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Lian B, Wu A, Wu H, Lv X, Sun M, Li Y, Lu Z, Li S, An L, Guo X, Wei F, Fu X, Lu J, Wang H, Ma L, Wei H, Yu S. GhVOZ1-AVP1 module positively regulates salt tolerance in upland cotton (Gossypium hirsutum L.). Int J Biol Macromol 2024; 258:129116. [PMID: 38171192 DOI: 10.1016/j.ijbiomac.2023.129116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024]
Abstract
Vascular Plant One‑zinc Finger (VOZ) transcription factor can respond to a variety of abiotic stresses, however its function in cotton and the molecular mechanisms of response to salt tolerance remained unclear. In this study, we found that GhVOZ1 is highly expressed in stamen and stem of cotton under normal conditions. The expression of GhVOZ1 increased significantly after 3 h of salt treatment in three-leaf staged upland cotton. Overexpressed transgenic lines of GhVOZ1 in Arabidopsis and upland cotton were treated with salt stress and we found that GhVOZ1 could respond positively to salt stress. GhVOZ1 can regulate Arabidopsis Vacuolar Proton Pump Pyrophosphatase (H+-PPase) gene (AVP1) expression through specific binding to GCGTCTAAAGTACGC site on GhAVP1 promoter, which was examined through Dual-luciferase assay and Electrophoretic mobility shift assay (EMSA). AVP1 expression was significantly increased in Arabidopsis with GhVOZ1 overexpression, while GhAVP1 expression was decreased in virus induced gene silenced (VIGS) cotton plants of GhVOZ1. Knockdown of GhAVP1 expression in cotton plants by VIGS showed decreased superoxide dismutase (SOD) and peroxidase (POD) activities, whereas an increased malondialdehyde (MDA) content and ultimately decreased salt tolerance. The GhVOZ1-AVP1 module could maintain sodium ion homeostasis through cell ion transport and positively regulate the salt tolerance in cotton, providing new ideas and insights for the study of salt tolerance.
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Affiliation(s)
- Boying Lian
- College of Agronomy, Northwest A&F University, Yangling 712100, Shannxi, China
| | - Aimin Wu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Hongmei Wu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xiaoyan Lv
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Mengxi Sun
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Yiran Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhengying Lu
- Handan Academy of Agricultural Sciences, Handan 056000, Hebei, China
| | - Shiyun Li
- Handan Academy of Agricultural Sciences, Handan 056000, Hebei, China
| | - Li An
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xiaohao Guo
- College of Agronomy, Northwest A&F University, Yangling 712100, Shannxi, China
| | - Fei Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xiaokang Fu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Jianhua Lu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Hantao Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Liang Ma
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Hengling Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Shuxun Yu
- College of Agronomy, Northwest A&F University, Yangling 712100, Shannxi, China.
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Yu H, Guo Q, Ji W, Wang H, Tao J, Xu P, Chen X, Ali W, Wu X, Shen X, Xie Y, Xu Z. Transcriptome Expression Profiling Reveals the Molecular Response to Salt Stress in Gossypium anomalum Seedlings. PLANTS (BASEL, SWITZERLAND) 2024; 13:312. [PMID: 38276767 PMCID: PMC10819910 DOI: 10.3390/plants13020312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024]
Abstract
Some wild cotton species are remarkably tolerant to salt stress, and hence represent valuable resources for improving salt tolerance of the domesticated allotetraploid species Gossypium hirsutum L. Here, we first detected salt-induced stress changes in physiological and biochemical indexes of G. anomalum, a wild African diploid cotton species. Under 350 mmol/L NaCl treatment, the photosynthetic parameters declined significantly, whereas hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents increased. Catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) activity and proline (PRO) content also significantly increased, reaching peak values at different stages of salt stress. We used RNA-Seq to characterize 15,476 differentially expressed genes in G. anomalum roots after 6, 12, 24, 72, and 144 h of salt stress. Gene Ontology enrichment analysis revealed these genes to be related to sequence-specific DNA and iron ion binding and oxidoreductase, peroxidase, antioxidant, and transferase activity; meanwhile, the top enriched pathways from the Kyoto Encyclopedia of Genes and Genomes database were plant hormone signal transduction, phenylpropanoid biosynthesis, fatty acid degradation, carotenoid biosynthesis, zeatin biosynthesis, starch and sucrose metabolism, and MAPK signaling. A total of 1231 transcription factors were found to be expressed in response to salt stress, representing ERF, MYB, WRKY, NAC, C2H2, bZIP, and HD-ZIP families. Nine candidate genes were validated by quantitative real-time PCR and their expression patterns were found to be consistent with the RNA-Seq data. These data promise to significantly advance our understanding of the molecular response to salt stress in Gossypium spp., with potential value for breeding applications.
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Affiliation(s)
- Huan Yu
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China;
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Qi Guo
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Wei Ji
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Heyang Wang
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Jingqi Tao
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Peng Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xianglong Chen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Wuzhimu Ali
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xuan Wu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xinlian Shen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Yinfeng Xie
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China;
| | - Zhenzhen Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
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Wang H, Ye L, Zhou L, Yu J, Pang B, Zuo D, Gu L, Zhu B, Du X, Wang H. Co-Expression Network Analysis of the Transcriptome Identified Hub Genes and Pathways Responding to Saline-Alkaline Stress in Sorghum bicolor L. Int J Mol Sci 2023; 24:16831. [PMID: 38069156 PMCID: PMC10706439 DOI: 10.3390/ijms242316831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Soil salinization, an intractable problem, is becoming increasingly serious and threatening fragile natural ecosystems and even the security of human food supplies. Sorghum (Sorghum bicolor L.) is one of the main crops growing in salinized soil. However, the tolerance mechanisms of sorghum to saline-alkaline soil are still ambiguous. In this study, RNA sequencing was carried out to explore the gene expression profiles of sorghum treated with sodium bicarbonate (150 mM, pH = 8.0, treated for 0, 6, 12 and 24 h). The results show that 6045, 5122, 6804, 7978, 8080 and 12,899 differentially expressed genes (DEGs) were detected in shoots and roots after 6, 12 and 24 h treatments, respectively. GO, KEGG and weighted gene co-expression analyses indicate that the DEGs generated by saline-alkaline stress were primarily enriched in plant hormone signal transduction, the MAPK signaling pathway, starch and sucrose metabolism, glutathione metabolism and phenylpropanoid biosynthesis. Key pathway and hub genes (TPP1, WRKY61, YSL1 and NHX7) are mainly related to intracellular ion transport and lignin synthesis. The molecular and physiological regulation processes of saline-alkali-tolerant sorghum are shown by these results, which also provide useful knowledge for improving sorghum yield and quality under saline-alkaline conditions.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (H.W.); (L.Y.); (L.Z.); (J.Y.); (B.P.); (D.Z.); (L.G.); (B.Z.)
| | - Huinan Wang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (H.W.); (L.Y.); (L.Z.); (J.Y.); (B.P.); (D.Z.); (L.G.); (B.Z.)
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Abdul Aziz M, Masmoudi K. Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms. Int J Mol Sci 2023; 24:9813. [PMID: 37372961 DOI: 10.3390/ijms24129813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023] Open
Abstract
The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na+ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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5
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Ju F, Sun L, Xiong C, Wang Z, Yu H, Pang J, Bai H, Zhao W, Zhou Z, Chen B. Weighted gene co-expression network analysis revealed the key pathways and hub genes of potassium regulating cotton root adaptation to salt stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1132877. [PMID: 36938049 PMCID: PMC10014550 DOI: 10.3389/fpls.2023.1132877] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Soil salinization is one of the main abiotic stresses affecting cotton yield and planting area. Potassium application has been proven to be an important strategy to reduce salt damage in agricultural production. However, the mechanism of potassium regulating the salt adaptability of cotton has not been fully elucidated. In the present research, the appropriate potassium application rate for alleviating salt damage of cotton based on different K+/Na+ ratios we screened, and a gene co-expression network based on weighted gene co-expression network analysis (WGCNA) using the transcriptome data sets treated with CK (0 mM NaCl), S (150 mM NaCl), and SK8 (150 mM NaCl + 9.38 mM K2SO4) was constructed. In this study, four key modules that are highly related to potassium regulation of cotton salt tolerance were identified, and the mitogen-activated protein kinase (MAPK) signaling pathway, tricarboxylic acid (TCA) cycle and glutathione metabolism pathway were identified as the key biological processes and metabolic pathways for potassium to improve cotton root salt adaptability. In addition, 21 hub genes and 120 key candidate genes were identified in this study, suggesting that they may play an important role in the enhancement of salt adaptability of cotton by potassium. The key modules, key biological pathways and hub genes discovered in this study will provide a new understanding of the molecular mechanism of potassium enhancing salinity adaptability in cotton, and lay a theoretical foundation for the improvement and innovation of high-quality cotton germplasm.
