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Wang J, Chen X, Chu S, Hayat K, Chi Y, Liao X, Zhang H, Xie Y, Zhou P, Zhang D. Conjoint analysis of physio-biochemical, transcriptomic, and metabolomic reveals the response characteristics of solanum nigrum L. to cadmium stress. BMC PLANT BIOLOGY 2024; 24:567. [PMID: 38880885 PMCID: PMC11181532 DOI: 10.1186/s12870-024-05278-z] [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: 03/27/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
Cadmium (Cd) is a nonessential element in plants and has adverse effects on the growth and development of plants. However, the molecular mechanisms of Cd phytotoxicity, tolerance and accumulation in hyperaccumulators Solanum nigrum L. has not been well understood. Here, physiology, transcriptome, and metabolome analyses were conducted to investigate the influence on the S. nigrum under 0, 25, 50, 75 and 100 µM Cd concentrations for 7 days. Pot experiments demonstrated that compared with the control, Cd treatment significantly inhibited the biomass, promoted the Cd accumulation and translocation, and disturbed the balance of mineral nutrient metabolism in S. nigrum, particularly at 100 µM Cd level. Moreover, the photosynthetic pigments contents were severely decreased, while the content of total protein, proline, malondialdehyde (MDA), H2O2, and antioxidant enzyme activities generally increased first and then slightly declined with increasing Cd concentrations, in both leaves and roots. Furthermore, combined with the previous transcriptomic data, numerous crucial coding-genes related to mineral nutrients and Cd ion transport, and the antioxidant enzymes biosynthesis were identified, and their expression pattern was regulated under different Cd stress. Simultaneously, metabolomic analyses revealed that Cd treatment significantly changed the expression level of many metabolites related to amino acid, lipid, carbohydrate, and nucleotide metabolism. Metabolic pathway analysis also showed that S. nigrum roots activated some differentially expressed metabolites (DEMs) involved in energy metabolism, which may enhance the energy supply for detoxification. Importantly, central common metabolism pathways of DEGs and DEMs, including the "TCA cycle", "glutathione metabolic pathway" and "glyoxylate and dicarboxylate metabolism" were screened using conjoint transcriptomics and metabolomics analysis. Our results provide some novel evidences on the physiological and molecular mechanisms of Cd tolerance in hyperaccumulator S. nigrum plants.
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Affiliation(s)
- Juncai Wang
- Guizhou Academy of Sciences, Guiyang, Guizhou, 550001, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- The Land Greening Remediation Engineering Research Center of Guizhou Province, Guiyang, 550001, China
| | - Xunfeng Chen
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shaohua Chu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kashif Hayat
- Key Laboratory of Pollution Exposure and Health Intervention, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, 310015, China
| | - Yaowei Chi
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaofeng Liao
- Guizhou Academy of Sciences, Guiyang, Guizhou, 550001, China
- The Land Greening Remediation Engineering Research Center of Guizhou Province, Guiyang, 550001, China
- Guizhou University, Guiyang, 550025, China
| | - Hongliang Zhang
- Guizhou Academy of Sciences, Guiyang, Guizhou, 550001, China
- The Land Greening Remediation Engineering Research Center of Guizhou Province, Guiyang, 550001, China
| | - Yuangui Xie
- Guizhou Academy of Sciences, Guiyang, Guizhou, 550001, China.
- The Land Greening Remediation Engineering Research Center of Guizhou Province, Guiyang, 550001, China.
| | - Pei Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Wang Z, Chen Z, Wu Y, Mu M, Jiang J, Nie W, Zhao S, Cui G, Yin X. Genome-wide identification and characterization of NAC transcription factor family members in Trifolium pratense and expression analysis under lead stress. BMC Genomics 2024; 25:128. [PMID: 38297198 PMCID: PMC10829316 DOI: 10.1186/s12864-023-09944-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/26/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND The NAC TF family is widely involved in plant responses to various types of stress. Red clover (Trifolium pratense) is a high-quality legume, and the study of NAC genes in red clover has not been comprehensive. The aim of this study was to analyze the NAC gene family of red clover at the whole-genome level and explore its potential role in the Pb stress response. RESULTS In this study, 72 TpNAC genes were identified from red clover; collinearity analysis showed that there were 5 pairs of large fragment replicators of TpNAC genes, and red clover was found to be closely related to Medicago truncatula. Interestingly, the TpNAC genes have more homologs in Arabidopsis thaliana than in soybean (Glycine max). There are many elements in the TpNAC genes promoters that respond to stress. Gene expression analysis showed that all the TpNAC genes responded to Pb stress. qRT-PCR showed that the expression levels of TpNAC29 and TpNAC42 were significantly decreased after Pb stress. Protein interaction network analysis showed that 21 TpNACs and 23 other genes participated in the interaction. In addition, the TpNAC proteins had three possible 3D structures, and the secondary structure of these proteins were mainly of other types. These results indicated that most TpNAC members were involved in the regulation of Pb stress in red clover. CONCLUSION These results suggest that most TpNAC members are involved in the regulation of Pb stress in red clover. TpNAC members play an important role in the response of red clover to Pb stress.
