1
|
Ye Q, Zhang L, Li Q, Ji Y, Zhou Y, Wu Z, Hu Y, Ma Y, Wang J, Zhang C. Genome and GWAS analysis identified genes significantly related to phenotypic state of Rhododendron bark. HORTICULTURE RESEARCH 2024; 11:uhae008. [PMID: 38487544 PMCID: PMC10939351 DOI: 10.1093/hr/uhae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/01/2024] [Indexed: 03/17/2024]
Abstract
As an important horticultural plant, Rhododendron is often used in urban greening and landscape design. However, factors such as the high rate of genetic recombination, frequent outcrossing in the wild, weak linkage disequilibrium, and the susceptibility of gene expression to environmental factors limit further exploration of functional genes related to important horticultural traits, and make the breeding of new varieties require a longer time. Therefore, we choose bark as the target trait which is not easily affected by environmental factors, but also has ornamental properties. Genome-wide association study (GWAS) of Rhododendron delavayi (30 samples), R. irroratum (30 samples) and their F1 generation R. agastum (200 samples) was conducted on the roughness of bark phenotypes. Finally, we obtained 2416.31 Gbp of clean data and identified 5 328 800 high-quality SNPs. According to the P-value and the degree of linkage disequilibrium of SNPs, we further identified 4 out of 11 candidate genes that affect bark roughness. The results of gene differential expression analysis further indicated that the expression levels of Rhdel02G0243600 and Rhdel08G0220700 in different bark phenotypes were significantly different. Our study identified functional genes that influence important horticultural traits of Rhododendron, and illustrated the powerful utility and great potential of GWAS in understanding and exploiting wild germplasm genetic resources of Rhododendron.
Collapse
Affiliation(s)
- Qiannan Ye
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Yunnan Academy of Agricultural Sciences Kunming 650000, China
| | - Qing Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaliang Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Yanli Zhou
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
| | - Zhenzhen Wu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanting Hu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Yunnan Academy of Agricultural Sciences Kunming 650000, China
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan 650201, China
- Haiyan Engineering & Technology Center, Zhejiang Institute of Advanced Technology, Jiaxing 314022, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| |
Collapse
|
2
|
Jiang W, He J, Babla M, Wu T, Tong T, Riaz A, Zeng F, Qin Y, Chen G, Deng F, Chen ZH. Molecular evolution and interaction of 14-3-3 proteins with H+-ATPases in plant abiotic stresses. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:689-707. [PMID: 37864845 DOI: 10.1093/jxb/erad414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/20/2023] [Indexed: 10/23/2023]
Abstract
Environmental stresses severely affect plant growth and crop productivity. Regulated by 14-3-3 proteins (14-3-3s), H+-ATPases (AHAs) are important proton pumps that can induce diverse secondary transport via channels and co-transporters for the abiotic stress response of plants. Many studies demonstrated the roles of 14-3-3s and AHAs in coordinating the processes of plant growth, phytohormone signaling, and stress responses. However, the molecular evolution of 14-3-3s and AHAs has not been summarized in parallel with evolutionary insights across multiple plant species. Here, we comprehensively review the roles of 14-3-3s and AHAs in cell signaling to enhance plant responses to diverse environmental stresses. We analyzed the molecular evolution of key proteins and functional domains that are associated with 14-3-3s and AHAs in plant growth and hormone signaling. The results revealed evolution, duplication, contraction, and expansion of 14-3-3s and AHAs in green plants. We also discussed the stress-specific expression of those 14-3-3and AHA genes in a eudicotyledon (Arabidopsis thaliana), a monocotyledon (Hordeum vulgare), and a moss (Physcomitrium patens) under abiotic stresses. We propose that 14-3-3s and AHAs respond to abiotic stresses through many important targets and signaling components of phytohormones, which could be promising to improve plant tolerance to single or multiple environmental stresses.
Collapse
Affiliation(s)
- Wei Jiang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Jing He
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Mohammad Babla
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Ting Wu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Tao Tong
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Adeel Riaz
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Fanrong Zeng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Yuan Qin
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Fenglin Deng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| |
Collapse
|
3
|
Zhao L, Li Y, Li Y, Chen W, Yao J, Fang S, Lv Y, Zhang Y, Zhu S. Systematical Characterization of the Cotton Di19 Gene Family and the Role of GhDi19-3 and GhDi19-4 as Two Negative Regulators in Response to Salt Stress. Antioxidants (Basel) 2022; 11:2225. [PMID: 36421411 PMCID: PMC9686973 DOI: 10.3390/antiox11112225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2023] Open
Abstract
Drought-induced 19 (Di19) protein is a Cys2/His2 (C2H2) type zinc-finger protein, which plays a crucial role in plant development and in response to abiotic stress. This study systematically investigated the characteristics of the GhDi19 gene family, including the member number, gene structure, chromosomal distribution, promoter cis-elements, and expression profiles. Transcriptomic analysis indicated that some GhDi19s were up-regulated under heat and salt stress. Particularly, two nuclear localized proteins, GhDi19-3 and GhDi19-4, were identified as being in potential salt stress responsive roles. GhDi19-3 and GhDi19-4 decreased sensitivity under salt stress through virus-induced gene silencing (VIGS), and showed significantly lower levels of H2O2, malondialdehyde (MDA), and peroxidase (POD) as well as significantly increased superoxide dismutase (SOD) activity. This suggested that their abilities were improved to effectively reduce the reactive oxygen species (ROS) damage. Furthermore, certain calcium signaling and abscisic acid (ABA)-responsive gene expression levels showed up- and down-regulation changes in target gene-silenced plants, suggesting that GhDi19-3 and GhDi19-4 were involved in calcium signaling and ABA signaling pathways in response to salt stress. In conclusion, GhDi19-3 and GhDi19-4, two negative transcription factors, were found to be responsive to salt stress through calcium signaling and ABA signaling pathways.
