers and thinner cell walls. The GhHOX3-GhTCP4 complex may represent a general mechanism of cellular development in plants since both are conserved factors in many species, thus providing us a potential molecular tool for the design of fiber traits.
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Affiliation(s)
- Jun-Feng Cao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Plant Stress Biology Center, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Bo Zhao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Chao-Chen Huang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhi-Wen Chen
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ting Zhao
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hong-Ru Liu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guan-Jing Hu
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Xiao-Xia Shangguan
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chun-Min Shan
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Ling-Jian Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tian-Zhen Zhang
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Xue-Ying Guan
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Plant Science Research Center, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
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15
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Gě Q, Cūi Y, Lǐ J, Gōng J, Lú Q, Lǐ P, Shí Y, Shāng H, Liú À, Dèng X, Pān J, Chén Q, Yuán Y, Gǒng W. Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species. BMC Genomics 2020; 21:379. [PMID: 32482161 PMCID: PMC7262775 DOI: 10.1186/s12864-020-6773-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/06/2020] [Indexed: 11/26/2022] Open
Abstract
Background Fructose-1,6-bisphosphatase (FBP) is a key enzyme in the plant sucrose synthesis pathway, in the Calvin cycle, and plays an important role in photosynthesis regulation in green plants. However, no systemic analysis of FBPs has been reported in Gossypium species. Results A total of 41 FBP genes from four Gossypium species were identified and analyzed. These FBP genes were sorted into two groups and seven subgroups. Results revealed that FBP family genes were under purifying selection pressure that rendered FBP family members as being conserved evolutionarily, and there was no tandem or fragmental DNA duplication in FBP family genes. Collinearity analysis revealed that a FBP gene was located in a translocated DNA fragment and the whole FBP gene family was under disequilibrium evolution that led to a faster evolutionary progress of the members in G. barbadense and in At subgenome than those in other Gossypium species and in the Dt subgenome, respectively, in this study. Through RNA-seq analyses and qRT-PCR verification, different FBP genes had diversified biological functions in cotton fiber development (two genes in 0 DPA and 1DPA ovules and four genes in 20–25 DPA fibers), in plant responses to Verticillium wilt onset (two genes) and to salt stress (eight genes). Conclusion The FBP gene family displayed a disequilibrium evolution pattern in Gossypium species, which led to diversified functions affecting not only fiber development, but also responses to Verticillium wilt and salt stress. All of these findings provide the foundation for further study of the function of FBP genes in cotton fiber development and in environmental adaptability.
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Affiliation(s)
- Qún Gě
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China, 311 Nongda East Road, Urumqi, 830052, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yànli Cūi
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China, 311 Nongda East Road, Urumqi, 830052, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jùnwén Lǐ
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jǔwǔ Gōng
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China, 311 Nongda East Road, Urumqi, 830052, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Quánwěi Lú
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,Research Base, State Key Laboratory of Cotton Biology, Anyang Institute of Technology, Anyang, China
| | - Péngtāo Lǐ
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,Research Base, State Key Laboratory of Cotton Biology, Anyang Institute of Technology, Anyang, China
| | - Yùzhēn Shí
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hǎihóng Shāng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Àiyīng Liú
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiǎoyīng Dèng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jìngtāo Pān
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qúanjiā Chén
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China, 311 Nongda East Road, Urumqi, 830052, China.
| | - Yǒulù Yuán
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China, 311 Nongda East Road, Urumqi, 830052, China. .,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
| | - Wànkuí Gǒng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China. .,Research Base, State Key Laboratory of Cotton Biology, Anyang Institute of Technology, Anyang, China.
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16
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Yang Z, Qanmber G, Wang Z, Yang Z, Li F. Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement. TRENDS IN PLANT SCIENCE 2020; 25:488-500. [PMID: 31980282 DOI: 10.1016/j.tplants.2019.12.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/19/2019] [Accepted: 12/09/2019] [Indexed: 05/23/2023]
Abstract
Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs.
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Affiliation(s)
- Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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17
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Azizi P, Hanafi MM, Sahebi M, Harikrishna JA, Taheri S, Yassoralipour A, Nasehi A. Epigenetic changes and their relationship to somaclonal variation: a need to monitor the micropropagation of plantation crops. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:508-523. [PMID: 32349860 DOI: 10.1071/fp19077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 02/23/2020] [Indexed: 06/11/2023]
Abstract
Chromatin modulation plays important roles in gene expression regulation and genome activities. In plants, epigenetic changes, including variations in histone modification and DNA methylation, are linked to alterations in gene expression. Despite the significance and potential of in vitro cell and tissue culture systems in fundamental research and marketable applications, these systems threaten the genetic and epigenetic networks of intact plant organs and tissues. Cell and tissue culture applications can lead to DNA variations, methylation alterations, transposon activation, and finally, somaclonal variations. In this review, we discuss the status of the current understanding of epigenomic changes that occur under in vitro conditions in plantation crops, including coconut, oil palm, rubber, cotton, coffee and tea. It is hoped that comprehensive knowledge of the molecular basis of these epigenomic variations will help researchers develop strategies to enhance the totipotent and embryogenic capabilities of tissue culture systems for plantation crops.