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Affiliation(s)
- Zicheng Wang
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Zirui Chen
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Yuchen Wu
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Meiqi Mu
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Jingwen Jiang
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Wanting Nie
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Siwen Zhao
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Guowen Cui
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Xiujie Yin
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China.
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Hussain Q, Ye T, Shang C, Li S, Khan A, Nkoh JN, Mustafa AEZMA, Elshikh MS. NRAMP gene family in Kandelia obovata: genome-wide identification, expression analysis, and response to five different copper stress conditions. FRONTIERS IN PLANT SCIENCE 2024; 14:1318383. [PMID: 38239217 PMCID: PMC10794735 DOI: 10.3389/fpls.2023.1318383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/14/2023] [Indexed: 01/22/2024]
Abstract
Natural resistance-associated macrophage proteins (NRAMPs) are a class of metal transporters found in plants that exhibit diverse functions across different species. Transporter proteins facilitate the absorption, distribution, and sequestration of metallic elements within various plant tissues. Despite the extensive identification of NRAMP family genes in various species, a full analysis of these genes in tree species is still necessary. Genome-wide identification and bioinformatics analysis were performed to understand the roles of NRAMP genes in copper (CuCl2) stress in Kandelia obovata (Ko). In Arachis hypogaea L., Populus trichocarpa, Vitis vinifera, Phaseolus vulgaris L., Camellia sinensis, Spirodela polyrhiza, Glycine max L. and Solanum lycopersicum, a genome-wide study of the NRAMP gene family was performed earlier. The domain and 3D structural variation, phylogenetic tree, chromosomal distributions, gene structure, motif analysis, subcellular localization, cis-regulatory elements, synteny and duplication analysis, and expression profiles in leaves and CuCl2 were all investigated in this research. In order to comprehend the notable functions of the NRAMP gene family in Kandelia obovata, a comprehensive investigation was conducted at the genomic level. This study successfully found five NRAMP genes, encompassing one gene pair resulting from whole-genome duplication and a gene that had undergone segmental duplication. The examination of chromosomal position revealed an unequal distribution of the KoNRAMP genes across chromosomes 1, 2, 5, 7, and 18. The KoNRAMPs can be classified into three subgroups (I, II, and SLC) based on phylogeny and synteny analyses, similar to Solanum lycopersicum. Examining cis-regulatory elements in the promoters revealed five hormone-correlated responsive elements and four stress-related responsive elements. The genomic architecture and properties of 10 highly conserved motifs are similar among members of the NRAMP gene family. The conducted investigations demonstrated that the expression levels of all five genes exhibited alterations in response to different levels of CuCl2 stress. The results of this study offer crucial insights into the roles of KoNRAMPs in the response of Kandelia obovata to CuCl2 stress.
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Affiliation(s)
- Quaid Hussain
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform for Collaborative Innovation of Marine Algae Industry, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Ting Ye
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform for Collaborative Innovation of Marine Algae Industry, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Chenjing Shang
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform for Collaborative Innovation of Marine Algae Industry, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Sihui Li
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform for Collaborative Innovation of Marine Algae Industry, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Asadullah Khan
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform for Collaborative Innovation of Marine Algae Industry, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jackson Nkoh Nkoh
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen Public Service Platform for Collaborative Innovation of Marine Algae Industry, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | | | - Mohamed S. Elshikh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Nestor BJ, Bayer PE, Fernandez CGT, Edwards D, Finnegan PM. Approaches to increase the validity of gene family identification using manual homology search tools. Genetica 2023; 151:325-338. [PMID: 37817002 PMCID: PMC10692271 DOI: 10.1007/s10709-023-00196-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/01/2023] [Indexed: 10/12/2023]
Abstract
Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species. Analysis of gene families is often used to form and support hypotheses on genetic patterns such as gene presence, absence, or functional divergence which underlie traits examined in functional studies. These analyses often require precise identification of all members in a targeted gene family. Manual pipelines where homology search and orthology assignment tools are used separately are the most common approach for identifying small gene families where accurate identification of all members is important. The ability to curate sequences between steps in manual pipelines allows for simple and precise identification of all possible gene family members. However, the validity of such manual pipeline analyses is often decreased by inappropriate approaches to homology searches including too relaxed or stringent statistical thresholds, inappropriate query sequences, homology classification based on sequence similarity alone, and low-quality proteome or genome sequences. In this article, we propose several approaches to mitigate these issues and allow for precise identification of gene family members and support for hypotheses linking genetic patterns to functional traits.