Collapse
Affiliation(s)
- Lanjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Youzhong Li
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, China
| | - Yan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jinbo Yao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shengtao Fang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Youjun Lv
- Anyang Institute of Technology, Anyang 455000, China
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| |
Collapse
|
4
|
Maryum Z, Luqman T, Nadeem S, Khan SMUD, Wang B, Ditta A, Khan MKR. An overview of salinity stress, mechanism of salinity tolerance and strategies for its management in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:907937. [PMID: 36275563 PMCID: PMC9583260 DOI: 10.3389/fpls.2022.907937] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/20/2022] [Indexed: 05/14/2023]
Abstract
Salinity stress is one of the primary threats to agricultural crops resulting in impaired crop growth and development. Although cotton is considered as reasonably salt tolerant, it is sensitive to salt stress at some critical stages like germination, flowering, boll formation, resulting in reduced biomass and fiber production. The mechanism of partial ion exclusion (exclusion of Na+ and/or Cl-) in cotton appears to be responsible for the pattern of uptake and accumulation of harmful ions (Na+ and Cl) in tissues of plants exposed to saline conditions. Maintaining high tissue K+/Na+ and Ca2+/Na+ ratios has been proposed as a key selection factor for salt tolerance in cotton. The key adaptation mechanism in cotton under salt stress is excessive sodium exclusion or compartmentation. Among the cultivated species of cotton, Egyptian cotton (Gossypium barbadense L.) exhibit better salt tolerance with good fiber quality traits as compared to most cultivated cotton and it can be used to improve five quality traits and transfer salt tolerance into Upland or American cotton (Gossypium hirsutum L.) by interspecific introgression. Cotton genetic studies on salt tolerance revealed that the majority of growth, yield, and fiber traits are genetically determined, and controlled by quantitative trait loci (QTLs). Molecular markers linked to genes or QTLs affecting key traits have been identified, and they could be utilized as an indirect selection criterion to enhance breeding efficiency through marker-assisted selection (MAS). Transfer of genes for compatible solute, which are an important aspect of ion compartmentation, into salt-sensitive species is, theoretically, a simple strategy to improve tolerance. The expression of particular stress-related genes is involved in plant adaptation to environmental stressors. As a result, enhancing tolerance to salt stress can be achieved by marker assisted selection added with modern gene editing tools can boost the breeding strategies that defend and uphold the structure and function of cellular components. The intent of this review was to recapitulate the advancements in salt screening methods, tolerant germplasm sources and their inheritance, biochemical, morpho-physiological, and molecular characteristics, transgenic approaches, and QTLs for salt tolerance in cotton.
Collapse
Affiliation(s)
- Zahra Maryum
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
| | - Tahira Luqman
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
| | - Sahar Nadeem
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
| | - Sana Muhy Ud Din Khan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Allah Ditta
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| |
Collapse
|
5
|
Chen X, Xu Z, Zhao B, Yang Y, Mi J, Zhao Z, Liu J. Physiological and Proteomic Analysis Responsive Mechanisms for Salt Stress in Oat. FRONTIERS IN PLANT SCIENCE 2022; 13:891674. [PMID: 35783977 PMCID: PMC9240473 DOI: 10.3389/fpls.2022.891674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Oat is considered as a moderately salt-tolerant crop that can be used to improve saline and alkaline soils. Previous studies have focused on short-term salt stress exposure, and the molecular mechanisms of salt tolerance in oat have not yet been elucidated. In this study, the salt-tolerant oat cultivar Vao-9 and the salt-sensitive oat cultivar Bai5 were treated with 6 days of 0 and 150 mmol L-1 salt stress (nNaCl:nNa2SO4 = 1:1). Label-Free technology was then used to analyze the differentially expressed proteins in leaves under 0 and 150 mmol L-1 salt stress. The obtained results indicated that total of 2,631 proteins were identified by mass spectrometry in the four samples. The salt-tolerant cultivar Vao-9 mainly enhances its carbohydrate and energy metabolism through the pentose and glucuronate interconversions, and carbon fixation pathways in prokaryotes, thereby reducing the damage caused by salt stress. In addition, the down-regulation of ribosomes expression and the up-regulated expression of HSPs and CRT are all through the regulation of protein synthesis in response to salt stress. However, GABA metabolism presents a different synthesis pattern in Bai5 and Vao-9. The main KEGG function of differential expressed protein (DEP) in Bai5 is classified into protein processing in the endoplasmic reticulum, estrogen signaling pathway, antigen processing and presentation, longevity regulating pathway-multiple species, arginine and proline metabolism, beta-alanine metabolism, vitamin B6 metabolism, salmonella infection, chloroalkane and chloroalkene degradation, and limonene and pinene degradation. Moreover, the main KEGG functions of DEP in Vao-9 are classified as ribosome and carbon fixation pathways in prokaryotes, pentose and glucuronate interconversions, GABA ergic synapse, and taurine and hypotaurine metabolism. The results obtained in this study provide an important basis for further research on the underlying mechanisms of salt response and tolerance in oat and other plant species.