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Affiliation(s)
- Parisa Azizi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamed M Hanafi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Corresponding author.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Jennifer A Harikrishna
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sima Taheri
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ali Yassoralipour
- Department of Agricultural and Food Science, Faculty of Science (Kampar Campus), Universiti Tunku Abdul Rahman (UTAR), Jalan Universiti, Bandar Barat, 31900 Kampar, Perak, Malaysia
| | - Abbas Nasehi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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Cavé-Radet A, Giraud D, Lima O, El Amrani A, Aïnouche M, Salmon A. Evolution of small RNA expression following hybridization and allopolyploidization: insights from Spartina species (Poaceae, Chloridoideae). PLANT MOLECULAR BIOLOGY 2020; 102:55-72. [PMID: 31748889 DOI: 10.1007/s11103-019-00931-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
Differential expression of mi-RNAs targeting developmental processes and progressive downregulation of repeat-associated siRNAs following genome merger and genome duplication in the context of allopolyploid speciation in Spartina. The role of small RNAs on gene expression regulation and genome stability is arousing increased interest and is being explored in various plant systems. In spite of prominence of reticulate evolution and polyploidy that affects the evolutionary history of all plant lineages, very few studies analysed RNAi mechanisms with this respect. Here, we explored small RNAs diversity and expression in the context of recent allopolyploid speciation, using the Spartina system, which offers a unique opportunity to explore the immediate changes following hybridization and genome duplication. Small RNA-Seq analyses were conducted on hexaploid parental species (S. alterniflora and S. maritima), their F1 hybrid S. x townsendii, and the neoallododecaploid S. anglica. We identified 594 miRNAs, 2197 miRNA-target genes, and 3730 repeat-associated siRNAs (mostly targeting Class I/Copia-Ivana- Copia-SIRE and LINEs elements). For both mi- and ra-siRNAs, we detected differential expression patterns following genome merger and genome duplication. These misregulations include non-additive expression of miRNAs in the F1 hybrid and additional changes in the allopolyploid targeting developmental processes. Expression of repeat-associated siRNAs indicates a strengthen of transposable element repression during the allopolyploidization process. Altogether, these results confirm the central role small RNAs play in shaping regulatory changes in naturally formed recent allopolyploids.
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Affiliation(s)
- Armand Cavé-Radet
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Delphine Giraud
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Oscar Lima
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Abdelhak El Amrani
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Malika Aïnouche
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Armel Salmon
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France.
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Wang L, Liu X, Wang X, Pan Z, Geng X, Chen B, Liu B, Du X, Song X. Identification and characterization analysis of sulfotransferases (SOTs) gene family in cotton (Gossypium) and its involvement in fiber development. BMC PLANT BIOLOGY 2019; 19:595. [PMID: 31888489 PMCID: PMC6938023 DOI: 10.1186/s12870-019-2190-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/08/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Sulfotransferases (SOTs) (EC 2.8.2.-) play a crucial role in the sulphate conjugation reaction involved in plant growth, vigor, stress resistance and pathogen infection. SOTs in Arabidopsis have been carried out and divided into 8 groups. However, the systematic analysis and functional information of SOT family genes in cotton have rarely been reported. RESULTS According to the results of BLASTP and HMMER, we isolated 46, 46, 76 and 77 SOT genes in the genome G. arboreum, G. raimondii, G. barbadense and G. hirsutum, respectively. A total of 170 in 245 SOTs were further classified into four groups based on the orthologous relationships comparing with Arabidopsis, and tandem replication primarily contributed to the expansion of SOT gene family in G. hirsutum. Expression profiles of the GhSOT showed that most genes exhibited a high level of expression in the stem, leaf, and the initial stage of fiber development. The localization analysis indicated that GhSOT67 expressed in cytoplasm and located in stem and leaf tissue. Additionally, the expression of GhSOT67 were induced and the length of stem and leaf hairs were shortened after gene silencing mediated by Agrobacterium, compared with the blank and negative control plants. CONCLUSIONS Our findings indicated that SOT genes might be associated with fiber development in cotton and provided valuable information for further studies of SOT genes in Gossypium.
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Affiliation(s)
- Liyuan Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, 271018, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiyan Liu
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, 271018, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoli Geng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Baoshen Liu
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, 271018, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xianliang Song
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, 271018, China.
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Ayubov MS, Mirzakhmedov MH, Sripathi VR, Buriev ZT, Ubaydullaeva KA, Usmonov DE, Norboboyeva RB, Emani C, Kumpatla SP, Abdurakhmonov IY. Role of MicroRNAs and small RNAs in regulation of developmental processes and agronomic traits in Gossypium species. Genomics 2019; 111:1018-1025. [PMID: 30026106 DOI: 10.1016/j.ygeno.2018.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/10/2018] [Accepted: 07/14/2018] [Indexed: 02/08/2023]
Abstract
Small RNAs (sRNAs) are short, non-coding, 17-24 nucleotides long RNA molecules that play vital roles in regulating gene expression in every known organism investigated to date including cotton (Gossypium ssp.). These tiny RNA molecules target diverse categories of genes from different bioliogical and metabolic processes and have been reported in the three domains of life. Small RNAs, including miRNAs, are involved in ovule and fiber development, biotic and abiotic stresses, fertility, and other biochemical processes in cotton species. Also, sRNAs are the critical components in RNA interference pathway. In this article, we have reviewed the research efforts related to the isolation and characterization of miRNAs using molecular and genomic approaches. The progress made in understanding the functional roles of miRNAs in regulation, alteration, and inactivation of fundamental plant processes and traits of importance in cotton are presented here.
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Affiliation(s)
- Mirzakamol S Ayubov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | - Mukhammad H Mirzakhmedov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan; Faculty of Agricultural Science, University of Hohenheim, Germany
| | - Venkateswara R Sripathi
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama A and M University, AL, USA
| | - Zabardast T Buriev
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | | | - Dilshod E Usmonov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | - Risolat B Norboboyeva
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
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21
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Fambrini M, Pugliesi C. The Dynamic Genetic-Hormonal Regulatory Network Controlling the Trichome Development in Leaves. PLANTS (BASEL, SWITZERLAND) 2019; 8:E253. [PMID: 31357744 PMCID: PMC6724107 DOI: 10.3390/plants8080253] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 02/05/2023]
Abstract
Plant trichomes are outgrowths developed from an epidermal pavement cells of leaves and other organs. Trichomes (also called 'hairs') play well-recognized roles in defense against insect herbivores, forming a physical barrier that obstructs insect movement and mediating chemical defenses. In addition, trichomes can act as a mechanosensory switch, transducing mechanical stimuli (e.g., insect movement) into physiological signals, helping the plant to respond to insect attacks. Hairs can also modulate plant responses to abiotic stresses, such as water loss, an excess of light and temperature, and reflect light to protect plants against UV radiation. The structure of trichomes is species-specific and this trait is generally related to their function. These outgrowths are easily analyzed and their origin represents an outstanding subject to study epidermal cell fate and patterning in plant organs. In leaves, the developmental control of the trichomatous complement has highlighted a regulatory network based on four fundamental elements: (i) genes that activate and/or modify the normal cell cycle of epidermal pavement cells (i.e., endoreduplication cycles); (ii) transcription factors that create an activator/repressor complex with a central role in determining cell fate, initiation, and differentiation of an epidermal cell in trichomes; (iii) evidence that underlines the interplay of the aforesaid complex with different classes of phytohormones; (iv) epigenetic mechanisms involved in trichome development. Here, we reviewed the role of genes in the development of trichomes, as well as the interaction between genes and hormones. Furthermore, we reported basic studies about the regulation of the cell cycle and the complexity of trichomes. Finally, this review focused on the epigenetic factors involved in the initiation and development of hairs, mainly on leaves.