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Affiliation(s)
- Feiyan Ju
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing, China
| | - Liyuan Sun
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing, China
| | - Cai Xiong
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing, China
| | - Zhuo Wang
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing, China
| | - Huilian Yu
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing, China
| | - Jiali Pang
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing, China
| | - Hua Bai
- School of Agricultural Sciences, Northwest Missouri State University, Maryville, MO, United States
| | - Wengqing Zhao
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing, China
| | - Zhiguo Zhou
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing, China
| | - Binglin Chen
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing, China
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Sun K, Mehari TG, Fang H, Han J, Huo X, Zhang J, Chen Y, Wang D, Zhuang Z, Ditta A, Khan MK, Zhang J, Wang K, Wang B. Transcriptome, proteome and functional characterization reveals salt stress tolerance mechanisms in upland cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1092616. [PMID: 36875590 PMCID: PMC9978342 DOI: 10.3389/fpls.2023.1092616] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/03/2023] [Indexed: 06/05/2023]
Abstract
Uncovering the underlying mechanism of salt tolerance is important to breed cotton varieties with improved salt tolerance. In this study, transcriptome and proteome sequencing were performed on upland cotton (Gossypium hirsutum L.) variety under salt stress, and integrated analysis was carried out to exploit salt-tolerance genes in cotton. Enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed on differentially expressed genes (DEGs) obtained from transcriptome and proteome sequencing. GO enrichment was carried out mainly in the cell membrane, organelle, cellular process, metabolic process, and stress response. The expression of 23,981 genes was changed in physiological and biochemical processes such as cell metabolism. The metabolic pathways obtained by KEGG enrichment included glycerolipid metabolism, sesquiterpene and triterpenoid biosynthesis, flavonoid production, and plant hormone signal transduction. Combined transcriptome and proteome analysis to screen and annotate DEGs yielded 24 candidate genes with significant differential expression. The quantitative real-time polymerase chain reaction (qRT-PCR) validation of the candidate genes showed that two genes (Gh_D11G0978 and Gh_D10G0907) responded significantly to the induction of NaCl, and these two genes were further selected as target genes for gene cloning and functional validation through virus-induced gene silencing (VIGS). The silenced plants exhibited early wilting with a greater degree of salt damage under salt treatment. Moreover, they showed higher levels of reactive oxygen species (ROS) than the control. Therefore, we can infer that these two genes have a pivotal role in the response to salt stress in upland cotton. The findings in this research will facilitate the breeding of salt tolerance cotton varieties that can be grown on saline alkaline lands.
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Affiliation(s)
- Kangtai Sun
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | | | - Hui Fang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Xuehan Huo
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Dongmei Wang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Zhimin Zhuang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Allah Ditta
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Muhammad K.R. Khan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
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7
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Bano N, Fakhrah S, Lone RA, Mohanty CS, Bag SK. Genome-wide identification and expression analysis of the HD2 protein family and its response to drought and salt stress in Gossypium species. FRONTIERS IN PLANT SCIENCE 2023; 14:1109031. [PMID: 36860898 PMCID: PMC9968887 DOI: 10.3389/fpls.2023.1109031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Histone deacetylase 2 (HD2) proteins play an important role in the regulation of gene expression. This helps with the growth and development of plants and also plays a crucial role in responses to biotic and abiotic stress es. HD2s comprise a C2H2-type Zn2+ finger at their C-terminal and an HD2 label, deacetylation and phosphorylation sites, and NLS motifs at their N-terminal. In this study, a total of 27 HD2 members were identified, using Hidden Markov model profiles, in two diploid cotton genomes (Gossypium raimondii and Gossypium arboretum) and two tetraploid cotton genomes (Gossypium hirsutum and Gossypium barbadense). These cotton HD2 members were classified into 10 major phylogenetic groups (I-X), of which group III was found to be the largest with 13 cotton HD2 members. An evolutionary investigation showed that the expansion of HD2 members primarily occurred as a result of segmental duplication in paralogous gene pairs. Further qRT-PCR validation of nine putative genes using RNA-Seq data suggested that GhHDT3D.2 exhibits significantly higher levels of expression at 12h, 24h, 48h, and 72h of exposure to both drought and salt stress conditions compared to a control measure at 0h. Furthermore, gene ontology, pathways, and co-expression network study of GhHDT3D.2 gene affirmed their significance in drought and salt stress responses.
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Affiliation(s)
- Nasreen Bano
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shafquat Fakhrah
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Rayees Ahmad Lone
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chandra Sekhar Mohanty
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sumit Kumar Bag
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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8
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Hou R, Yang L, Wuyun T, Chen S, Zhang L. Genes related to osmoregulation and antioxidation play important roles in the response of Trollius chinensis seedlings to saline-alkali stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1080504. [PMID: 36778702 PMCID: PMC9911134 DOI: 10.3389/fpls.2023.1080504] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Saline-alkali stress is one of the main abiotic stress factors affecting plant growth and development. Trollius chinensis is a perennial herbal medicinal plant with high values for garden application. However, its response and tolerance to saline-alkali stress is unclear. In this study, we mixed four salts (NaCl: Na2SO4: NaHCO3: Na2CO3) with a concentration ratio of 1:9:9:1, and applied low (40 and 80 mM) and high (120 and 160 mM) saline-alkali stress to analyze osmotic regulation substances, antioxidant systems and the gene expression of T. chinensis. Along with higher saline-alkali stress, the leaf relative water content (RWC) started to decrease only from high stress, while the malondialdehyde (MDA) content in leaves decreased continuously, and the contents of proline (Pro), soluble sugar (SS) and soluble protein (SP) increased compared with control. The activities of antioxidant enzymes and the contents of non-enzymatic antioxidants were increased positively with the accumulation of superoxide anion (O2 •-) and hydrogen peroxide (H2O2). For instance, the ascorbic acid-glutathione (AsA-GSH) cycle was enhanced in T. chinensis seedling leaves subject to saline-alkali stress. Principal Component Analysis (PCA) indicates that MDA, Pro, SS, SP, H2O2, O2 •-, and GSH are important indexes to evaluate the response and tolerance of T. chinensis to saline-alkali stress. Through RNA-Seq, a total of 474 differentially expressed genes (DEGs) were found in plant under low saline-alkaline stress (40 mM, MSA1) vs. control. Among them, 364 genes were up-regulated and 110 genes were down-regulated. DEGs were extensively enriched in carbohydrate transport, transferase activity, zeatin biosynthesis, ABC transporters, and spliceosome. The transcription factor family MYB, BZIP, WRKY, and NAC were related to its saline-alkali tolerance. In addition, some DEGs encode key enzymes in the processes of osmoregulation and antioxidation, including betaine aldehyde dehydrogenase (BADH), inositol monophosphatase (IMP), chloroperoxidase (CPO), thioredoxin (Trx), and germin-like protein (GLPs) were found. Overall, these findings provide new insights into the physiological changes and molecular mechanism of T. chinensis to saline-alkali stress and lay a foundation for application of T. chinensis in saline-alkali environment.