Collapse
Affiliation(s)
- Xiaojing Chen
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Zhongshan Xu
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Baoping Zhao
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Yanming Yang
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Junzhen Mi
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Zhou Zhao
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| | - Jinghui Liu
- Cereal Industry Collaborative Innovation Center, Inner Mongolia Agricultural University, Hohhot, China
- National Outstanding Talents in Agricultural Research and Their Innovative Teams, Hohhot, China
| |
Collapse
|
6
|
Zhao N, Wang W, Grover CE, Jiang K, Pan Z, Guo B, Zhu J, Su Y, Wang M, Nie H, Xiao L, Guo A, Yang J, Cheng C, Ning X, Li B, Xu H, Adjibolosoo D, Aierxi A, Li P, Geng J, Wendel JF, Kong J, Hua J. Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fibre length, lint percentage and Fusarium wilt resistance. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:691-710. [PMID: 34800075 PMCID: PMC8989498 DOI: 10.1111/pbi.13747] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 05/04/2023]
Abstract
Sea Island cotton (Gossypium barbadense) is the source of the world's finest fibre quality cotton, yet relatively little is understood about genetic variations among diverse germplasms, genes underlying important traits and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fibre quality, yield, disease resistance, maturity and plant architecture. The highest number of associated loci was for fibre quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments, we confirmed the roles of five candidate genes regulating four key traits, that is disease resistance, fibre length, fibre strength and lint percentage. Geographical and temporal considerations demonstrated selection for the superior fibre quality (fibre length and fibre strength), and high lint percentage in improving G. barbadense in China. Pedigree selection breeding increased Fusarium wilt disease resistance and separately improved fibre quality and yield. Our work provides a foundation for understanding genomic variation and selective breeding of Sea Island cotton.
Collapse
Affiliation(s)
- Nan Zhao
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Weiran Wang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIAUSA
| | - Kaiyun Jiang
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Zhuanxia Pan
- Institute of Cotton ResearchShanxi Agricultural UniversityShanxiChina
| | - Baosheng Guo
- Cotton Research InstituteHebei Academy of Agriculture and Forestry SciencesHebeiChina
| | - Jiahui Zhu
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Ying Su
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Meng Wang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Hushuai Nie
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Li Xiao
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Anhui Guo
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jing Yang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Cheng Cheng
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xinmin Ning
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Bin Li
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Haijiang Xu
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Daniel Adjibolosoo
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Alifu Aierxi
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Pengbo Li
- Institute of Cotton ResearchShanxi Agricultural UniversityShanxiChina
| | - Junyi Geng
- Cotton Research InstituteHebei Academy of Agriculture and Forestry SciencesHebeiChina
| | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIAUSA
| | - Jie Kong
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Jinping Hua
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| |
Collapse
|
7
|
Yang R, Li M, Harrison MT, Fahad S, Wei M, Li X, Yin L, Sha A, Zhou M, Liu K, Wang X. iTRAQ Proteomic Analysis of Wheat ( Triticum aestivum L.) Genotypes Differing in Waterlogging Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:890083. [PMID: 35548301 PMCID: PMC9084233 DOI: 10.3389/fpls.2022.890083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 03/25/2022] [Indexed: 05/11/2023]
Abstract
Transient and chronic waterlogging constrains crop production in many regions of the world. Here, we invoke a novel iTRAQ-based proteomic strategy to elicit protein synthesis and regulation responses to waterlogging in tolerant (XM 55) and sensitive genotypes (YM 158). Of the 7,710 proteins identified, 16 were distinct between the two genotypes under waterlogging, partially defining a proteomic basis for waterlogging tolerance (and sensitivity). We found that 11 proteins were up-regulated and 5 proteins were down-regulated; the former included an Fe-S cluster assembly factor, heat shock cognate 70, GTP-binding protein SAR1A-like and CBS domain-containing protein. Down-regulated proteins contained photosystem II reaction center protein H, carotenoid 9, 10 (9', 10')-cleavage dioxygenase-like, psbP-like protein 1 and mitochondrial ATPase inhibitor. We showed that nine proteins responded to waterlogging with non-cultivar specificity: these included 3-isopropylmalate dehydratase large subunit, solanesyl-diphosphate synthase 2, DEAD-box ATP-dependent RNA helicase 3, and 3 predicted or uncharacterized proteins. Sixteen of the 28 selected proteins showed consistent expression patterns between mRNA and protein levels. We conclude that waterlogging stress may redirect protein synthesis, reduce chlorophyll synthesis and enzyme abundance involved in photorespiration, thus influencing synthesis of other metabolic enzymes. Collectively, these factors accelerate the accumulation of harmful metabolites in leaves in waterlogging-susceptible genotypes. The differentially expressed proteins enumerated here could be used as biological markers for enhancing waterlogging tolerance as part of future crop breeding programs.
Collapse
Affiliation(s)
- Rui Yang
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
| | - Murong Li
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
| | - Matthew Tom Harrison
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, TAS, Australia
| | - Shah Fahad
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- Department of Agronomy, The University of Haripur, Haripur, Pakistan
- *Correspondence: Shah Fahad,
| | - Mingmei Wei
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
| | - Xiu Li
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
| | - Lijun Yin
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
| | - Aihua Sha
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, TAS, Australia
| | - Ke Liu
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, TAS, Australia
- Ke Liu,
| | - Xiaoyan Wang
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Agriculture College, Yangtze University, Jingzhou, China
- Xiaoyan Wang,
| |
Collapse
|
8
|
Ding G, Yang Q, Ruan X, Si T, Yuan B, Zheng W, Xie Q, Souleymane OA, Wang X. Proteomics analysis of the effects for different salt ions in leaves of true halophyte Sesuvium portulacastrum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:234-248. [PMID: 34920320 DOI: 10.1016/j.plaphy.2021.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 05/25/2023]
Abstract
Sesuvium portulacastrum is a true halophyte and shows an optimal development under moderate salinity with large amounts of salt ions in its leaves. However, the specific proteins in response to salt ions are remained unknown. In this study, comparative physiological and proteomic analyses of different leaves subject to NaCl, KCl, NaNO3 and KNO3 were performed. Chlorophyll content was decreased under the above four kinds of salt treatments. Starch and soluble sugar contents changed differently under different salt treatments. A total of 53 differentially accumulated proteins (DAPs) were identified by mass spectrometry. Among them, 13, 25, 26 and 25 DAPs were identified after exposure to KCl, NaCl, KNO3, and NaNO3, respectively. These DAPs belong to 47 unique genes, and 37 of them are involved in protein-protein interactions. These DAPs displayed different expression patterns after treating with different salt ions. Functional annotation revealed they are mainly involved in photosynthesis, carbohydrate and energy metabolism, lipid metabolism, and biosynthesis of secondary metabolites. Genes and proteins showed different expression profiles under different salt treatments. Enzyme activity analysis indicated P-ATPase was induced by KCl, NaCl and NaNO3, V-ATPase was induced by KCl and NaCl, whereas V-PPase activity was significantly increased after application of KNO3, but sharply inhibited by NaCl. These results might deepen our understanding of responsive mechanisms in the leaves of S. portulacastrum upon different salt ions.