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Affiliation(s)
- Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124 Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124 Pisa, Italy.
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Cheng H, Sun G, He S, Gong W, Peng Z, Wang R, Lin Z, Du X. Comparative effect of allopolyploidy on transposable element composition and gene expression between Gossypium hirsutum and its two diploid progenitors. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:45-59. [PMID: 30565413 DOI: 10.1111/jipb.12763] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/15/2018] [Indexed: 05/20/2023]
Abstract
An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements (TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes. Gypsy was the most abundant TE type and most TEs were located ∼500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs (siRNAs) that targeted TEs. TEs, particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.
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Affiliation(s)
- Hua Cheng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, the Chinese Academy of Agricultural Science, Anyang 455000, China
- College of Plant Science & Technology of Huazhong Agricultural University, Wuhan 430070, China
| | - Gaofei Sun
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, the Chinese Academy of Agricultural Science, Anyang 455000, China
| | - Shoupu He
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, the Chinese Academy of Agricultural Science, Anyang 455000, China
| | - Wenfang Gong
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, the Chinese Academy of Agricultural Science, Anyang 455000, China
| | - Zhen Peng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, the Chinese Academy of Agricultural Science, Anyang 455000, China
| | - Ruiping Wang
- Department of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Zhongxu Lin
- College of Plant Science & Technology of Huazhong Agricultural University, Wuhan 430070, China
| | - Xiongming Du
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, the Chinese Academy of Agricultural Science, Anyang 455000, China
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Genome-Wide Analysis of LRR-RLK Gene Family in Four Gossypium Species and Expression Analysis during Cotton Development and Stress Responses. Genes (Basel) 2018; 9:genes9120592. [PMID: 30501109 PMCID: PMC6316826 DOI: 10.3390/genes9120592] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 11/26/2022] Open
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) have been reported to play important roles in plant growth, development, and stress responses. However, no comprehensive analysis of this family has been performed in cotton (Gossypium spp.), which is an important economic crop that suffers various stresses in growth and development. Here we conducted a comprehensive analysis of LRR-RLK family in four Gossypium species (Gossypium arboreum, Gossypium barbadense, Gossypium hirsutum, and Gossypium raimondii). A total of 1641 LRR-RLK genes were identified in the four Gossypium species involved in our study. The maximum-likelihood phylogenetic tree revealed that all the LRR-RLK genes were divided into 21 subgroups. Exon-intron organization structure of LRR-RLK genes kept relatively conserved within subfamilies and between Arabidopsis and Gossypium genomes. Notably, subfamilies XI and XII were found dramatically expanded in Gossypium species. Tandem duplication acted as an important mechanism in expansion of the Gossypium LRR-RLK gene family. Functional analysis suggested that GossypiumLRR-RLK genes were enriched for plant hormone signaling and plant-pathogen interaction pathways. Promoter analysis revealed that GossypiumLRR-RLK genes were extensively regulated by transcription factors (TFs), phytohormonal, and various environmental stimuli. Expression profiling showed that GossypiumLRR-RLK genes were widely involved in stress defense and diverse developmental processes including cotton fiber development and provides insight into potential functional divergence within and among subfamilies. Our study provided valuable information for further functional study of GossypiumLRR-RLK genes.
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24
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Shao GM, Li XY, Wang Y, Wang ZW, Li Z, Zhang XJ, Zhou L, Gui JF. Whole Genome Incorporation and Epigenetic Stability in a Newly Synthetic Allopolyploid of Gynogenetic Gibel Carp. Genome Biol Evol 2018; 10:2394-2407. [PMID: 30085110 PMCID: PMC6143163 DOI: 10.1093/gbe/evy165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 12/23/2022] Open
Abstract
Allopolyploidization plays an important role in speciation, and some natural or synthetic allopolyploid fishes have been extensively applied to aquaculture. Although genetic and epigenetic inheritance and variation associated with plant allopolyploids have been well documented, the relative research in allopolyploid animals is scarce. In this study, the genome constitution and DNA methylation inheritance in a newly synthetic allopolyploid of gynogenetic gibel carp were analyzed. The incorporation of a whole genome of paternal common carp sperm in the allopolyploid was confirmed by genomic in situ hybridization, chromosome localization of 45S rDNAs, and sequence comparison. Pooled sample-based methylation sensitive amplified polymorphism (MSAP) revealed that an overwhelming majority (98.82%) of cytosine methylation patterns in the allopolyploid were inherited from its parents of hexaploid gibel carp clone D and common carp. Compared to its parents, 11 DNA fragments in the allopolyploid were proved to be caused by interindividual variation, recombination, deletion, and mutation through individual sample-based MSAP and sequencing. Contrast to the rapid and remarkable epigenetic changes in most of analyzed neopolyploids, no cytosine methylation variation was detected in the gynogenetic allopolyploid. Therefore, the newly synthetic allopolyploid of gynogenetic gibel carp combined genomes from its parents and maintained genetic and epigenetic stability after its formation and subsequently seven successive gynogenetic generations. Our current results provide a paradigm for recurrent polyploidy consequences in the gynogenetic allopolyploid animals.