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Affiliation(s)
- Rongmiao Hou
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Lizhi Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Tana Wuyun
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Shiyao Chen
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
| | - Lu Zhang
- College of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang A&F University, Hangzhou, China
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9
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Ma D, Cai J, Ma Q, Wang W, Zhao L, Li J, Su L. Comparative time-course transcriptome analysis of two contrasting alfalfa ( Medicago sativa L.) genotypes reveals tolerance mechanisms to salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1070846. [PMID: 36570949 PMCID: PMC9773191 DOI: 10.3389/fpls.2022.1070846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Salt stress is a major abiotic stress affecting plant growth and crop yield. For the successful cultivation of alfalfa (Medicago sativa L.), a key legume forage, in saline-affected areas, it's essential to explore genetic modifications to improve salt-tolerance.Transcriptome assay of two comparative alfalfa genotypes, Adina and Zhaodong, following a 4 h and 8 h's 300 mM NaCl treatment was conducted in this study in order to investigate the molecular mechanism in alfalfa under salt stress conditions. Results showed that we obtained 875,023,571 transcripts and 662,765,594 unigenes were abtained from the sequenced libraries, and 520,091 assembled unigenes were annotated in at least one database. Among them, we identified 1,636 differentially expression genes (DEGs) in Adina, of which 1,426 were up-regulated and 210 down-regulated, and 1,295 DEGs in Zhaodong, of which 565 were up-regulated and 730 down-regulated. GO annotations and KEGG pathway enrichments of the DEGs based on RNA-seq data indicated that DEGs were involved in (1) ion and membrane homeostasis, including ABC transporter, CLC, NCX, and NHX; (2) Ca2+ sensing and transduction, including BK channel, EF-hand domain, and calmodulin binding protein; (3) phytohormone signaling and regulation, including TPR, FBP, LRR, and PP2C; (4) transcription factors, including zinc finger proteins, YABBY, and SBP-box; (5) antioxidation process, including GST, PYROX, and ALDH; (6) post-translational modification, including UCH, ubiquitin family, GT, MT and SOT. The functional roles of DEGs could explain the variations in salt tolerance performance observed between the two alfalfa genotypes Adina and Zhaodong. Our study widens the understanding of the sophisticated molecular response and tolerance mechanism to salt stress, providing novel insights on candidate genes and pathways for genetic modification involved in salt stress adaptation in alfalfa.
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Affiliation(s)
- Dongmei Ma
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Jinjun Cai
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Qiaoli Ma
- Agricultural College, Ningxia University, Yinchuan, China
| | - Wenjing Wang
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Lijuan Zhao
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Jiawen Li
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
| | - Lina Su
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
- Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China
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10
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Guo X, Ullah A, Siuta D, Kukfisz B, Iqbal S. Role of WRKY Transcription Factors in Regulation of Abiotic Stress Responses in Cotton. Life (Basel) 2022; 12:life12091410. [PMID: 36143446 PMCID: PMC9504182 DOI: 10.3390/life12091410] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental factors are the major constraints in sustainable agriculture. WRKY proteins are a large family of transcription factors (TFs) that regulate various developmental processes and stress responses in plants, including cotton. On the basis of Gossypium raimondii genome sequencing, WRKY TFs have been identified in cotton and characterized for their functions in abiotic stress responses. WRKY members of cotton play a significant role in the regulation of abiotic stresses, i.e., drought, salt, and extreme temperatures. These TFs either activate or repress various signaling pathways such as abscisic acid, jasmonic acid, salicylic acid, mitogen-activated protein kinases (MAPK), and the scavenging of reactive oxygen species. WRKY-associated genes in cotton have been genetically engineered in Arabidopsis, Nicotiana, and Gossypium successfully, which subsequently enhanced tolerance in corresponding plants against abiotic stresses. Although a few review reports are available for WRKY TFs, there is no critical report available on the WRKY TFs of cotton. Hereby, the role of cotton WRKY TFs in environmental stress responses is studied to enhance the understanding of abiotic stress response and further improve in cotton plants.
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Affiliation(s)
- Xiaoqiang Guo
- College of Life Science and Technology, Longdong University, Qingyang 745000, China
- Correspondence: (X.G.); (A.U.)
| | - Abid Ullah
- Department of Botany, Post Graduate College Dargai, Malakand 23060, Khyber Pakhtunkhwa, Pakistan
- Correspondence: (X.G.); (A.U.)
| | - Dorota Siuta
- Faculty of Process and Environmental Engineering, Lodz University of Technology, Wolczanska Str. 213, 90-924 Lodz, Poland
| | - Bożena Kukfisz
- Faculty of Security Engineering and Civil Protection, The Main School of Fire Service, 01-629 Warsaw, Poland
| | - Shehzad Iqbal
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China
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11
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Li N, Zhang Z, Gao S, Lv Y, Chen Z, Cao B, Xu K. Different responses of two Chinese cabbage (Brassica rapa L. ssp. pekinensis) cultivars in photosynthetic characteristics and chloroplast ultrastructure to salt and alkali stress. PLANTA 2021; 254:102. [PMID: 34671899 DOI: 10.1007/s00425-021-03754-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Salt and alkali stress affected the photosynthetic characteristics of Chinese cabbages. A salt-tolerant cultivar maintained its tolerance by ensuring the high ability of photosynthesis. The synthesis of organic acids and carbohydrates in leaves played important roles in improving the photosynthetic capacity of alkali-tolerant plants. Soil salinization has become an increasingly serious ecological problem, which limits the quality and yield of crops. As an important economic vegetable in winter, however, little is known about the response of Chinese cabbage to salt, alkali and salt-alkali stress in photosynthetic characteristics and chloroplast ultrastructure. Thus, two Chinese cabbage cultivars, 'Qinghua' (salt-tolerant-alkali-sensitive) and 'Biyu' (salt-sensitive-alkali-tolerant) were investigated under stresses to clarify the similarities and differences between salt tolerance and alkali tolerance pathways in Chinese cabbage. We found that the root of Qinghua, the leaf ultrastructure and net photosynthetic rate (Pn), stomatal conductance (Gs), water use efficiency (WUE), maximum photochemical quantum yield of PSII (Fv/Fm) and nonphotochemical quenching (NPQ) were not affected by salt stress. However, Biyu was seriously affected under salt stress. Its growth indexes decreased by between 60 and 30% compared with the control and the photosynthetic indexes were also seriously affected under salt stress. This indicated that the salt-tolerant cultivar Qinghua improved the photosynthetic fluorescence ability to promote the synthesis of organic matter resulting in salt tolerance. In contrast, under alkali treatment, the root of Biyu was affected by alkali stress, but could still maintain good growth, and root and leaf structure were not seriously affected and could maintain the normal operations. Biyu improved its tolerance by improving the water use efficiency, regulating the synthesis of organic acids and carbohydrates, ensuring the synthesis of organic matter and ensured the normal growth of the plant.
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Affiliation(s)
- Na Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production in Shandong, Tai'an, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, People's Republic of China
- State Key Laboratory of Crop Biology, Tai'an, 271018, China
| | - Zhihuan Zhang
- Qingdao Academy of Agricultural Sciences, Qingdao, China
| | - Song Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production in Shandong, Tai'an, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, People's Republic of China
- State Key Laboratory of Crop Biology, Tai'an, 271018, China
| | - Yao Lv
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production in Shandong, Tai'an, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, People's Republic of China
- State Key Laboratory of Crop Biology, Tai'an, 271018, China
| | - Zijing Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production in Shandong, Tai'an, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, People's Republic of China
- State Key Laboratory of Crop Biology, Tai'an, 271018, China
| | - Bili Cao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
- Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production in Shandong, Tai'an, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, People's Republic of China
- State Key Laboratory of Crop Biology, Tai'an, 271018, China
| | - Kun Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
- Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production in Shandong, Tai'an, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, People's Republic of China.
- State Key Laboratory of Crop Biology, Tai'an, 271018, China.