Collapse
Affiliation(s)
- Guohua Ding
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Qian Yang
- South Subtropical Crop Research Institute, China Academy of Tropical Agricultural Sciences, China
| | - Xueyu Ruan
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Tingting Si
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Boxuan Yuan
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan, 571158, China; Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Wenwei Zheng
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Ousmane Ahmat Souleymane
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Xuchu Wang
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan, 571158, China.
| |
Collapse
|
9
|
Mustafa G, Komatsu S. Plant proteomic research for improvement of food crops under stresses: a review. Mol Omics 2021; 17:860-880. [PMID: 34870299 DOI: 10.1039/d1mo00151e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Crop improvement approaches have been changed due to technological advancements in traditional plant-breeding methods. Abiotic and biotic stresses limit plant growth and development, which ultimately lead to reduced crop yield. Proteins encoded by genomes have a considerable role in the endurance and adaptation of plants to different environmental conditions. Biotechnological applications in plant breeding depend upon the information generated from proteomic studies. Proteomics has a specific advantage to contemplate post-translational modifications, which indicate the functional effects of protein modifications on crop production. Subcellular proteomics helps in exploring the precise cellular responses and investigating the networking among subcellular compartments during plant development and biotic/abiotic stress responses. Large-scale mass spectrometry-based plant proteomic studies with a more comprehensive overview are now possible due to dramatic improvements in mass spectrometry, sample preparation procedures, analytical software, and strengthened availability of genomes for numerous plant species. Development of stress-tolerant or resilient crops is essential to improve crop productivity and growth. Use of high throughput techniques with advanced instrumentation giving efficient results made this possible. In this review, the role of proteomic studies in identifying the stress-response processes in different crops is summarized. Advanced techniques and their possible utilization on plants are discussed in detail. Proteomic studies accelerate marker-assisted genetic augmentation studies on crops for developing high yielding stress-tolerant lines or varieties under stresses.
Collapse
Affiliation(s)
- Ghazala Mustafa
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
| |
Collapse
|
10
|
Bai LWD, Liu J, Dai LF, Deng QW, Chen YL, Xie JK, Luo XD. Identification and characterisation of cold stress-related proteins in Oryza rufipogon at the seedling stage using label-free quantitative proteomic analysis. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:542-555. [PMID: 33487217 DOI: 10.1071/fp20046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
In this study, label-free quantitative proteomics were used to study cold stress-related proteins in Dongxiang wild rice (Oryza rufipogon Griff., DWR) and cold sensitive cultivated rice 'Xieqingzao B'(Oryza sativa L. ssp. indica cv., XB). The results demonstrated the presence of 101 and 216 differentially expressed proteins (DEPs) were detected in DWR and XB, respectively, after cold stress. Bioinformatics analysis showed that DWR and XB differed significantly in their ability to scavenge reactive oxygen species (ROS) and regulate energy metabolism. Of the 101 DEPs of DWR, 46 DEPs related to differential expressed genes were also detected by transcriptome analysis. And 13 out of 101 DEPs were located in previous cold related quantitative trait loci (QTL). Quantitative real-time PCR analysis indicated that protein expression and transcription patterns were not similar in XB and DWR. Protein-protein interaction (PPI) network was constituted using the DEPs of DWR and XB, and the following three centre proteins were identified: Q8H3I3, Q9LDN2, and Q2QXR8. Next, we selected a centre protein and two of the 37 DEPs with high levels of differential expression (fold change ≥ 2) were used for cloning and prokaryotic expression. We found that Q5Z9Q8 could significantly improve the cold tolerance of Escherichia coli.