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Affiliation(s)
- Guang-Ming Shao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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25
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Kumar V, Singh B, Singh SK, Rai KM, Singh SP, Sable A, Pant P, Saxena G, Sawant SV. Role of GhHDA5 in H3K9 deacetylation and fiber initiation in Gossypium hirsutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1069-1083. [PMID: 29952050 DOI: 10.1111/tpj.14011] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 05/28/2023]
Abstract
Cotton fibers are single-celled trichomes that initiate from the epidermal cells of the ovules at or before anthesis. Here, we identified that the histone deacetylase (HDAC) activity is essential for proper cotton fiber initiation. We further identified 15 HDACs homoeologs in each of the A- and D-subgenomes of Gossypium hirsutum. Few of these HDAC homoeologs expressed preferentially during the early stages of fiber development [-1, 0 and 6 days post-anthesis (DPA)]. Among them, GhHDA5 expressed significantly at the time of fiber initiation (-1 and 0 DPA). The in vitro assay for HDAC activity indicated that GhHDA5 primarily deacetylates H3K9 acetylation marks. Moreover, the reduced expression of GhHDA5 also suppresses fiber initiation and lint yield in the RNA interference (RNAi) lines. The 0 DPA ovules of GhHDA5RNAi lines also showed alterations in reactive oxygen species homeostasis and elevated autophagic cell death in the developing fibers. The differentially expressed genes (DEGs) identified through RNA-seq of RNAi line (DEP12) and their pathway analysis showed that GhHDA5 modulates expression of many stress and development-related genes involved in fiber development. The reduced expression of GhHDA5 in the RNAi lines also resulted in H3K9 hyper-acetylation on the promoter region of few DEGs assessed by chromatin immunoprecipitation assay. The positively co-expressed genes with GhHDA5 showed cumulative higher expression during fiber initiation, and gene ontology annotation suggests their involvement in fiber development. Furthermore, the predicted protein interaction network in the positively co-expressed genes indicates HDA5 modulates fiber initiation-specific gene expression through a complex involving reported repressors.
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Affiliation(s)
- Verandra Kumar
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Babita Singh
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI, Lucknow, India
| | - Sunil K Singh
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
| | - Krishan M Rai
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
| | - Surendra P Singh
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Anshulika Sable
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
| | - Poonam Pant
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI, Lucknow, India
| | - Gauri Saxena
- Department of Botany, University of Lucknow, Lucknow, India
| | - Samir V Sawant
- Plant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI, Lucknow, India
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Bateman RM, Guy JJ, Rudall PJ, Leitch IJ, Pellicer J, Leitch AR. Evolutionary and functional potential of ploidy increase within individual plants: somatic ploidy mapping of the complex labellum of sexually deceptive bee orchids. ANNALS OF BOTANY 2018; 122:133-150. [PMID: 29672665 PMCID: PMC6025197 DOI: 10.1093/aob/mcy048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 03/15/2018] [Indexed: 05/07/2023]
Abstract
Background and Aims Recent tissue-level observations made indirectly via flow cytometry suggest that endoreplication (duplication of the nuclear genome within the nuclear envelope in the absence of subsequent cell division) is widespread within the plant kingdom. Here, we also directly observe ploidy variation among cells within individual petals, relating size of nucleus to cell micromorphology and (more speculatively) to function. Methods We compared the labella (specialized pollinator-attracting petals) of two European orchid genera: Dactylorhiza has a known predisposition to organismal polyploidy, whereas Ophrys exhibits exceptionally complex epidermal patterning that aids pseudocopulatory pollination. Confocal microscopy using multiple staining techniques allowed us to observe directly both the sizes and the internal structures of individual nuclei across each labellum, while flow cytometry was used to test for progressively partial endoreplication. Key Results In Dactylorhiza, endoreplication was comparatively infrequent, reached only low levels, and appeared randomly located across the labellum, whereas in Ophrys endoreplication was commonplace, being most frequent in large peripheral trichomes. Endoreplicated nuclei reflected both endomitosis and endocycling, the latter reaching the third round of genome doubling (16C) to generate polytene nuclei. All Ophrys individuals studied exhibited progressively partial endoreplication. Conclusions Comparison of the two genera failed to demonstrate the hypothesized pattern of frequent polyploid speciation in genera showing extensive endoreplication. Endoreplication in Ophrys appears more strongly positively correlated with cell size/complexity than with cell location or secretory role. Epigenetic control of gene overexpression by localized induction of endoreplication within individual plant organs may represent a significant component of a plant's developmental programme, contributing substantially to organ plasticity.
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Affiliation(s)
| | - Jessica J Guy
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Biological Sciences, University of Reading, Reading, UK
| | - Paula J Rudall
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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27
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Zhang Z, Ge X, Luo X, Wang P, Fan Q, Hu G, Xiao J, Li F, Wu J. Simultaneous Editing of Two Copies of Gh14-3-3d Confers Enhanced Transgene-Clean Plant Defense Against Verticillium dahliae in Allotetraploid Upland Cotton. FRONTIERS IN PLANT SCIENCE 2018; 9:842. [PMID: 30013582 PMCID: PMC6036271 DOI: 10.3389/fpls.2018.00842] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/30/2018] [Indexed: 05/02/2023]
Abstract
Gossypium hirsutum is an allotetraploid species, meaning that mutants that are difficult to be generated by classical approaches due to gene redundancy. The CRISPR/Cas9 genome editing system is a robust and highly efficient tool for generating target gene mutants, by which the genes of interest may be functionally dissected and applied through genotype-to-phenotype approaches. In this study, the CRISPR/Cas9 genome editing system was developed in G. hirsutum through editing the Gh14-3-3d gene. In T0 transgenic plants, lots of insertions and deletions (indels) in Gh14-3-3d at the expected target site were detected in the allotetraploid cotton At or Dt subgenomes. The results of the PCR, T7EI digestion and sequencing analyses showed that the indels in Gh14-3-3d gene can be stably transmitted to the next generation. Additionally, the indels in the At and Dt subgenomes were segregated in the T1 transgenic plants following Mendelian law, independing on the T-DNA segregation. Two homozygous Gh14-3-3d-edited plants free of T-DNA were chosen by PCR and sequencing assays in the T1 plants, which were called transgene-clean editing plants and were designated ce1 and ce2 in the T2 lines showed higher resistance to Verticillium dahliae infestation compared to the wild-type plants. Thus, the two transgene-clean edited lines can be used as a germplasm to breed disease-resistant cotton cultivars, possibly avoiding complex and expensive safety assessments of the transgenic plants.