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12
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Razzaq A, Saleem F, Wani SH, Abdelmohsen SAM, Alyousef HA, Abdelbacki AMM, Alkallas FH, Tamam N, Elansary HO. De-novo Domestication for Improving Salt Tolerance in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:681367. [PMID: 34603347 PMCID: PMC8481614 DOI: 10.3389/fpls.2021.681367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/12/2021] [Indexed: 05/21/2023]
Abstract
Global agriculture production is under serious threat from rapidly increasing population and adverse climate changes. Food security is currently a huge challenge to feed 10 billion people by 2050. Crop domestication through conventional approaches is not good enough to meet the food demands and unable to fast-track the crop yields. Also, intensive breeding and rigorous selection of superior traits causes genetic erosion and eliminates stress-responsive genes, which makes crops more prone to abiotic stresses. Salt stress is one of the most prevailing abiotic stresses that poses severe damages to crop yield around the globe. Recent innovations in state-of-the-art genomics and transcriptomics technologies have paved the way to develop salinity tolerant crops. De novo domestication is one of the promising strategies to produce superior new crop genotypes through exploiting the genetic diversity of crop wild relatives (CWRs). Next-generation sequencing (NGS) technologies open new avenues to identifying the unique salt-tolerant genes from the CWRs. It has also led to the assembly of highly annotated crop pan-genomes to snapshot the full landscape of genetic diversity and recapture the huge gene repertoire of a species. The identification of novel genes alongside the emergence of cutting-edge genome editing tools for targeted manipulation renders de novo domestication a way forward for developing salt-tolerance crops. However, some risk associated with gene-edited crops causes hurdles for its adoption worldwide. Halophytes-led breeding for salinity tolerance provides an alternative strategy to identify extremely salt tolerant varieties that can be used to develop new crops to mitigate salinity stress.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Shabir Hussain Wani
- Division of Genetics and Plant Breeding, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Shaimaa A. M. Abdelmohsen
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Haifa A. Alyousef
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | - Fatemah H. Alkallas
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nissren Tamam
- Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Hosam O. Elansary
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
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13
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Wang Q, Lu X, Chen X, Zhao L, Han M, Wang S, Zhang Y, Fan Y, Ye W. Genome-wide identification and function analysis of HMAD gene family in cotton (Gossypium spp.). BMC PLANT BIOLOGY 2021; 21:386. [PMID: 34416873 PMCID: PMC8377987 DOI: 10.1186/s12870-021-03170-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The abiotic stress such as soil salinization and heavy metal toxicity has posed a major threat to sustainable crop production worldwide. Previous studies revealed that halophytes were supposed to tolerate other stress including heavy metal toxicity. Though HMAD (heavy-metal-associated domain) was reported to play various important functions in Arabidopsis, little is known in Gossypium. RESULTS A total of 169 G. hirsutum genes were identified belonging to the HMAD gene family with the number of amino acids ranged from 56 to 1011. Additionally, 84, 76 and 159 HMAD genes were identified in each G. arboreum, G. raimondii and G. barbadense, respectively. The phylogenetic tree analysis showed that the HMAD gene family were divided into five classes, and 87 orthologs of HMAD genes were identified in four Gossypium species, such as genes Gh_D08G1950 and Gh_A08G2387 of G. hirsutum are orthologs of the Gorai.004G210800.1 and Cotton_A_25987 gene in G. raimondii and G. arboreum, respectively. In addition, 15 genes were lost during evolution. Furthermore, conserved sequence analysis found the conserved catalytic center containing an anion binding (CXXC) box. The HMAD gene family showed a differential expression levels among different tissues and developmental stages in G. hirsutum with the different cis-elements for abiotic stress. CONCLUSIONS Current study provided important information about HMAD family genes under salt-stress in Gossypium genome, which would be useful to understand its putative functions in different species of cotton.
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Affiliation(s)
- Qinqin Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000 China
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14
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Bano N, Fakhrah S, Mohanty CS, Bag SK. Genome-Wide Identification and Evolutionary Analysis of Gossypium Tubby-Like Protein (TLP) Gene Family and Expression Analyses During Salt and Drought Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:667929. [PMID: 34367198 PMCID: PMC8335595 DOI: 10.3389/fpls.2021.667929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/09/2021] [Indexed: 06/02/2023]
Abstract
Tubby-like proteins (TLPs) possess a highly conserved closed β barrel tubby domain at C-terminal and N-terminal F-box. The role of TLP gene family members has been widely discussed in numerous organisms; however, the detailed genome-wide study of this gene family in Gossypium species has not been reported till date. Here, we systematically identified 105 TLP gene family members in cotton (Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense) genomes and classified them into eight phylogenetic groups. Cotton TLP12 gene family members clustered into two groups, 4 and 8. They experienced higher evolutionary pressure in comparison to others, indicating the faster evolution in both diploid as well as in tetraploid cotton. Cotton TLP gene family members expanded mainly due to segmental duplication, while only one pair of tandem duplication was found in cotton TLPs paralogous gene pairs. Subsequent qRT-PCR validation of seven putative key candidate genes of GhTLPs indicated that GhTLP11A and GhTLP12A.1 genes were highly sensitive to salt and drought stress. The co-expression network, pathways, and cis-regulatory elements of GhTLP11A and GhTLP12A.1 genes confirmed their functional importance in salt and drought stress responses. This study proposes the significance of GhTLP11A and GhTLP12A.1 genes in exerting control over salt and drought stress responses in G. hirsutum and also provides a reference for future research, elaborating the biological roles of G. hirsutum TLPs in both stress responses.
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Affiliation(s)
- Nasreen Bano
- Council of Scientific & Industrial Research-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shafquat Fakhrah
- Council of Scientific & Industrial Research-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
| | - Chandra Sekhar Mohanty
- Council of Scientific & Industrial Research-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sumit Kumar Bag
- Council of Scientific & Industrial Research-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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15
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Bolortuya B, Kawabata S, Yamagami A, Davaapurev BO, Takahashi F, Inoue K, Kanatani A, Mochida K, Kumazawa M, Ifuku K, Jigjidsuren S, Battogtokh T, Udval G, Shinozaki K, Asami T, Batkhuu J, Nakano T. Transcriptome Analysis of Chloris virgata, Which Shows the Fastest Germination and Growth in the Major Mongolian Grassland Plant. FRONTIERS IN PLANT SCIENCE 2021; 12:684987. [PMID: 34262584 PMCID: PMC8275185 DOI: 10.3389/fpls.2021.684987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/26/2021] [Indexed: 06/13/2023]
Abstract
Plants in Mongolian grasslands are exposed to short, dry summers and long, cold winters. These plants should be prepared for fast germination and growth activity in response to the limited summer rainfall. The wild plant species adapted to the Mongolian grassland environment may allow us to explore useful genes, as a source of unique genetic codes for crop improvement. Here, we identified the Chloris virgata Dornogovi accession as the fastest germinating plant in major Mongolian grassland plants. It germinated just 5 h after treatment for germination initiation and showed rapid growth, especially in its early and young development stages. This indicates its high growth potential compared to grass crops such as rice and wheat. By assessing growth recovery after animal bite treatment (mimicked by cutting the leaves with scissors), we found that C. virgata could rapidly regenerate leaves after being damaged, suggesting high regeneration potential against grazing. To analyze the regulatory mechanism involved in the high growth potential of C. virgata, we performed RNA-seq-based transcriptome analysis and illustrated a comprehensive gene expression map of the species. Through de novo transcriptome assembly with the RNA-seq reads from whole organ samples of C. virgata at the germination stage (2 days after germination, DAG), early young development stage (8 DAG), young development stage (17 DAG), and adult development stage (28 DAG), we identified 21,589 unified transcripts (contigs) and found that 19,346 and 18,156 protein-coding transcripts were homologous to those in rice and Arabidopsis, respectively. The best-aligned sequences were annotated with gene ontology groups. When comparing the transcriptomes across developmental stages, we found an over-representation of genes involved in growth regulation in the early development stage in C. virgata. Plant development is tightly regulated by phytohormones such as brassinosteroids, gibberellic acid, abscisic acid, and strigolactones. Moreover, our transcriptome map demonstrated the expression profiles of orthologs involved in the biosynthesis of these phytohormones and their signaling networks. We discuss the possibility that C. virgata phytohormone signaling and biosynthesis genes regulate early germination and growth advantages. Comprehensive transcriptome information will provide a useful resource for gene discovery and facilitate a deeper understanding of the diversity of the regulatory systems that have evolved in C. virgata while adapting to severe environmental conditions.