Collapse
Affiliation(s)
- Li-Wei-Dan Bai
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Jian Liu
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Liang-Fang Dai
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Qian-Wen Deng
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Ya-Ling Chen
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Jian-Kun Xie
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China; and Corresponding authors. ;
| | - Xiang-Dong Luo
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China; and Corresponding authors. ;
| |
Collapse
|
11
|
GhN/AINV13 positively regulates cotton stress tolerance by interacting with the 14-3-3 protein. Genomics 2020; 113:44-56. [PMID: 33276005 DOI: 10.1016/j.ygeno.2020.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 02/06/2023]
Abstract
Neutral/alkaline invertases (N/AINVs) are sucrose hydrolases with important roles in plants. In this study, 15, 15, 15, 29, and 30 N/AINVs were identified in the Gossypium species, G. raimondii, G. herbaceum, G. arboreum, G. hirsutum, and G. barbadense, respectively. Along with two previously discovered branches, α and β, a new clade γ was first discovered in our study. Investigation of gene collinearity showed that whole-genome duplication (WGD) and polyploidization were responsible for the expansion of the N/AINV gene family in allopolyploid Gossypium. Moreover, expression patterns revealed that GhN/AINV3/13/17/23/24/28 from the β clade is highly expressed during the period of fiber initiation. The invertase activity of GhN/AINV13 and GhN/AINV23 were confirmed by restoring defects of invertase-deficient yeast mutant SEY2102. Treatments of abiotic stress showed that most GhN/AINVs were induced in response to polyethylene glycol (PEG) or salt stress. A virus-induced gene-silencing (VIGS) experiment and yeast two-hybrid assay demonstrated that GhN/AINV13 may interact with their positive regulators Gh14-3-3 proteins and participate in the fiber initiation or stress tolerance of cotton. Our results provided fundamental information regarding N/AINVs and highlight their potential functions in cotton stress tolerance.
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Li P, Liu H, Yang H, Pu X, Li C, Huo H, Chu Z, Chang Y, Lin Y, Liu L. Translocation of Drought-Responsive Proteins from the Chloroplasts. Cells 2020; 9:E259. [PMID: 31968705 PMCID: PMC7017212 DOI: 10.3390/cells9010259] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/19/2022] Open
Abstract
Some chloroplast proteins are known to serve as messengers to transmit retrograde signals from chloroplasts to the nuclei in response to environmental stresses. However, whether particular chloroplast proteins respond to drought stress and serve as messengers for retrograde signal transduction are unclear. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) to monitor the proteomic changes in tobacco (Nicotiana benthamiana) treated with drought stress/re-watering. We identified 3936 and 1087 differentially accumulated total leaf and chloroplast proteins, respectively, which were grouped into 16 categories. Among these, one particular category of proteins, that includes carbonic anhydrase 1 (CA1), exhibited a great decline in chloroplasts, but a remarkable increase in leaves under drought stress. The subcellular localizations of CA1 proteins from moss (Physcomitrella patens), Arabidopsis thaliana and rice (Oryza sativa) in P. patens protoplasts consistently showed that CA1 proteins gradually diminished within chloroplasts but increasingly accumulated in the cytosol under osmotic stress treatment, suggesting that they could be translocated from chloroplasts to the cytosol and act as a signal messenger from the chloroplast. Our results thus highlight the potential importance of chloroplast proteins in retrograde signaling pathways and provide a set of candidate proteins for further research.
Collapse
Affiliation(s)
- Ping Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China; (P.L.); (H.L.); (C.L.)
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, China; (H.Y.); (X.P.)
| | - Haoju Liu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China; (P.L.); (H.L.); (C.L.)
| | - Hong Yang
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, China; (H.Y.); (X.P.)
| | - Xiaojun Pu
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, China; (H.Y.); (X.P.)
| | - Chuanhong Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China; (P.L.); (H.L.); (C.L.)
| | - Heqiang Huo
- Mid-Florida Research and Education Center, Department of Environmental Horticulture, University of Florida, Miami, FL 32703, USA;
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Taian 271018, China;
| | - Yuxiao Chang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China; (P.L.); (H.L.); (C.L.)
| | - Li Liu
- Key Laboratory for Economic Plants and Biotechnology, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, China; (H.Y.); (X.P.)
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430070, China
| |
Collapse
|
14
|
Frukh A, Siddiqi TO, Khan MIR, Ahmad A. Modulation in growth, biochemical attributes and proteome profile of rice cultivars under salt stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 146:55-70. [PMID: 31733605 DOI: 10.1016/j.plaphy.2019.11.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/06/2019] [Accepted: 11/06/2019] [Indexed: 05/06/2023]
Abstract
One of the major abiotic stresses that affect productivity of rice is salinity. Rice cultivars showed significant genetic variation in response to salt stress. In the present investigation, differential growth pattern and physio-chemical traits-based screening of high yielding rice cultivars of various salt affected areas of India was carried out, and salt-sensitive and salt-tolerant cultivars were identified. Differential responses of antioxidant enzyme activity and tolerance index at maximum level of salt treatment depicted that Jhelum and Vytilla-4 cultivars of rice were sensitive and tolerant to salt stress, respectively. Analysis of growth, morpho-physiological, and biochemical parameters also confirmed the salt-tolerant and salt-sensitive characters of cv. Vytilla-4 and cv. Jhelum, respectively. Nano-LCMS/MS-based proteome profile of these two cultivars was carried out to find out the mechanism lying behind the salt tolerance. A total number of 514 and 770 protein spots were reported in the most salt-tolerant (cv. Vytilla-4) and salt-sensitive (cv. Jhelum) cultivars, respectively. The differentially expressed proteins (DEPs) were found associated with major metabolic pathways including photosynthesis, energy metabolism, amino acid metabolism, nitrogen assimilation and stress and signalling pathways. The changes in the major proteins like Ribulose bisphosphate carboxylase small chain, chlorophyll a-b binding protein, phosphoglycerate kinase, cytochrome c oxidase subunit 5C, glutamine synthetase, glutathione S-transferase, peroxidase, and thioredoxin elucidated the mechanism activated by salt-tolerant cv. Vytilla-4. The transcriptional validation of some of the differentially expressed proteins through real-time quantitative PCR analysis further validated the proteomic results. Outcomes of this work could help in finding out the potential cross-links of different pathways involved in salt-tolerance mechanisms operating in the studied here rice cultivars under salt stress.