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Affiliation(s)
- Zhennan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoli Luo
- Institute of Cotton Research, Shanxi Academy of Agricultural Sciences, Yuncheng, China
| | - Peng Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qiang Fan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guang Hu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Juanli Xiao
- Institute of Cotton Research, Shanxi Academy of Agricultural Sciences, Yuncheng, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Fuguang Li, Jiahe Wu,
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Fuguang Li, Jiahe Wu,
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Wang X, Dong Q, Li X, Yuliang A, Yu Y, Li N, Liu B, Gong L. Cytonuclear Variation of Rubisco in Synthesized Rice Hybrids and Allotetraploids. THE PLANT GENOME 2017; 10. [PMID: 29293814 DOI: 10.3835/plantgenome2017.05.0041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The allopolyploid speciation process faces the genomic challenge of stoichiometric disruption caused by merging biparental nuclear genomes with only one (usually maternal) of the two sets of progenitor cytoplasmic genomes. The photosynthetic protein 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is composed of nuclear-encoded small subunits (SSUs) and plastome-encoded large subunits (LSUs), making it an ideal enzyme to explore the evolution process of cytonuclear accommodation. We investigated the variation of SSUs and their encoding genes in synthetic nascent rice ( L.) allotetraploid lineages, formed from the parental subspecies and of Asian rice. The evolution of genes in rice subspecies involves both mutation and concerted homogenization. Within reciprocal rice hybrids and allopolyploids, there was no consistent pattern of biased expression of alleles or homeologs, nor was there biased gene conversion favoring the maternal gene copies. Instead, we observed an apparently stochastic pattern of intergenomic gene conversions and biased expression of homeologs. We conclude that in young rice allopolyploids, cytonuclear coordination either is not selectively favored because of high parental sequence similarity or because there has been insufficient time for subtle selective effects to become observable.
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Tang J, Chu C. MicroRNAs in crop improvement: fine-tuners for complex traits. NATURE PLANTS 2017; 3:17077. [PMID: 28665396 DOI: 10.1038/nplants.2017.77] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/28/2017] [Indexed: 05/20/2023]
Abstract
One of the most common challenges for both conventional and modern crop improvement is that the appearance of one desirable trait in a new crop variety is always balanced by the impairment of one or more other beneficial characteristics. The best way to overcome this problem is the flexible utilization of regulatory genes, especially genes that provide more efficient and precise regulation in a targeted manner. MicroRNAs (miRNAs), a type of short non-coding RNA, are promising candidates in this area due to their role as master modulators of gene expression at the post-transcriptional level, targeting messenger RNAs for cleavage or directing translational inhibition in eukaryotes. We herein highlight the current understanding of the biological role of miRNAs in orchestrating distinct agriculturally important traits by summarizing recent functional analyses of 65 miRNAs in 9 major crops worldwide. The integration of current miRNA knowledge with conventional and modern crop improvement strategies is also discussed.
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Affiliation(s)
- Jiuyou Tang
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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MicroRNA expression profiles during cotton (Gossypium hirsutum L) fiber early development. Sci Rep 2017; 7:44454. [PMID: 28327647 PMCID: PMC5361117 DOI: 10.1038/srep44454] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/08/2017] [Indexed: 12/24/2022] Open
Abstract
The role of microRNAs (miRNAs) during cotton fiber development remains unclear. Here, a total of 54 miRNAs belonging to 39 families were selected to characterize miRNA regulatory mechanism in eight different fiber development stages in upland cotton cv BM-1. Among 54 miRNAs, 18 miRNAs were involved in cotton fiber initiation and eight miRNAs were related to fiber elongation and secondary wall biosynthesis. Additionally, 3,576 protein-coding genes were candidate target genes of these miRNAs, which are potentially involved in cotton fiber development. We also investigated the regulatory network of miRNAs and corresponding targets in fiber initiation and elongation, and secondary wall formation. Our Gene Ontology-based term classification and KEGG-based pathway enrichment analyses showed that the miRNA targets covered 220 biological processes, 67 molecular functions, 45 cellular components, and 10 KEGG pathways. Three of ten KEGG pathways were involved in lignan synthesis, cell elongation, and fatty acid biosynthesis, all of which have important roles in fiber development. Overall, our study shows the potential regulatory roles of miRNAs in cotton fiber development and the importance of miRNAs in regulating different cell types. This is helpful to design miRNA-based biotechnology for improving fiber quality and yield.