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Affiliation(s)
- Byambajav Bolortuya
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | | | - Ayumi Yamagami
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Bekh-Ochir Davaapurev
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Asaka Kanatani
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Minoru Kumazawa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kentaro Ifuku
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Sodnomdarjaa Jigjidsuren
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Tugsjargal Battogtokh
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Gombosuren Udval
- Research Institute of Animal Husbandry, Mongolian University of Life Science, Ulaanbaatar, Mongolia
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Tadao Asami
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
| | - Javzan Batkhuu
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Takeshi Nakano
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
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16
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Wang X, An M, Wang K, Fan H, Shi J, Chen K. Effects of Organic Polymer Compound Material on K + and Na + Distribution and Physiological Characteristics of Cotton Under Saline and Alkaline Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:636536. [PMID: 34122466 PMCID: PMC8194489 DOI: 10.3389/fpls.2021.636536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/29/2021] [Indexed: 05/05/2023]
Abstract
Soil salinization and alkalization greatly restrict crop growth and yield. In this study, NaCl (8 g kg-1) and Na2CO3 (8 g kg-1) were used to create saline stress and alkaline stress on cotton in pot cultivation in the field, and organic polymer compound material (OPCM) and stem girdling were applied before cotton sowing and at flowering and boll-forming stage, respectively, aiming to determine the effects of OPCM on K+ and Na+ absorption and transport and physiological characteristics of cotton leaf and root. The results showed that after applying the OPCM, the Na+ content in leaf of cotton under saline stress and alkaline stress were decreased by 7.72 and 6.49%, respectively, the K+/Na+ ratio in leaf were increased by 5.65 and 19.10%, respectively, the Na+ content in root were decreased by 9.57 and 0.53%, respectively, the K+/Na+ ratio in root were increased by 65.77 and 55.84%, respectively, and the transport coefficients of K+ and Na+ from leaf to root were increased by 39.59 and 21.38%, respectively. The activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), and the relative electrical conductivity (REC) in cotton leaf were significantly increased, while the content of malondialdehyde (MDA) was decreased; but the changes in those in root were not significant. The boll weights were increased by 11.40 and 13.37%, respectively, compared with those for the control. After stem girdling, the application of OPCM still promoted the ion transport of cotton organs; moreover, the CAT activity in root was increased by 25.09% under saline stress, and the SOD activity in leaf and CAT in root were increased by 42.22 and 6.91%, respectively under alkaline stress. Therefore, OPCM can significantly change the transport of K+ and Na+ to maintain the K+ and Na+ homeostasis in leaf and root, and regulate physiological and biochemical indicators to alleviate the stress-induced damage. Besides, the regulation effect of OPCM on saline stress was better than that on alkaline stress.
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Nie H, Wang Y, Wei C, Grover CE, Su Y, Wendel JF, Hua J. Embryogenic Calli Induction and Salt Stress Response Revealed by RNA-Seq in Diploid Wild Species Gossypium sturtianum and Gossypium raimondii. FRONTIERS IN PLANT SCIENCE 2021; 12:715041. [PMID: 34512696 PMCID: PMC8424188 DOI: 10.3389/fpls.2021.715041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/26/2021] [Indexed: 05/06/2023]
Abstract
Wild cotton species can contribute to a valuable gene pool for genetic improvement, such as genes related to salt tolerance. However, reproductive isolation of different species poses an obstacle to produce hybrids through conventional breeding. Protoplast fusion technology for somatic cell hybridization provides an opportunity for genetic manipulation and targeting of agronomic traits. Transcriptome sequencing analysis of callus under salt stress is conducive to study salt tolerance genes. In this study, calli were induced to provide materials for extracting protoplasts and also for screening salt tolerance genes. Calli were successfully induced from leaves of Gossypium sturtianum (C1 genome) and hypocotyls of G. raimondii (D5 genome), and embryogenic calli of G. sturtianum and G. raimondii were induced on a differentiation medium with different concentrations of 2, 4-D, KT, and IBA, respectively. In addition, embryogenic calli were also induced successfully from G. raimondii through suspension cultivation. Transcriptome sequencing analysis was performed on the calli of G. raimondii and G. sturtianum, which were treated with 200 mM NaCl at 0, 6, 12, 24, and 48 h, and a total of 12,524 genes were detected with different expression patterns under salt stress. Functional analysis showed that 3,482 genes, which were differentially expressed in calli of G. raimondii and G. sturtianum, were associated with biological processes of nucleic acid binding, plant hormone (such as ABA) biosynthesis, and signal transduction. We demonstrated that DEGs or TFs which related to ABA metabolism were involved in the response to salt stress, including xanthoxin dehydrogenase genes (ABA2), sucrose non-fermenting 1-related protein kinases (SnRK2), NAM, ATAT1/2, and CUC2 transcription factors (NAC), and WRKY class of zinc-finger proteins (WRKY). This research has successfully induced calli from two diploid cotton species and revealed new genes responding to salt stress in callus tissue, which will lay the foundation for protoplast fusion for further understanding of salt stress responses in cotton.
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Affiliation(s)
- Hushuai Nie
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yali Wang
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Chengcheng Wei
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Ying Su
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding/Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- *Correspondence: Jinping Hua
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18
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Wang D, Lu X, Chen X, Wang S, Wang J, Guo L, Yin Z, Chen Q, Ye W. Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum. BMC Genomics 2020; 21:838. [PMID: 33246403 PMCID: PMC7694341 DOI: 10.1186/s12864-020-07260-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Background Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. We studied a salt-tolerant upland cotton cultivar under temporal salt stress to unfold the salt tolerance molecular mechanisms. Biochemical response to salt stress (400 mM) was measured at 0 h, 3 h, 12 h, 24 h and 48 h post stress intervals and single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) combined with the unique molecular identifiers approach was used to identify differentially expressed genes (DEG). Results Antioxidant enzymes including, catalase (CAT), peroxidase (POD), superoxide dismutase (SOD) were found significantly induced under temporal salt stress, suggesting that reactive oxygen species scavenging antioxidant machinery is an essential component of salt tolerance mechanism in cotton. We identified a wealth of novel transcripts based on the PacBio long reads sequencing approach. Prolonged salt stress duration induces high number of DEGs. Significant numbers of DEGs were found under key terms related to stress pathways such as “response to oxidative stress”, “response to salt stress”, “response to water deprivation”, “cation transport”, “metal ion transport”, “superoxide dismutase”, and “reductase”. Key DEGs related to hormone (abscisic acid, ethylene and jasmonic acid) biosynthesis, ion homeostasis (CBL-interacting serine/threonine-protein kinase genes, calcium-binding proteins, potassium transporter genes, potassium channel genes, sodium/hydrogen exchanger or antiporter genes), antioxidant activity (POD, SOD, CAT, glutathione reductase), transcription factors (myeloblastosis, WRKY, Apetala 2) and cell wall modification were found highly active in response to salt stress in cotton. Expression fold change of these DEGs showed both positive and negative responses, highlighting the complex nature of salt stress tolerance mechanisms in cotton. Conclusion Collectively, this study provides a good insight into the regulatory mechanism under salt stress in cotton and lays the foundation for further improvement of salt stress tolerance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07260-z.
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Affiliation(s)
- Delong Wang
- College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, P. R. China.,State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Xuke Lu
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Xiugui Chen
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Shuai Wang
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Lixue Guo
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Zujun Yin
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, P. R. China
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology/Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China.