Collapse
Affiliation(s)
- Arajmand Frukh
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Tariq Omar Siddiqi
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - M Iqbal R Khan
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Altaf Ahmad
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India.
| |
Collapse
|
15
|
Zhou X, Hu W, Li B, Yang Y, Zhang Y, Thow K, Fan L, Qu Y. Proteomic profiling of cotton fiber developmental transition from cell elongation to secondary wall deposition. Acta Biochim Biophys Sin (Shanghai) 2019; 51:1168-1177. [PMID: 31620780 DOI: 10.1093/abbs/gmz111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 06/26/2019] [Accepted: 08/02/2019] [Indexed: 01/16/2023] Open
Abstract
Cotton fiber developmental transition from elongation to secondary cell wall biosynthesis is a critical growth shifting phase that affects fiber final length, strength, and other properties. Morphological dynamic analysis indicated an asynchronous fiber developmental pattern between two most important commercial cotton species, Gossypium hirsutum (Gh) and G. barbadense (Gb). Using isobaric tags for relative and absolute quantitation techniques, we examined the temporal changes of protein expression at three representative development periods (15-19, 19-23, and 23-27 dpa) in both species. Strikingly, a large proportion of differentially expressed proteins (DEPs) were identified at 19-23 dpa in Gh and at 23-27 dpa in Gb, corresponding to their fiber developmental transition timing. To better understand fiber transitional development, we comparatively analyzed those DEPs in 19-23 dpa of Gh vs. in 23-27 dpa of Gb, and noted that these cotton species indeed share fundamentally similar fiber developmental features under the biological processes. We also showed that there are limited overlaps in both specific upregulated and downregulated proteins between the two species, suggesting species-specific protein regulations in the development process. Proteomic profiling results revealed dynamic changes of several key proteins and biological processes that are potentially correlated with fiber developmental transition. During the transition, upregulated proteins are mainly involved in carbohydrate/energy metabolism, oxidation-reduction, cytoskeleton, protein turnover, Ca2+ signaling, etc., whereas important downregulated proteins are mostly involved in phenylpropanoid and flavonoid secondary metabolism pathways. The gene expressions of several changed proteins in this key stage were also examined by quantitative reverse transcription polymerase chain reaction. Overall, the present study provides accurate pictures of the regulatory networks of functional proteins during the fiber developmental transition, therefore highlighting candidate genes/proteins and related pathways for the cotton fiber improvement.
Collapse
Affiliation(s)
- Xiaoyun Zhou
- College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Wenran Hu
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Bo Li
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yang Yang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yong Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kieran Thow
- St Hugh’s College, University of Oxford, Gourdon, Montrose, UK
| | - Ling Fan
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yanying Qu
- College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| |
Collapse
|
16
|
Zhu L, Zheng B, Song W, Tao C, Jin X, Li H. Comparative Proteomic Analysis of Molecular Differences between Leaves of Wild-Type Upland Cotton and Its Fuzzless- Lintless Mutant. Molecules 2019; 24:molecules24203769. [PMID: 31635060 PMCID: PMC6832260 DOI: 10.3390/molecules24203769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/13/2019] [Accepted: 10/16/2019] [Indexed: 01/01/2023] Open
Abstract
Fuzzless-lintless mutant (fl) ovules of upland cotton have been used to investigate cotton fiber development for decades. However, the molecular differences of green tissues between fl and wild-type (WT) cotton were barely reported. Here, we found that gossypol content, the most important secondary metabolite of cotton leaves, was higher in Gossypium hirsutum L. cv Xuzhou-142 (Xu142) WT than in fl. Then, we performed comparative proteomic analysis of the leaves from Xu142 WT and its fl. A total of 4506 proteins were identified, of which 103 and 164 appeared to be WT- and fl-specific, respectively. In the 4239 common-expressed proteins, 80 and 74 were preferentially accumulated in WT and fl, respectively. Pathway enrichment analysis and protein–protein interaction network analysis of both variety-specific and differential abundant proteins showed that secondary metabolism and chloroplast-related pathways were significantly enriched. Quantitative real-time PCR confirmed that the expression levels of 12 out of 16 selected genes from representative pathways were consistent with their protein accumulation patterns. Further analyses showed that the content of chlorophyll a in WT, but not chlorophyll b, was significantly increased compared to fl. This work provides the leaf proteome profiles of Xu142 and its fl mutant, indicating the necessity of further investigation of molecular differences between WT and fl leaves.
Collapse
Affiliation(s)
- Liping Zhu
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
| | - Bowen Zheng
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
| | - Wangyang Song
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
| | - Chengcheng Tao
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
| | - Xiang Jin
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi 832003, China.
| |
Collapse
|
17
|
Xing J, Pan D, Wang L, Tan F, Chen W. Proteomic and physiological responses in mangrove Kandelia candel roots under short-term high-salinity stress. ACTA ACUST UNITED AC 2019; 43:314-325. [PMID: 31768104 PMCID: PMC6823913 DOI: 10.3906/biy-1906-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Kandelia candel is one of the mangrove species that are most resistant to environmental stress. As a typical nonsalt-secreting mangrove plant, K. candel is an ideal biological material to analyze the molecular mechanism of salt tolerance in woody plants. In this study, changes in protein abundance and expression profile in K. candel roots under high-salinity stress of 600 mmol L-1 NaCl were analyzed using isobaric tags for relative and absolute quantification (iTRAQ) assay. Moreover, the physiological parameters associated with metabolic pathways in which the differentially abundant proteins (DAPs) are involved were determined. A total of 5577 proteins were identified by iTRAQ analysis of the K. candel root proteins, of which 227 were DAPs with a fold change ratio >1.2 or a fold change ratio <0.83 and a P-value <0.05. A total of 227 DAPs consisting of 110 up-regulated and 117 down-regulated proteins were identified. Our Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the DAPs were primarily involved in biological processes including carbohydrate and energy metabolisms, stress response and defense, cell wall structure, and secondary metabolism. The results of the physiological parameters showed that their profile changes were consistent with those of the proteome analysis. The results of the proteome and physiological parameters showed that K. candel roots could resist high-salinity stress by maintaining a normal Embden-Meyerhof-Parnas and tricarboxylic acid (EMP-TCA) pathway, increasing the activities of various antioxidant enzymes and antioxidant contents, stabilizing the cell wall structure, and accumulating secondary metabolites such as triterpenoids.