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A high-efficiency CRISPR/Cas9 system for targeted mutagenesis in Cotton (Gossypium hirsutum L.). Sci Rep 2017; 7:43902. [PMID: 28256588 PMCID: PMC5335549 DOI: 10.1038/srep43902] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/30/2017] [Indexed: 12/26/2022] Open
Abstract
The complex allotetraploid genome is one of major challenges in cotton for repressing gene expression. Developing site-specific DNA mutation is the long-term dream for cotton breeding scientists. The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system is emerging as a robust biotechnology for targeted-DNA mutation. In this study, two sgRNAs, GhMYB25-like-sgRNA1 and GhMYB25-like-sgRNA2, were designed in the identical genomic regions of GhMYB25-like A and GhMYB25-like D, which were encoded by cotton A subgenome and the D subgenome, respectively, was assembled to direct Cas9-mediated allotetraploid cotton genome editing. High proportion (14.2–21.4%) CRISPR/Cas9-induced specific truncation events, either from GhMYB25-like A DNA site or from GhMYB25-like D DNA site, were detected in 50% examined transgenic cotton through PCR amplification assay and sequencing analyses. Sequencing results also demonstrated that 100% and 98.8% mutation frequency were occurred on GhMYB25-like-sgRNA1 and GhMYB25-like-sgRNA2 target site respectively. The off-target effect was evaluated by sequencing two putative off-target sites, which have 3 and 1 mismatched nucleotides with GhMYB25-like-sgRNA1 and GhMYB25-like-sgRNA2, respectively; all the examined samples were not detected any off-target-caused mutation events. Thus, these results demonstrated that CRISPR/Cas9 is qualified for generating DNA level mutations on allotetraploid cotton genome with high-efficiency and high-specificity.
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Miao Q, Deng P, Saha S, Jenkins JN, Hsu CY, Abdurakhmonov IY, Buriev ZT, Pepper A, Ma DP. Genome-wide identification and characterization of microRNAs differentially expressed in fibers in a cotton phytochrome A1 RNAi line. PLoS One 2017; 12:e0179381. [PMID: 28614407 PMCID: PMC5470697 DOI: 10.1371/journal.pone.0179381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/28/2017] [Indexed: 02/07/2023] Open
Abstract
Cotton fiber is an important commodity throughout the world. Fiber property determines fiber quality and commercial values. Previous studies showed that silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium hirsutum L. cv. Coker 312) had generated PHYA1 RNAi lines with simultaneous improvements in fiber quality (longer, stronger and finer fiber) and other key agronomic traits. Characterization of the altered molecular processes in these RNAi genotypes and its wild-type controls is a great interest to better understand the PHYA1 RNAi phenotypes. In this study, a total of 77 conserved miRNAs belonging to 61 families were examined in a PHYA1 RNAi line and its parental Coker 312 genotype by using multiplex sequencing. Of these miRNAs, seven (miR7503, miR7514, miR399c, miR399d, miR160, miR169b, and miR2950) were found to be differentially expressed in PHYA1 RNAi cotton. The target genes of these differentially expressed miRNAs were involved in the metabolism and signaling pathways of phytohormones, which included Gibberellin, Auxin and Abscisic Acid. The expression of several MYB transcription factors was also affected by miRNAs in RNAi cotton. In addition, 35 novel miRNAs (novel miR1-novel miR35) were identified in fibers for the first time in this study. Target genes of vast majority of these novel miRNAs were also predicted. Of these, nine novel miRNAs (novel-miR1, 2, 16, 19, 26, 27, 28, 31 and 32) were targeted to cytochrome P450-like TATA box binding protein (TBP). The qRT-PCR confirmed expression levels of several differentially regulated miRNAs. Expression patterns of four miRNAs-targets pairs were also examined via RNA deep sequencing. Together, the results imply that the regulation of miRNA expression might confer to the phenotype of the PHYA1 RNAi line(s) with improved fiber quality.
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Affiliation(s)
- Qing Miao
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, United States of America
| | - Peng Deng
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, United States of America
| | - Sukumar Saha
- USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS, United States of America
| | - Johnie N. Jenkins
- USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS, United States of America
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, United States of America
| | | | - Zabardast T. Buriev
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Alan Pepper
- Department of Biology, Texas A & M University, College Station, TX, United States of America
| | - Din-Pow Ma
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, United States of America
- * E-mail:
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Miao Q, Deng P, Saha S, Jenkins JN, Hsu CY, Abdurakhmonov IY, Buriev ZT, Pepper A, Ma DP. Transcriptome Analysis of Ten-DPA Fiber in an Upland Cotton (<i>Gossypium hirsutum</i>) Line with Improved Fiber Traits from Phytochrome A1 RNAi Plants. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/ajps.2017.810172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Yang H, Meng Y, Chen B, Zhang X, Wang Y, Zhao W, Zhou Z. How Integrated Management Strategies Promote Protein Quality of Cotton Embryos: High Levels of Soil Available N, N Assimilation and Protein Accumulation Rate. FRONTIERS IN PLANT SCIENCE 2016; 7:1118. [PMID: 27532007 PMCID: PMC4969568 DOI: 10.3389/fpls.2016.01118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/13/2016] [Indexed: 05/24/2023]
Abstract
Cottonseed is widely used as a source of ruminant feed and for industrial purposes. Therefore, there is a tremendous need to improve the nutritional value of cotton embryos. In this study, a conventional management (CM) and two integrated cotton management strategies (IMS1, IMS2) were performed at two soil fertility levels to study the relationships among soil N, N assimilation, embryonic protein accumulation and protein quality. The levels of proteins, essential amino acids, and semi-essential amino acids, especially those of glutamate, lysine, and methionine, were higher in IMS1 and IMS2 embryos than in CM embryos. These changes were significantly positively correlated with the soil-available N content, glutamine synthetase activity and peak value of protein accumulation rate and were negatively correlated with the free amino acid level. These results illustrated that integrated management strategies, especially the rates and timing of N application, raise the level of soil available N, which is beneficial for N assimilation in developing cotton embryos. The protein content was limited by the rate of protein accumulation rather than by the free amino acid content. The combination of target yield fertilization, a growth-driven N application schedule, a high plant density and the seedling raising with bio-organic fertilizer can substantially improve protein quality in cotton embryos, especially at a soil with low soil organic matter and total nitrogen.