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Xu Y, Magwanga RO, Jin D, Cai X, Hou Y, Juyun Z, Agong SG, Wang K, Liu F, Zhou Z. Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton. BMC PLANT BIOLOGY 2020; 20:518. [PMID: 33183239 PMCID: PMC7664088 DOI: 10.1186/s12870-020-02726-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/31/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Wild species of cotton are excellent resistance to abiotic stress. Diploid D-genome cotton showed abundant phenotypic diversity and was the putative donor species of allotetraploid cotton which produce the largest textile natural fiber. RESULTS A total of 41,053 genes were expressed in all samples by mapping RNA-seq Illumina reads of G. thurberi (D1), G. klotzschianum (D3-k), G. raimondii (D5) and G. trilobum (D8) to reference genome. The numbers of differently expressed genes (DEGs) were significantly higher under cold stress than salt stress. However, 34.1% DEGs under salt stress were overlapped with cold stress in four species. Notably, a potential shared network (cold and salt response, including 16 genes) was mined out by gene co-expression analysis. A total of 47,180-55,548 unique genes were identified in four diploid species by De novo assembly. Furthermore, 163, 344, 330, and 161 positively selected genes (PSGs) were detected in thurberi, G. klotzschianum, G. raimondii and G. trilobum by evolutionary analysis, respectively, and 9.5-17% PSGs of four species were DEGs in corresponding species under cold or salt stress. What's more, most of PSGs were enriched GO term related to response to stimulation. G. klotzschianum showed the best tolerance under both cold and salt stress. Interestingly, we found that a RALF-like protein coding gene not only is PSGs of G. klotzschianum, but also belongs to the potential shared network. CONCLUSION Our study provided new evidence that gene expression variations of evolution by natural selection were essential drivers of the morphological variations related to environmental adaptation during evolution. Additionally, there exist shared regulated networks under cold and salt stress, such as Ca2+ signal transduction and oxidation-reduction mechanisms. Our work establishes a transcriptomic selection mechanism for altering gene expression of the four diploid D-genome cotton and provides available gene resource underlying multi-abiotic resistant cotton breeding strategy.
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Affiliation(s)
- Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 40070 China
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- School of Biological, Physical, Mathematics and Actuarial sciences (SBPMAS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya
| | - Dingsha Jin
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Zheng Juyun
- Economic Crops Research Institute of Xinjiang Academy of Agricultural Science, Urumqi, Xinjiang province China
| | - Stephen Gaya Agong
- School of Biological, Physical, Mathematics and Actuarial sciences (SBPMAS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
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20
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An M, Wang X, Chang D, Wang S, Hong D, Fan H, Wang K. Application of compound material alleviates saline and alkaline stress in cotton leaves through regulation of the transcriptome. BMC PLANT BIOLOGY 2020; 20:462. [PMID: 33032521 PMCID: PMC7542905 DOI: 10.1186/s12870-020-02649-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/14/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Soil salinization and alkalinization are the main factors that affect the agricultural productivity. Evaluating the persistence of the compound material applied in field soils is an important part of the regulation of the responses of cotton to saline and alkaline stresses. RESULT To determine the molecular effects of compound material on the cotton's responses to saline stress and alkaline stress, cotton was planted in the salinized soil (NaCl 8 g kg- 1) and alkalized soil (Na2CO3 8 g kg- 1) after application of the compound material, and ion content, physiological characteristics, and transcription of new cotton leaves at flowering and boll-forming stage were analyzed. The results showed that compared with saline stress, alkaline stress increased the contents of Na+, K+, SOD, and MDA in leaves. The application of the compound material reduced the content of Na+ but increased the K+/Na+ ratio, the activities of SOD, POD, and CAT, and REC. Transcriptome analysis revealed that after the application of the compound material, the Na+/H+ exchanger gene in cotton leaves was down-regulated, while the K+ transporter, K+ channel, and POD genes were up-regulated. Besides, the down-regulation of genes related to lignin synthesis in phenylalanine biosynthesis pathway had a close relationship with the ion content and physiological characteristics in leaves. The quantitative analysis with PCR proved the reliability of the results of RNA sequencing. CONCLUSION These findings suggest that the compound material alleviated saline stress and alkaline stress on cotton leaves by regulating candidate genes in key biological pathways, which improves our understanding of the molecular mechanism of the compound material regulating the responses of cotton to saline stress and alkaline stress.
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Affiliation(s)
- Mengjie An
- Agricultural College, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Xiaoli Wang
- Agricultural College, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Doudou Chang
- Agricultural College, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Shuai Wang
- Agricultural College, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Dashuang Hong
- Agricultural College, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Hua Fan
- Agricultural College, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Kaiyong Wang
- Agricultural College, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China.
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21
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Zuo J, Grierson D, Courtney LT, Wang Y, Gao L, Zhao X, Zhu B, Luo Y, Wang Q, Giovannoni JJ. Relationships between genome methylation, levels of non-coding RNAs, mRNAs and metabolites in ripening tomato fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:980-994. [PMID: 32314448 DOI: 10.1111/tpj.14778] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/12/2020] [Accepted: 03/23/2020] [Indexed: 05/28/2023]
Abstract
Ripening of tomato fruit is a complex tightly orchestrated developmental process that involves multiple physiological and metabolic changes that render fruit attractive, palatable and nutritious. Ripening requires initiation, activation and coordination of key pathways at the transcriptional and post-transcriptional levels that lead to ethylene synthesis and downstream ripening events determining quality. We studied wild-type, Gr and r mutant fruits at the coding and non-coding transcriptomic, metabolomic and genome methylation levels. Numerous differentially expressed non-coding RNAs were identified and quantified and potential competing endogenous RNA regulation models were constructed. Multiple changes in gene methylation were linked to the ethylene pathway and ripening processes. A combined analysis of changes in genome methylation, long non-coding RNAs, circular RNAs, micro-RNAs and fruit metabolites revealed many differentially expressed genes (DEGs) with differentially methylated regions encoding transcription factors and key enzymes related to ethylene or carotenoid pathways potentially targeted by differentially expressed non-coding RNAs. These included ACO2 (targeted by MSTRG.59396.1 and miR396b), CTR1 (targeted by MSTRG.43594.1 and miR171b), ERF2 (targeted by MSTRG.183681.1), ERF5 (targeted by miR9470-3p), PSY1 (targeted by MSTRG.95226.7), ZISO (targeted by 12:66127788|66128276) and NCED (targeted by MSTRG.181568.2). Understanding the functioning of this intricate genetic regulatory network provides new insights into the underlying integration and relationships between the multiple events that collectively determine the ripe phenotype.
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Affiliation(s)
- Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- United States Department of Agriculture - Agricultural Research Service and Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY, 14853, USA
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Lance T Courtney
- United States Department of Agriculture - Agricultural Research Service and Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY, 14853, USA
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - James J Giovannoni
- United States Department of Agriculture - Agricultural Research Service and Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY, 14853, USA
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22
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Dong Y, Hu G, Yu J, Thu SW, Grover CE, Zhu S, Wendel JF. Salt-tolerance diversity in diploid and polyploid cotton (Gossypium) species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1135-1151. [PMID: 31642116 DOI: 10.1111/tpj.14580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/21/2019] [Accepted: 10/14/2019] [Indexed: 05/22/2023]
Abstract
The development of salt-tolerant genotypes is pivotal for the effective utilization of salinized land and to increase global crop productivity. Several cotton species comprise the most important source of textile fibers globally, and these are increasingly grown on marginal or increasingly saline agroecosystems. The allopolyploid cotton species also provide a model system for polyploid research, of relevance here because polyploidy was suggested to be associated with increased adaptation to stress. To evaluate the genetic variation of salt tolerance among cotton species, 17 diverse accessions of allopolyploid (AD-genome) and diploid (A- and D-genome) Gossypium were evaluated for a total of 29 morphological and physiological traits associated with salt tolerance. For most morphological and physiological traits, cotton accessions showed highly variable responses to 2 weeks of exposure to moderate (50 mm NaCl) and high (100 mm NaCl) hydroponic salinity treatments. Our results showed that the most salt-tolerant species were the allopolyploid Gossypium mustelinum from north-east Brazil, the D-genome diploid Gossypium klotzschianum from the Galapagos Islands, followed by the A-genome diploids of Africa and Asia. Generally, A-genome accessions outperformed D-genome cottons under salinity conditions. Allopolyploid accessions from either diploid genomic group did not show significant differences in salt tolerance, but they were more similar to one of the two progenitor lineages. Our findings demonstrate that allopolyploidy in itself need not be associated with increased salinity stress tolerance and provide information for using the secondary Gossypium gene pool to breed for improved salt tolerance.