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Affiliation(s)
- Benjamin J Nestor
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia.
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Cassandria G Tay Fernandez
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Patrick M Finnegan
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
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Ma X, Yang H, Bu Y, Zhang Y, Sun N, Wu X, Jing Y. Genome-wide identification of the NRAMP gene family in Populus trichocarpa and their function as heavy metal transporters. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 261:115110. [PMID: 37300917 DOI: 10.1016/j.ecoenv.2023.115110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/12/2023]
Abstract
The natural resistance-associated macrophage protein (NRAMP) gene family plays a key role in essential mineral nutrient homeostasis, as well as toxic metal accumulation, translocation, and detoxification. Although the NRAMP family genes have been widely identified in various species, they still require to be analyzed comprehensively in tree species. In this study, a total of 11 NRAMP members (PtNRAMP1-11) were identified in Populus trichocarpa, a woody model plant, and further subdivided into three groups based on phylogenetic analysis. Chromosomal location analysis indicated that the PtNRAMP genes were unevenly distributed on six of the 19 Populus chromosomes. Gene expression analysis indicated that the PtNRAMP genes were differentially responsive to metal stress, including iron (Fe) and manganese (Mn) deficiency, as well as Fe, Mn, zinc (Zn), and cadmium (Cd) toxicity. Furthermore, the PtNRAMP gene functions were characterized using a heterologous yeast expression system. The results showed that PtNRAMP1, PtNRAMP2, PtNRAMP4, PtNRAMP9, PtNRAMP10, and PtNRAMP11 displayed the ability to transport Cd into yeast cells. In addition, PtNRAMP1, PtNRAMP6, and PtNRAMP7 complemented the Mn uptake mutant, while PtNRAMP1, PtNRAMP6, PtNRAMP7, and PtNRAMP9 complemented the Fe uptake mutant. In conclusion, our findings revealed the respective functions of PtNRAMPs during metal transport as well as their potential role in micronutrient biofortification and phytoremediation.
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Affiliation(s)
- Xiaocen Ma
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Haobo Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Yufen Bu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Na Sun
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Xinyuan Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China
| | - Yanping Jing
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing 100083, China; National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083,China.
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He G, Saleem M, Deng T, Zhong Z, He T, Wu J. Unraveling the Mechanism of StWRKY6 in Potato ( Solanum tuberosum)'s Cadmium Tolerance for Ensuring Food Safety. Foods 2023; 12:2303. [PMID: 37372512 DOI: 10.3390/foods12122303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The WRKY transcription factor plays a crucial role in plant stress adaptation. Our research has found that WRKY6 in Solanum tuberosum (potatoes) is closely related to cadmium (Cd) tolerance. Therefore, investigating the mechanism of StWRKY6 in plant resistance to Cd toxicity is of great scientific importance for food safety. This research further analyzed the gene structure and functional regions of the nuclear transcription factor WRKY6 in potatoes, discovering that StWRKY6 contains W box, GB/box, ABRE, and other elements that can act as a nuclear transcription regulatory factor to execute multiple functional regulations. The results of the heterologous expression of StWRKY6 in Arabidopsis under Cd stress showed that the overexpression line (StWRKY6-OE) had significantly higher SAPD values and content of reactive oxygen species scavenging enzymes than the wild type, indicating that StWRKY6 plays a crucial role in protecting the photosynthetic system and promoting carbohydrate synthesis. Transcriptome analysis also revealed that the Cd-induced expression of StWRKY6 up-regulated many potential gene targets, including APR2, DFRA, ABCG1, VSP2, ERF013, SAUR64/67, and BBX20, which are involved in Cd chelation (APR2, DFRA), plant defense (VSP2, PDF1.4), toxic substance efflux (ABCG1), light morphology development (BBX20), and auxin signal (SAUR64/67). These genes coordinate the regulation of Cd tolerance in the StWRKY6 overexpression line. In summary, this study identified a potential gene set of the co-expression module of StWRKY6, providing useful evidence for the remediation of Cd-contaminated soil and the genetic breeding of low Cd-accumulating crops, thereby ensuring food safety.