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Affiliation(s)
| | | | - BingLin Chen
- Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Nanjing Agricultural University and Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing, China
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Wan Q, Guan X, Yang N, Wu H, Pan M, Liu B, Fang L, Yang S, Hu Y, Ye W, Zhang H, Ma P, Chen J, Wang Q, Mei G, Cai C, Yang D, Wang J, Guo W, Zhang W, Chen X, Zhang T. Small interfering RNAs from bidirectional transcripts of GhMML3_A12 regulate cotton fiber development. THE NEW PHYTOLOGIST 2016; 210:1298-310. [PMID: 26832840 DOI: 10.1111/nph.13860] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 12/09/2015] [Indexed: 05/18/2023]
Abstract
Natural antisense transcripts (NATs) are commonly observed in eukaryotic genomes, but only a limited number of such genes have been identified as being involved in gene regulation in plants. In this research, we investigated the function of small RNA derived from a NAT in fiber cell development. Using a map-based cloning strategy for the first time in tetraploid cotton, we cloned a naked seed mutant gene (N1 ) encoding a MYBMIXTA-like transcription factor 3 (MML3)/GhMYB25-like in chromosome A12, GhMML3_A12, that is associated with fuzz fiber development. The extremely low expression of GhMML3_A12 in N1 is associated with NAT production, driven by its 3' antisense promoter, as indicated by the promoter-driven histochemical staining assay. In addition, small RNA deep sequencing analysis suggested that the bidirectional transcriptions of GhMML3_A12 form double-stranded RNAs and generate 21-22 nt small RNAs. Therefore, in a fiber-specific manner, small RNA derived from the GhMML3_A12 locus can mediate GhMML3_A12 mRNA self-cleavage and result in the production of naked seeds followed by lint fiber inhibition in N1 plants. The present research reports the first observation of gene-mediated NATs and siRNA directly controlling fiber development in cotton.
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Affiliation(s)
- Qun Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xueying Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nannan Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huaitong Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengqiao Pan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingliang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lei Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shouping Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hua Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peiyong Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiedan Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gaofu Mei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Caiping Cai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Donglei Yang
- National Laboratory of Plant Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiawei Wang
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenhua Zhang
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
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Gallagher JP, Grover CE, Hu G, Wendel JF. Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis. Mol Ecol 2016; 25:2644-60. [PMID: 27027619 DOI: 10.1111/mec.13626] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/09/2016] [Accepted: 03/22/2016] [Indexed: 12/18/2022]
Abstract
Polyploidy is a widespread phenomenon throughout eukaryotes, with important ecological and evolutionary consequences. Although genes operate as components of complex pathways and networks, polyploid changes in genes and gene expression have typically been evaluated as either individual genes or as a part of broad-scale analyses. Network analysis has been fruitful in associating genomic and other 'omic'-based changes with phenotype for many systems. In polyploid species, network analysis has the potential not only to facilitate a better understanding of the complex 'omic' underpinnings of phenotypic and ecological traits common to polyploidy, but also to provide novel insight into the interaction among duplicated genes and genomes. This adds perspective to the global patterns of expression (and other 'omic') change that accompany polyploidy and to the patterns of recruitment and/or loss of genes following polyploidization. While network analysis in polyploid species faces challenges common to other analyses of duplicated genomes, present technologies combined with thoughtful experimental design provide a powerful system to explore polyploid evolution. Here, we demonstrate the utility and potential of network analysis to questions pertaining to polyploidy with an example involving evolution of the transgressively superior cotton fibres found in polyploid Gossypium hirsutum. By combining network analysis with prior knowledge, we provide further insights into the role of profilins in fibre domestication and exemplify the potential for network analysis in polyploid species.
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Affiliation(s)
- Joseph P Gallagher
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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37
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Li C, Zhang B. MicroRNAs in Control of Plant Development. J Cell Physiol 2016; 231:303-13. [PMID: 26248304 DOI: 10.1002/jcp.25125] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 08/04/2015] [Indexed: 12/19/2022]
Abstract
In the long evolutionary history, plant has evolved elaborate regulatory network to control functional gene expression for surviving and thriving, such as transcription factor-regulated transcriptional programming. However, plenty of evidences from the past decade studies demonstrate that the 21-24 nucleotides small RNA molecules, majorly microRNAs (miRNAs) play dominant roles in post-transcriptional gene regulation through base pairing with their complementary mRNA targets, especially prefer to target transcription factors in plants. Here, we review current progresses on miRNA-controlled plant development, from miRNA biogenesis dysregulation-caused pleiotropic developmental defects to specific developmental processes, such as SAM regulation, leaf and root system regulation, and plant floral transition. We also summarize some miRNAs that are experimentally proved to greatly affect crop plant productivity and quality. In addition, recent reports show that a single miRNA usually displays multiple regulatory roles, such as organ development, phase transition, and stresses responses. Thus, we infer that miRNA may act as a node molecule to coordinate the balance between plant development and environmental clues, which may shed the light on finding key regulator or regulatory pathway for uncovering the mysterious molecular network.
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Affiliation(s)
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, 27858, North Carolina
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Gao JS, Wu N, Shen ZL, Lv K, Qian SH, Guo N, Sun X, Cai YP, Lin Y. Molecular cloning, expression analysis and subcellular localization of a Transparent Testa 12 ortholog in brown cotton (Gossypium hirsutum L.). Gene 2016; 576:763-9. [DOI: 10.1016/j.gene.2015.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 10/16/2015] [Accepted: 11/02/2015] [Indexed: 11/26/2022]
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Song Q, Guan X, Chen ZJ. Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton. PLoS Genet 2015; 11:e1005724. [PMID: 26710171 PMCID: PMC4692501 DOI: 10.1371/journal.pgen.1005724] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/14/2015] [Indexed: 11/19/2022] Open
Abstract
DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites via distinct pathways. Cotton is an allotetraploid consisting of two progenitor genomes. Each cotton fiber is a rapidly-elongating cell derived from the ovule epidermis, but the molecular basis for this developmental transition is unknown. Here we analyzed methylome, transcriptome, and small RNAome and revealed distinct changes in CHH methylation during ovule and fiber development. In ovules, CHH hypermethylation in promoters correlated positively with siRNAs, inducing RNA-dependent DNA methylation (RdDM), and up-regulation of ovule-preferred genes. In fibers, the ovule-derived cells generated additional heterochromatic CHH hypermethylation independent of RdDM, which repressed transposable elements (TEs) and nearby genes including fiber-related genes. Furthermore, CHG and CHH methylation in genic regions contributed to homoeolog expression bias in ovules and fibers. Inhibiting DNA methylation using 5-aza-2'-deoxycytidine in cultured ovules has reduced fiber cell number and length, suggesting a potential role for DNA methylation in fiber development. Thus, RdDM-dependent methylation in promoters and RdDM-independent methylation in TEs and nearby genes could act as a double-lock feedback mechanism to mediate gene and TE expression, potentiating the transition from epidermal to fiber cells during ovule and seed development. Cotton is the world’s largest source of renewable textile fiber and is an allotetraploid crop consisting of two progenitor genomes. In plants, de novo CHH (H = A, T, or C) methylation depends on RNA-directed DNA methylation (RdDM) and CHROMOMETHYLASE2 (CMT2)-mediated pathways. The biological significance of the two pathways is largely unknown. Here we show dynamic roles of these two pathways in ovule and fiber development. RdDM-dependent CHH methylation is linked to gene activation in ovules, and additional CMT2-dependent methylation leads to silencing of transposons and nearby genes in fibers. Moreover, DNA methylation affects expression bias of homoeologous genes and fiber development. These findings provide novel insights into epigenetic regulation of organ development and polyploid evolution.