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Affiliation(s)
- Yating Dong
- Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- 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
| | - Jingwen Yu
- Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sandi Win Thu
- Department of Genetics, Development, and Cell 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
| | - Shuijin Zhu
- Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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Genetic regulatory networks for salt-alkali stress in Gossypium hirsutum with differing morphological characteristics. BMC Genomics 2020; 21:15. [PMID: 31906862 PMCID: PMC6945603 DOI: 10.1186/s12864-019-6375-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/08/2019] [Indexed: 12/13/2022] Open
Abstract
Background Cotton grows in altering environments that are often unfavorable or stressful for its growth and development. Consequently, the plant must cope with abiotic stresses such as soil salinity, drought, and excessive temperatures. Alkali-salt stress response remains a cumbersome biological process and is regulated via a multifaceted transcriptional regulatory network in cotton. Results To discover the molecular mechanisms of alkali-salt stress response in cotton, a comprehensive transcriptome analysis was carried out after alkali-salt stress treatment in three accessions of Gossypium hirsutum with contrasting phenotype. Expression level analysis proved that alkali-salt stress response presented significant stage-specific and tissue-specific. GO enrichment analysis typically suggested that signal transduction process involved in salt-alkali stress response at SS3 and SS12 stages in leaf; carbohydrate metabolic process and oxidation-reduction process involved in SS48 stages in leaf; the oxidation-reduction process involved at all three phases in the root. The Co-expression analysis suggested a potential GhSOS3/GhCBL10-SOS2 network was involved in salt-alkali stress response. Furthermore, Salt-alkali sensitivity was increased in GhSOS3 and GhCBL10 Virus-induced Gene Silencing (VIGS) plants. Conclusion The findings may facilitate to elucidate the underlying mechanisms of alkali-salt stress response and provide an available resource to scrutinize the role of candidate genes and signaling pathway governing alkali-salt stress response.
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Deep Transcriptome Analysis Reveals Reactive Oxygen Species (ROS) Network Evolution, Response to Abiotic Stress, and Regulation of Fiber Development in Cotton. Int J Mol Sci 2019; 20:ijms20081863. [PMID: 30991750 PMCID: PMC6514600 DOI: 10.3390/ijms20081863] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 12/03/2022] Open
Abstract
Reactive oxygen species (ROS) are important molecules in the plant, which are involved in many biological processes, including fiber development and adaptation to abiotic stress in cotton. We carried out transcription analysis to determine the evolution of the ROS genes and analyzed their expression levels in various tissues of cotton plant under abiotic stress conditions. There were 515, 260, and 261 genes of ROS network that were identified in Gossypium hirsutum (AD1 genome), G. arboreum (A genome), and G. raimondii (D genome), respectively. The ROS network genes were found to be distributed in all the cotton chromosomes, but with a tendency of aggregating on either the lower or upper arms of the chromosomes. Moreover, all the cotton ROS network genes were grouped into 17 families as per the phylogenetic tress analysis. A total of 243 gene pairs were orthologous in G. arboreum and G. raimondii. There were 240 gene pairs that were orthologous in G. arboreum, G. raimondii, and G. hirsutum. The synonymous substitution value (Ks) peaks of orthologous gene pairs between the At subgenome and the A progenitor genome (G. arboreum), D subgenome and D progenitor genome (G. raimondii) were 0.004 and 0.015, respectively. The Ks peaks of ROS network orthologous gene pairs between the two progenitor genomes (A and D genomes) and two subgenomes (At and Dt subgenome) were 0.045. The majority of Ka/Ks value of orthologous gene pairs between the A, D genomes and two subgenomes of TM-1 were lower than 1.0. RNA seq. analysis and RT-qPCR validation, showed that, CSD1,2,3,5,6; FSD1,2; MSD1,2; APX3,11; FRO5.6; and RBOH6 played a major role in fiber development while CSD1, APX1, APX2, MDAR1, GPX4-6-7, FER2, RBOH6, RBOH11, and FRO5 were integral for enhancing salt stress in cotton. ROS network-mediated signal pathway enhances the mechanism of fiber development and regulation of abiotic stress in Gossypium. This study will enhance the understanding of ROS network and form the basic foundation in exploring the mechanism of ROS network-involving the fiber development and regulation of abiotic stress in cotton.
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Zhang J, Wang F, Zhang C, Zhang J, Chen Y, Liu G, Zhao Y, Hao F, Zhang J. A novel VIGS method by agroinoculation of cotton seeds and application for elucidating functions of GhBI-1 in salt-stress response. PLANT CELL REPORTS 2018; 37:1091-1100. [PMID: 29868984 DOI: 10.1007/s00299-018-2294-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/10/2018] [Indexed: 05/21/2023]
Abstract
A VIGS method by agroinoculation of cotton seeds was developed for gene silencing in young seedlings and roots, and applied in functional analysis of GhBI-1 in response to salt stress. Virus-induced gene silencing (VIGS) has been widely used to investigate the functions of genes expressed in mature leaves, but not yet in young seedlings or roots of cotton (Gossypium hirsutum L.). Here, we developed a simple and effective VIGS method for silencing genes in young cotton seedlings and roots by soaking naked seeds in Agrobacterium cultures carrying tobacco rattle virus (TRV)-VIGS vectors. When the naked seeds were soaked in Agrobacterium cultures with an OD600 of 1.5 for 90 min, it was optimal for silencing genes effectively in young seedlings as clear photo-bleaching phenotype in the newly emerging leaves of pTRV:GhCLA1 seedlings were observed at 12-14 days post inoculation. Silencing of GhPGF (cotton pigment gland formation) by this method resulted in a 90% decrease in transcript abundances of the gene in roots at the early development stage. We further used the tool to investigate function of GhBI-1 (cotton Bax inhibitor-1) gene in response to salt stress and demonstrated that GhBI-1 might play a protective role under salt stress by suppressing stress-induced cell death in cotton. Our results showed that the newly established VIGS method is a powerful tool for elucidating functions of genes in cotton, especially the genes expressed in young seedlings and roots.
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Affiliation(s)
- Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Furong Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Chuanyun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Junhao Zhang
- Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Guodong Liu
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yanxiu Zhao
- College of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Fushun Hao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China.
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture, Cotton Research Center of Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
- College of Life Science, Shandong Normal University, Jinan, 250014, China.
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Mammadov J, Buyyarapu R, Guttikonda SK, Parliament K, Abdurakhmonov IY, Kumpatla SP. Wild Relatives of Maize, Rice, Cotton, and Soybean: Treasure Troves for Tolerance to Biotic and Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2018; 9:886. [PMID: 30002665 PMCID: PMC6032925 DOI: 10.3389/fpls.2018.00886] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 06/07/2018] [Indexed: 02/05/2023]
Abstract
Global food demand is expected to nearly double by 2050 due to an increase in the world's population. The Green Revolution has played a key role in the past century by increasing agricultural productivity worldwide, however, limited availability and continued depletion of natural resources such as arable land and water will continue to pose a serious challenge for global food security in the coming decades. High yielding varieties with proven tolerance to biotic and abiotic stresses, superior nutritional profiles, and the ability to adapt to the changing environment are needed for continued agricultural sustainability. The narrow genetic base of modern cultivars is becoming a major bottleneck for crop improvement efforts and, therefore, the use of crop wild relatives (CWRs) is a promising approach to enhance genetic diversity of cultivated crops. This article provides a review of the efforts to date on the exploration of CWRs as a source of tolerance to multiple biotic and abiotic stresses in four global crops of importance; maize, rice, cotton, and soybean. In addition to the overview of the repertoire and geographical spread of CWRs in each of the respective crops, we have provided a comprehensive discussion on the morphological and/or genetic basis of the traits along with some examples, when available, of the research in the transfer of traits from CWRs to cultivated varieties. The emergence of modern molecular and genomic technologies has not only accelerated the pace of dissecting the genetics underlying the traits found in CWRs, but also enabled rapid and efficient trait transfer and genome manipulation. The potential and promise of these technologies has also been highlighted in this review.