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Affiliation(s)
- Guandi He
- College of Agriculture, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Academy of Agricultural Sciences, Animal Husbandry and Veterinary Research Institute, Guiyang 550005, China
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Office 314, 1627 Harris Way, Montgomery, AL 36104, USA
| | - Tingfei Deng
- National Products Research Center of Guizhou Province, Guiyang 550025, China
| | - Zhuoyan Zhong
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Tengbing He
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Jiahai Wu
- Guizhou Provincial Academy of Agricultural Sciences, Animal Husbandry and Veterinary Research Institute, Guiyang 550005, China
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Angelin-Bonnet O, Thomson S, Vignes M, Biggs PJ, Monaghan K, Bloomer R, Wright K, Baldwin S. Investigating the genetic components of tuber bruising in a breeding population of tetraploid potatoes. BMC PLANT BIOLOGY 2023; 23:238. [PMID: 37147582 PMCID: PMC10161554 DOI: 10.1186/s12870-023-04255-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 04/27/2023] [Indexed: 05/07/2023]
Abstract
BACKGROUND Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economic importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still much to learn about this complex phenotype. Here, we used capture sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis (GWAS) for tuber bruising. In addition, we collected transcriptomic data to enrich the GWAS results. However, there is currently no satisfactory method to represent both GWAS and transcriptomics analysis results in a single visualisation and to compare them with existing knowledge about the biological system under study. RESULTS When investigating population structure, we found that the STRUCTURE algorithm yielded greater insights than discriminant analysis of principal components (DAPC). Importantly, we found that markers with the highest (though non-significant) association scores were consistent with previous findings on tuber bruising. In addition, new genomic regions were found to be associated with tuber bruising. The GWAS results were backed by the transcriptomics differential expression analysis. The differential expression notably highlighted for the first time the role of two genes involved in cellular strength and mechanical force sensing in tuber resistance to bruising. We proposed a new visualisation, the HIDECAN plot, to integrate the results from the genomics and transcriptomics analyses, along with previous knowledge about genomic regions and candidate genes associated with the trait. CONCLUSION This study offers a unique genome-wide exploration of the genetic components of tuber bruising. The role of genetic components affecting cellular strength and resistance to physical force, as well as mechanosensing mechanisms, was highlighted for the first time in the context of tuber bruising. We showcase the usefulness of genomic data from breeding programmes in identifying genomic regions whose association with the trait of interest merit further investigation. We demonstrate how confidence in these discoveries and their biological relevance can be increased by integrating results from transcriptomics analyses. The newly proposed visualisation provides a clear framework to summarise of both genomics and transcriptomics analyses, and places them in the context of previous knowledge on the trait of interest.
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Affiliation(s)
- Olivia Angelin-Bonnet
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, 4442, New Zealand.
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Christchurch, 8140, New Zealand
| | - Matthieu Vignes
- School of Mathematical and Computational Sciences, Massey University, Palmerston North, 4412, New Zealand
| | - Patrick J Biggs
- School of Natural Sciences, Massey University, Palmerston North, 4412, New Zealand
- School of Veterinary Science, Massey University, Palmerston North, 4412, New Zealand
| | - Katrina Monaghan
- The New Zealand Institute for Plant and Food Research Limited, Christchurch, 8140, New Zealand
| | - Rebecca Bloomer
- The New Zealand Institute for Plant and Food Research Limited, Christchurch, 8140, New Zealand
| | - Kathryn Wright
- The New Zealand Institute for Plant and Food Research Limited, Christchurch, 8140, New Zealand
| | - Samantha Baldwin
- The New Zealand Institute for Plant and Food Research Limited, Christchurch, 8140, New Zealand
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8
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Liu Y, He G, He Y, Tang Y, Zhao F, He T. Discovery of cadmium-tolerant biomacromolecule (StCAX1/4 transportproteins) in potato and its potential regulatory relationship with WRKY transcription factors. Int J Biol Macromol 2023; 228:385-399. [PMID: 36581029 DOI: 10.1016/j.ijbiomac.2022.12.232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/04/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022]
Abstract
The cation/H+ exchanger (CAX) involved in Ca2+, Mg2+ and Mn2+ transport is a special class of vacuolar transporters that play an important role in maintaining ion homeostasis in plant cells. However, it has been rarely reported whether CAX proteins have unique tolerance to cadmium stress. In our research, the cadmium-resistant potato variety "Yunshu 505" was taken as the object, through biological etc. methods, explored 1: response mode of StCAXs to cadmium stress; 2: the evolutionary characteristics and Cd ion binding sites of StCAXs; and 3: possible upstream regulatory pathways of StCAXs. The results showed that cadmium stress significantly induced the expression of StCAX1/4, and there were specific mutations in the evolution process, thus the possible main binding site of Cd ion (EDEE/DH/GxxxxxS/EEEE) was speculated. StCAX1/4 interacts with several proteins, and be regulated by transcription factors, especially the WRKY6. This synergistic regulation through WRKY6 may be an important pathway through which StCAX1/4 imparts high cadmium tolerance to potato. These results provide certain support for understanding the binding sites and specific evolutionary mechanisms of key amino acid residues of cadmium ion in StCAXs, also provide new clues for the identification and regulatory model of potato CAX key positive stress-responsive proteins under cadmium stress.