Collapse
Affiliation(s)
- Jianhong Xing
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian China.,College of Resources and Chemical Engineering, Sanming University, Sanming, Fujian China
| | - Dezhuo Pan
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Lingxia Wang
- College of Life Sciences, Ningxia University, Yinchuan, Ningxia China
| | - Fanglin Tan
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian China
| | - Wei Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| |
Collapse
|
18
|
Wang XQ, Han LH, Zhou W, Tao M, Hu QQ, Zhou YN, Li XB, Li DD, Huang GQ. GhEIN3, a cotton (Gossypium hirsutum) homologue of AtEIN3, is involved in regulation of plant salinity tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:83-93. [PMID: 31491703 DOI: 10.1016/j.plaphy.2019.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/16/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Ethylene insensitive 3 (EIN3), a key transcription factor in ethylene signal transduction, play important roles in plant stress signaling pathways. In this study, we isolated and characterized an EIN3-like gene from cotton (Gossypium hirsutum), designated as GhEIN3. GhEIN3 is highly expressed in vegetative tissues, and its expression is induced by 1-aminocyclopropane-1-carboxylic acid (ACC) and NaCl. Ectopic expression of GhEIN3 in Arabidopsis elevated plants' response to ethylene, which exhibit smaller leaves, more root hairs, shorter roots and hypocotyls. The germination rate, survival rate and root length of GhEIN3 transgenic plants were significantly improved compared to wild type under salt stress. GhEIN3 transgenic plants accumulated less H2O2 and malondialdehyde (MDA), while higher superoxide dismutase (SOD) and peroxidase (POD) activities were detected under salt stress. In addition, expression of several genes related to reactive oxygen species (ROS) pathway and ABA signaling pathway was increased in the GhEIN3 transgenic plants under salt stress. In contrast, virus-induced gene silencing (VIGS) of GhEIN3 in cotton enhanced the sensitivity of transgenic plants to salt stress, accumulating higher H2O2 and MDA and lower SOD and POD activities compared to control plants. Collectively, our results revealed that GhEIN3 might be involved in the regulation of plant response to salt stress by regulating ABA and ROS pathway during plant growth and development.
Collapse
Affiliation(s)
- Xiao-Qian Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Li-Hong Han
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Wei Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Miao Tao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Qian-Qian Hu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ying-Nan Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Xue-Bao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Deng-Di Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Geng-Qing Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| |
Collapse
|
19
|
Sharif I, Aleem S, Farooq J, Rizwan M, Younas A, Sarwar G, Chohan SM. Salinity stress in cotton: effects, mechanism of tolerance and its management strategies. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:807-820. [PMID: 31402811 PMCID: PMC6656830 DOI: 10.1007/s12298-019-00676-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/15/2019] [Accepted: 05/13/2019] [Indexed: 05/21/2023]
Abstract
Cotton is classified as moderately salt tolerant crop with salinity threshold level of 7.7 dS m-1. Salinity is a serious threat for cotton growth, yield and fiber quality. The sensitivity to salt stress depends upon growth stage and type of salt. Understanding of cotton response to salinity, its resistance mechanism and looking into management techniques may assist in formulating strategies to improve cotton performance under saline condition. The studies have showed that germination, emergence and seedling stages are more sensitive to salinity stress as compared to later stages. Salt stress results in delayed flowering, less fruiting positions, fruit shedding and reduced boll weight which ultimately affect seed cotton yield. Depressed activities of metabolic enzymes viz: acidic invertase, alkaline invertase and sucrose phophate synthase lead to fiber quality deterioration in salinity. Excessive sodium exclusion or its compartmentation is the main adaptive mechanism in cotton under salt stress. Up regulation of enzymatic and non-enzymatic antioxidants genes offer important adaptive potential to develop salt tolerant cotton varieties. Seed priming is also an effective approach for improving cotton germination in saline soils. Intra and inter variation in cotton germplasm could be used to develop salt tolerant varieties with the aid of marker assisted selection. Furthermore, transgenic approach could be the promising option for enhancing cotton production under saline condition. It is suggested that future research may be carried out with the combination of conventional and advance molecular technology to develop salt tolerant cultivars.