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Affiliation(s)
- Qingxin Song
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
| | - Xueying Guan
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Z. Jeffrey Chen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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40
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Li AL, Geng SF, Zhang LQ, Liu DC, Mao L. Making the Bread: Insights from Newly Synthesized Allohexaploid Wheat. MOLECULAR PLANT 2015; 8:847-59. [PMID: 25747845 DOI: 10.1016/j.molp.2015.02.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/13/2015] [Accepted: 02/25/2015] [Indexed: 05/27/2023]
Abstract
Bread wheat (or common wheat, Triticum aestivum) is an allohexaploid (AABBDD, 2n = 6x = 42) that arose by hybridization between a cultivated tetraploid wheat T. turgidum (AABB, 2n = 4x = 28) and the wild goatgrass Aegilops tauschii (DD, 2n = 2x = 14). Polyploidization provided niches for rigorous genome modification at cytogenetic, genetic, and epigenetic levels, rendering a broader spread than its progenitors. This review summarizes the latest advances in understanding gene regulation mechanisms in newly synthesized allohexaploid wheat and possible correlation with polyploid growth vigor and adaptation. Cytogenetic studies reveal persistent association of whole-chromosome aneuploidy with nascent allopolyploids, in contrast to the genetic stability in common wheat. Transcriptome analysis of the euploid wheat shows that small RNAs are driving forces for homoeo-allele expression regulation via genetic and epigenetic mechanisms. The ensuing non-additively expressed genes and those with expression level dominance to the respective progenitor may play distinct functions in growth vigor and adaptation in nascent allohexaploid wheat. Further genetic diploidization of allohexaploid wheat is not random. Regional asymmetrical gene distribution, rather than subgenome dominance, is observed in both synthetic and natural allohexaploid wheats. The combinatorial effects of diverged genomes, subsequent selection of specific gene categories, and subgenome-specific traits are essential for the successful establishment of common wheat.
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Affiliation(s)
- Ai-li Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai-Feng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lian-quan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Deng-cai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol 2015; 33:531-7. [PMID: 25893781 DOI: 10.1038/nbt.3207] [Citation(s) in RCA: 1014] [Impact Index Per Article: 112.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 03/15/2015] [Indexed: 02/06/2023]
Abstract
Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.
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Hu H, Yu D, Liu H. Bioinformatics analysis of small RNAs in pima (Gossypium barbadense L.). PLoS One 2015; 10:e0116826. [PMID: 25679373 PMCID: PMC4332481 DOI: 10.1371/journal.pone.0116826] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/12/2014] [Indexed: 11/24/2022] Open
Abstract
Small RNAs (sRNAs) are ~20 to 24 nucleotide single-stranded RNAs that play crucial roles in regulation of gene expression. In plants, sRNAs are classified into microRNAs (miRNAs), repeat-associated siRNAs (ra-siRNAs), phased siRNAs (pha-siRNAs), cis and trans natural antisense transcript siRNAs (cis- and trans-nat siRNAs). Pima (Gossypium barbadense L.) is one of the most economically important fiber crops, producing the best and longest spinnable fiber. Although some miRNAs are profiled in Pima, little is known about siRNAs, the largest subclass of plant sRNAs. In order to profile these gene regulators in Pima, a comprehensive analysis of sRNAs was conducted by mining publicly available sRNA data, leading to identification of 678 miRNAs, 3,559,126 ra-siRNAs, 627 pha-siRNAs, 136,600 cis-nat siRNAs and 79,994 trans-nat siRNAs. The 678 miRNAs, belonging to 98 conserved and 402 lineage-specific families, were produced from 2,138 precursors, of which 297 arose from introns, exons, or intron/UTR-exon junctions of protein-coding genes. Ra-siRNAs were produced from various repeat loci, while most (97%) were yielded from retrotransposons, especially LTRs (long terminal repeats). The genes encoding auxin-signaling-related proteins, NBS-LRRs and transcription factors were major sources of pha-siRNAs, while two conserved TAS3 homologs were found as well. Most cis-NATs in Pima overlapped in enclosed and convergent orientations, while a few hybridized in divergent and coincided orientations. Most cis- and trans-nat siRNAs were produced from overlapping regions. Additionally, characteristics of length and the 5’-first nucleotide of each sRNA class were analyzed as well. Results in this study created a valuable molecular resource that would facilitate studies on mechanism of controlling gene expression.
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Affiliation(s)
- Hongtao Hu
- Center for Bio-Pesticide Research, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
- Department of Biological Engineering, Hubei Vocational College of Biological Sciences and Technology, Wuhan, Hubei, China
| | - Dazhao Yu
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Hong Liu
- College of Life Sciences, Hunan University of Arts and Sciences, Changde, Hunan, China
- College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
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