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Affiliation(s)
- Yao Liu
- College of Agricultural, Guizhou University, Guiyang 550025, PR China.
| | - Guandi He
- College of Agricultural, Guizhou University, Guiyang 550025, PR China; Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, PR China.
| | - Yeqing He
- College of Agricultural, Guizhou University, Guiyang 550025, PR China.
| | - Yueyue Tang
- College of Agricultural, Guizhou University, Guiyang 550025, PR China.
| | - Fulin Zhao
- College of Agricultural, Guizhou University, Guiyang 550025, PR China.
| | - Tengbing He
- College of Agricultural, Guizhou University, Guiyang 550025, PR China; Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, PR China; Institute of New Rural Development of Guizhou University, Guiyang 550025, PR China.
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Identification of the Major Effector StSROs in Potato: A Potential StWRKY- SRO6 Regulatory Pathway Enhances Plant Tolerance to Cadmium Stress. Int J Mol Sci 2022; 23:ijms232214318. [PMID: 36430795 PMCID: PMC9698690 DOI: 10.3390/ijms232214318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/07/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
SIMILAR TO RCD-ONE (SRO) family members and transcription factors (TFs) often improve plant antioxidant capacity through interaction and co-regulation and participate in plant resistance to drought and high-salt stress. However, whether SROs are involved in the response to heavy metal stress, especially SRO genes with a specific response and tolerance characteristics to cadmium (Cd) stress, remains unclear. We first identified six SRO genes in the potato genome by PARP and RST domains. Special and conserved StSROs were found, and the spatio temporal tissue-specific expression patterns and co-expression network diagrams of StSROs under the stress of 5 heavy metals were constructed. Second, we identified StSRO6 as a major effector gene (StSRO6-MEG) and StSRO5 as a secondary effector gene (StSRO5-SEG) through a comprehensive analysis. Interestingly, they may hold true for various physiological or stress responses in plants. In addition, using systematic genomics and comparative omics techniques, the key gene StSRO6 that affects the difference in Cd accumulation was discovered, cloned in the low-Cd accumulation "Yunshu 505", and transformed into the yeast mutant ycf1 for overexpression. The results proved that StSRO6 could confer Cd tolerance. Finally, through transient expression and in vitro culture tests, we hypothesized that StSROs 5/6 are regulated by the transcription factor StWRKY6 and mediates the reactive oxygen species (ROS) system to confer Cd tolerance. These findings offer a new perspective for understanding the mechanisms underlying Cd tolerance in plants, and simultaneously provide clues for the development of biological agents for preventing and controlling Cd migration and transformation.
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Metalloprotein-Specific or Critical Amino Acid Residues: Perspectives on Plant-Precise Detoxification and Recognition Mechanisms under Cadmium Stress. Int J Mol Sci 2022; 23:ijms23031734. [PMID: 35163656 PMCID: PMC8836122 DOI: 10.3390/ijms23031734] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 12/15/2022] Open
Abstract
Cadmium (Cd) pollution in cultivated land is caused by irresistible geological factors and human activities; intense diffusion and migration have seriously affected the safety of food crops. Plants have evolved mechanisms to control excessive influx of Cd in the environment, such as directional transport, chelation and detoxification. This is done by some specific metalloproteins, whose key amino acid motifs have been investigated by scientists one by one. The application of powerful cell biology, crystal structure science, and molecular probe targeted labeling technology has identified a series of protein families involved in the influx, transport and detoxification of the heavy metal Cd. This review summarizes them as influx proteins (NRAMP, ZIP), chelating proteins (MT, PDF), vacuolar proteins (CAX, ABCC, MTP), long-distance transport proteins (OPT, HMA) and efflux proteins (PCR, ABCG). We selected representative proteins from each family, and compared their amino acid sequence, motif structure, subcellular location, tissue specific distribution and other characteristics of differences and common points, so as to summarize the key residues of the Cd binding target. Then, we explain its special mechanism of action from the molecular structure. In conclusion, this review is expected to provide a reference for the exploration of key amino acid targets of Cd, and lay a foundation for the intelligent design and breeding of crops with high/low Cd accumulation.
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