Collapse
Affiliation(s)
- Iram Sharif
- Cotton Research Station, AARI, Faisalabad, Pakistan
| | - Saba Aleem
- Vegetable Research Institute, AARI, Faisalabad, Pakistan
| | | | | | - Abia Younas
- Cotton Research Station, AARI, Faisalabad, Pakistan
| | | | | |
Collapse
|
20
|
Wu GQ, Wang JL, Feng RJ, Li SJ, Wang CM. iTRAQ-Based Comparative Proteomic Analysis Provides Insights into Molecular Mechanisms of Salt Tolerance in Sugar Beet ( Beta vulgaris L.). Int J Mol Sci 2018; 19:ijms19123866. [PMID: 30518064 PMCID: PMC6321137 DOI: 10.3390/ijms19123866] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/31/2018] [Accepted: 10/31/2018] [Indexed: 01/24/2023] Open
Abstract
Salinity is one of the major abiotic stress factors that limit plant growth and crop yield worldwide. To understand the molecular mechanisms and screen the key proteins in response of sugar beet (Beta vulgaris L.) to salt, in the present study, the proteomics of roots and shoots in three-week-old sugar beet plants exposed to 50 mM NaCl for 72 h was investigated by isobaric Tags for Relative and Absolute Quantitation (iTRAQ) technology. The results showed that 105 and 30 differentially expressed proteins (DEPs) were identified in roots and shoots of salt-treated plants compared with untreated plants, respectively. There were 46 proteins up-regulated and 59 proteins down-regulated in roots; and 13 up-regulated proteins and 17 down-regulated proteins found in shoots, respectively. These DEPs were mainly involved in carbohydrate metabolism, energy metabolism, lipid metabolism, biosynthesis of secondary metabolites, transcription, translation, protein folding, sorting, and degradation as well as transport. It is worth emphasizing that some novel salt-responsive proteins were identified, such as PFK5, MDH, KAT2, ACAD10, CYP51, F3H, TAL, SRPR, ZOG, V-H+-ATPase, V-H+-PPase, PIPs, TIPs, and tubulin α-2/β-1 chain. qRT-PCR analysis showed that six of the selected proteins, including BvPIP1-4, BvVP and BvVAP in root and BvTAL, BvURO-D1, and BvZOG in shoot, displayed good correlation between the expression levels of protein and mRNA. These novel proteins provide a good starting point for further research into their functions using genetic or other approaches. These findings should significantly improve the understanding of the molecular mechanisms involved in salt tolerance of sugar beet plants.
Collapse
Affiliation(s)
- Guo-Qiang Wu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Jin-Long Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Rui-Jun Feng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Shan-Jia Li
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Chun-Mei Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, CAAS, Lanzhou 730050, China.
| |
Collapse
|
21
|
Niu L, Xu X, Liu H, Wu X, Wang W. On the Promising Role of Enzyme Activity Assay in Interpreting Comparative Proteomic Data in Plants. Proteomics 2018; 18:e1800234. [PMID: 30179302 DOI: 10.1002/pmic.201800234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/18/2018] [Indexed: 11/09/2022]
Abstract
Comparative proteomics is widely used to detect protein changes, especially differential abundance proteins (DAPs) that are involved in plant responses to development, disease, or environment. Once DAPs are identified, it is essential to validate any change in their abundance, and their role in the biological process under study. In addition to common confirmation by quantitative RT-PCR, immunoblot, and multiple reaction monitoring analysis, it has been proposed that enzyme activity assay (EAA) can be complementary to the standard proteomics results, especially regarding the elucidation of protein (enzyme) function and the mechanism of enzyme-associated biochemical or metabolic pathways. The enzymes discussed here are the DAPs identified in comparative plant proteomics. Despite the small number of enzymes in a proteome, they often make up a substantial proportion of the DAPs identified in comparative studies. Currently, only a few studies have performed EAA to complement the interpretation of proteomic data, especially activity-based protein profiling. This viewpoint aims to arouse the attention of proteomic researchers on the promising role of EAA in plant proteomics and highlights the need for high-throughput assays of enzyme activities in comparative plant proteomics.
Collapse
Affiliation(s)
- Liangjie Niu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangru Xu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hui Liu
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaolin Wu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wei Wang
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China.,College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| |
Collapse
|
22
|
Diouf L, Magwanga RO, Gong W, He S, Pan Z, Jia YH, Kirungu JN, Du X. QTL Mapping of Fiber Quality and Yield-Related Traits in an Intra-Specific Upland Cotton Using Genotype by Sequencing (GBS). Int J Mol Sci 2018; 19:E441. [PMID: 29389902 PMCID: PMC5855663 DOI: 10.3390/ijms19020441] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/12/2018] [Accepted: 01/28/2018] [Indexed: 01/04/2023] Open
Abstract
Fiber quality and yield improvement are crucial for cotton domestication and breeding. With the transformation in spinning techniques and multiplicity needs, the development of cotton fiber quality and yield is of great importance. A genetic map of 5178 Single Nucleotide Polymorphism (SNP) markers were generated using 277 F2:3 population, from an intra-specific cross between two upland cotton accessions, CCRI35 a high fiber quality as female and Nan Dan Ba Di Da Hua (NH), with good yield properties as male parent. The map spanned 4768.098 cM with an average distance of 0.92 cM. A total of 110 Quantitative Traits Loci (QTLs) were identified for 11 traits, but only 30 QTLs were consistent in at least two environments. The highest percentage of phenotypic variance explained by a single QTL was 15.45%. Two major cluster regions were found, cluster 1 (chromosome17-D03) and cluster 2 (chromosome26-D12). Five candidate genes were identified in the two QTL cluster regions. Based on GO functional annotation, all the genes were highly correlated with fiber development, with functions such as protein kinase and phosphorylation. The five genes were associated with various fiber traits as follows: Gh_D03G0889 linked to qFM-D03_cb, Gh_D12G0093, Gh_D12G0410, Gh_D12G0435 associated with qFS-D12_cb and Gh_D12G0969 linked to qFY-D12_cb. Further structural annotation and fine mapping is needed to determine the specific role played by the five identified genes in fiber quality and yield related pathway.
Collapse
Affiliation(s)
- Latyr Diouf
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
- Senegalese River Valley Development Agency (SAED), Saint-Louis Bp74, Senegal.
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
- School of Physical and Biological Sciences (SPBS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Main Campus, P.O. Box 210-40601, Bondo, Kenya.
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yin Hua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Joy Nyangasi Kirungu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| |
Collapse
|