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Affiliation(s)
- Jafar Mammadov
- Agriculture Division of DowDuPont™, Corteva Agriscience™, Johnston, IA, United States
| | - Ramesh Buyyarapu
- Agriculture Division of DowDuPont™, Corteva Agriscience™, Johnston, IA, United States
| | - Satish K. Guttikonda
- Agriculture Division of DowDuPont™, Corteva Agriscience™, Johnston, IA, United States
| | - Kelly Parliament
- Agriculture Division of DowDuPont™, Corteva Agriscience™, Johnston, IA, United States
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Siva P. Kumpatla
- Agriculture Division of DowDuPont™, Corteva Agriscience™, Johnston, IA, United States
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Peng Z, He S, Gong W, Xu F, Pan Z, Jia Y, Geng X, Du X. Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton. BMC PLANT BIOLOGY 2018; 18:128. [PMID: 29925319 PMCID: PMC6011603 DOI: 10.1186/s12870-018-1350-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/12/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Salinity is a major abiotic stress that limits upland cotton growth and reduces fibre production worldwide. To reveal genetic regulation via transcript and protein levels after salt stress, we comprehensively analysed the global changes in mRNA, miRNA, and protein profiles in response to salt stress in two contrasting salt-tolerant cotton genotypes. RESULTS In the current study, proteomic and mRNA-seq data were combined to reveal that some genes are differentially expressed at both the proteomic and mRNA levels. However, we observed no significant change in mRNA corresponding to most of the strongly differentially abundant proteins. This finding may have resulted from global changes in alternative splicing events and miRNA levels under salt stress conditions. Evidence was provided indicating that several salt stress-responsive proteins can alter miRNAs and modulate alternative splicing events in upland cotton. The results of the stringent screening of the mRNA-seq and proteomic data between the salt-tolerant and salt-sensitive genotypes identified 63 and 85 candidate genes/proteins related to salt tolerance after 4 and 24 h of salt stress, respectively, between the tolerant and sensitive genotype. Finally, we predicted an interaction network comprising 158 genes/proteins and then discovered that two main clusters in the network were composed of ATP synthase (CotAD_74681) and cytochrome oxidase (CotAD_46197) in mitochondria. The results revealed that mitochondria, as important organelles involved in energy metabolism, play an essential role in the synthesis of resistance proteins during the process of salt exposure. CONCLUSION We provided a plausible schematic for the systematic salt tolerance model; this schematic reveals multiple levels of gene regulation in response to salt stress in cotton and provides a list of salt tolerance-related genes/proteins. The information here will facilitate candidate gene discovery and molecular marker development for salt tolerance breeding in cotton.
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Affiliation(s)
- Zhen Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Feifei Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Xiaoli Geng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
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Zuo J, Wang Y, Zhu B, Luo Y, Wang Q, Gao L. Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit. Genes (Basel) 2018; 9:genes9050266. [PMID: 29883429 PMCID: PMC5977206 DOI: 10.3390/genes9050266] [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: 04/03/2018] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an essential feature of epigenetic regulation and plays a role in various physiological and biochemical processes at CG, CHG, and CHH sites in plants. LeERF1 is an ethylene response factor (ERF) found in tomatoes which plays an important role in ethylene signal transduction. To explore the characteristics of DNA methylation in the ethylene pathway, sense-/antisense-LeERF1 transgenic tomato fruit were chosen for deep sequencing and bioinformatics parsing. The methylation type with the greatest distribution was CG, (71.60–72.80%) and CHH was found least frequently (10.70–12.50%). The level of DNA methylation was different among different tomato genomic regions. The differentially methylated regions (DMRs) and the differentially expressed genes (DEGs) were conjointly analyzed and 3030 different expressed genes were found, of which several are involved in ethylene synthesis and signaling transduction (such as ACS, ACO, MADS-Box, ERFs, and F-box). Furthermore, the relationships between DNA methylation and microRNAs (miRNAs) were also deciphered, providing basic information for the further study of DNA methylation and small RNAs involved in the ethylene pathway.
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Affiliation(s)
- Jinhua Zuo
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY 14853, USA.
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China.
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Qing Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Lipu Gao
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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Gao W, Xu FC, Guo DD, Zhao JR, Liu J, Guo YW, Singh PK, Ma XN, Long L, Botella JR, Song CP. Calcium-dependent protein kinases in cotton: insights into early plant responses to salt stress. BMC PLANT BIOLOGY 2018; 18:15. [PMID: 29343239 PMCID: PMC5772696 DOI: 10.1186/s12870-018-1230-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 01/11/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Soil salinization is one of the major environmental constraints to plant growth and agricultural production worldwide. Signaling components involving calcium (Ca2+) and the downstream calcium-dependent protein kinases (CPKs) play key roles in the perception and transduction of stress signals. However, the study of CPKs in cotton and their functions in response to salt stress remain unexplored. RESULTS A total of 98 predicted CPKs were identified from upland cotton (Gossypium hirsutum L. 'TM-1'), and phylogenetic analyses classified them into four groups. Gene family distribution studies have revealed the substantial impacts of the genome duplication events to the total number of GhCPKs. Transcriptome analyses showed a wide distribution of CPKs' expression among different organs. A total of 19 CPKs were selected for their rapid responses to salt stress at the transcriptional level, most of which were also incduced by the thylene-releasing chemical ethephon, suggesting a partal overlap of the salinity and ethylene responses. Silencing of 4 of the 19 CPKs (GhCPK8, GhCPK38, GhCPK54, and GhCPK55) severely compromised the basal cotton resistance to salt stress. CONCLUSIONS Our genome-wide expression analysis of CPK genes from up-land cotton suggests that CPKs are involved in multiple developmental responses as well as the response to different abiotic stresses. A cluster of the cotton CPKs was shown to participate in the early signaling events in cotton responses to salt stress. Our results provide significant insights on functional analysis of CPKs in cotton, especially in the context of cotton adaptions to salt stress.
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Affiliation(s)
- Wei Gao
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Fu-Chun Xu
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Dan-Dan Guo
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Jing-Ruo Zhao
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000 People’s Republic of China
| | - Ya-Wei Guo
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Prashant Kumar Singh
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Xiao-Nan Ma
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Lu Long
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Chun-Peng Song
- State Key Laboratory of Cotton Biology; Henan Key Laboratory of Plant Stress Biology; School of Life Science, Henan University, Kaifeng, Henan 475004 People’s Republic of China
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Kirungu JN, Deng Y, Cai X, Magwanga RO, Zhou Z, Wang X, Wang Y, Zhang Z, Wang K, Liu F. Simple Sequence Repeat (SSR) Genetic Linkage Map of D Genome Diploid Cotton Derived from an Interspecific Cross between Gossypium davidsonii and Gossypium klotzschianum. Int J Mol Sci 2018; 19:E204. [PMID: 29324636 PMCID: PMC5796153 DOI: 10.3390/ijms19010204] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/06/2018] [Accepted: 01/07/2018] [Indexed: 12/22/2022] Open
Abstract
The challenge in tetraploid cotton cultivars is the narrow genetic base and therefore, the bottleneck is how to obtain interspecific hybrids and introduce the germplasm directly from wild cotton to elite cultivars. Construction of genetic maps has provided insight into understanding the genome structure, interrelationships between organisms in relation to evolution, and discovery of genes that carry important agronomic traits in plants. In this study, we generated an interspecific hybrid between two wild diploid cottons, Gossypium davidsonii and Gossypium klotzschianum, and genotyped 188 F2:3 populations in order to develop a genetic map. We screened 12,560 SWU Simple Sequence Repeat (SSR) primers and obtained 1000 polymorphic markers which accounted for only 8%. A total of 928 polymorphic primers were successfully scored and only 728 were effectively linked across the 13 chromosomes, but with an asymmetrical distribution. The map length was 1480.23 cM, with an average length of 2.182 cM between adjacent markers. A high percentage of the markers on the map developed, and for the physical map of G. raimondii, exhibited highly significant collinearity, with two types of duplication. High level of segregation distortion was observed. A total of 27 key genes were identified with diverse roles in plant hormone signaling, development, and defense reactions. The achievement of developing the F2:3 population and its genetic map constructions may be a landmark in establishing a new tool for the genetic improvement of cultivars from wild plants in cotton. Our map had an increased recombination length compared to other maps developed from other D genome cotton species.
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Affiliation(s)
- Joy Nyangasi Kirungu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yanfeng Deng
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
- School of Biological and Physical Sciences (SBPS), Main Campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Main Campus, P.O. Box 210-40601 Bondo, Kenya.
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhenmei Zhang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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