1
|
Yu H, Li W, Liu X, Song Q, Li J, Xu J. Physiological and molecular bases of the nickel toxicity responses in tomato. STRESS BIOLOGY 2024; 4:25. [PMID: 38722370 PMCID: PMC11082119 DOI: 10.1007/s44154-024-00162-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/15/2024] [Indexed: 05/12/2024]
Abstract
Nickel (Ni), a component of urease, is a micronutrient essential for plant growth and development, but excess Ni is toxic to plants. Tomato (Solanum lycopersicum L.) is one of the important vegetables worldwide. Excessive use of fertilizers and pesticides led to Ni contamination in agricultural soils, thus reducing yield and quality of tomatoes. However, the molecular regulatory mechanisms of Ni toxicity responses in tomato plants have largely not been elucidated. Here, we investigated the molecular mechanisms underlying the Ni toxicity response in tomato plants by physio-biochemical, transcriptomic and molecular regulatory network analyses. Ni toxicity repressed photosynthesis, induced the formation of brush-like lateral roots and interfered with micronutrient accumulation in tomato seedlings. Ni toxicity also induced reactive oxygen species accumulation and oxidative stress responses in plants. Furthermore, Ni toxicity reduced the phytohormone concentrations, including auxin, cytokinin and gibberellic acid, thereby retarding plant growth. Transcriptome analysis revealed that Ni toxicity altered the expression of genes involved in carbon/nitrogen metabolism pathways. Taken together, these results provide a theoretical basis for identifying key genes that could reduce excess Ni accumulation in tomato plants and are helpful for ensuring food safety and sustainable agricultural development.
Collapse
Affiliation(s)
- Hao Yu
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Germplasm Resources Innovation and Utilization of Vegetable and Flower, Taiyuan, 030031, China
| | - Weimin Li
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Germplasm Resources Innovation and Utilization of Vegetable and Flower, Taiyuan, 030031, China
| | - Xiaoxiao Liu
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Germplasm Resources Innovation and Utilization of Vegetable and Flower, Taiyuan, 030031, China
| | - Qianqian Song
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Germplasm Resources Innovation and Utilization of Vegetable and Flower, Taiyuan, 030031, China
| | - Junjun Li
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Germplasm Resources Innovation and Utilization of Vegetable and Flower, Taiyuan, 030031, China
| | - Jin Xu
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China.
- Shanxi Key Laboratory of Germplasm Resources Innovation and Utilization of Vegetable and Flower, Taiyuan, 030031, China.
| |
Collapse
|
2
|
Li RT, Yang YJ, Liu WJ, Liang WW, Zhang M, Dong SC, Shu YJ, Guo DL, Guo CH, Bi YD. MsNRAMP2 Enhances Tolerance to Iron Excess Stress in Nicotiana tabacum and MsMYB Binds to Its Promoter. Int J Mol Sci 2023; 24:11278. [PMID: 37511038 PMCID: PMC10379929 DOI: 10.3390/ijms241411278] [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: 05/30/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Iron(Fe) is a trace metal element necessary for plant growth, but excess iron is harmful to plants. Natural resistance-associated macrophage proteins (NRAMPs) are important for divalent metal transport in plants. In this study, we isolated the MsNRAMP2 (MN_547960) gene from alfalfa, the perennial legume forage. The expression of MsNRAMP2 is specifically induced by iron excess. Overexpression of MsNRAMP2 conferred transgenic tobacco tolerance to iron excess, while it conferred yeast sensitivity to excess iron. Together with the MsNRAMP2 gene, MsMYB (MN_547959) expression is induced by excess iron. Y1H indicated that the MsMYB protein could bind to the "CTGTTG" cis element of the MsNRAMP2 promoter. The results indicated that MsNRAMP2 has a function in iron transport and its expression might be regulated by MsMYB. The excess iron tolerance ability enhancement of MsNRAMP2 may be involved in iron transport, sequestration, or redistribution.
Collapse
Affiliation(s)
- Run-Tian Li
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Yun-Jiao Yang
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Wen-Jun Liu
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Wen-Wei Liang
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
- Institute of Crops Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Miao Zhang
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Shi-Chen Dong
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Yong-Jun Shu
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Dong-Lin Guo
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Chang-Hong Guo
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Ying-Dong Bi
- Institute of Crops Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| |
Collapse
|
3
|
Singh G, Ambreen H, Jain P, Chakraborty A, Singh B, Manivannan A, Bhatia S. Comparative transcriptomic and metabolite profiling reveals genotype-specific responses to Fe starvation in chickpea. PHYSIOLOGIA PLANTARUM 2023; 175:e13897. [PMID: 36960640 DOI: 10.1111/ppl.13897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Iron deficiency is a major nutritional stress that severely impacts crop productivity worldwide. However, molecular intricacies and subsequent physiological and metabolic changes in response to Fe starvation, especially in leguminous crops like chickpea, remain elusive. In the present study, we investigated physiological, transcriptional, and metabolic reprogramming in two chickpea genotypes (H6013 and L4958) with contrasting seed iron concentrations upon Fe deficiency. Our findings revealed that iron starvation affected growth and physiological parameters of both chickpea genotypes. Comparative transcriptome analysis led to the identification of differentially expressed genes between the genotypes related to strategy I uptake, metal ions transporters, reactive oxygen species-associated genes, transcription factors, and protein kinases that could mitigate Fe deficiency. Our gene correlation network discovered several putative candidate genes like CIPK25, CKX3, WRKY50, NAC29, MYB4, and PAP18, which could facilitate the investigation of the molecular rationale underlying Fe tolerance in chickpea. Furthermore, the metabolite analysis also illustrated the differential accumulation of organic acids, amino acids and other metabolites associated with Fe mobilization in chickpea genotypes. Overall, our study demonstrated the comparative transcriptional dynamics upon Fe starvation. The outcomes of the current endeavor will enable the development of Fe deficiency tolerant chickpea cultivars.
Collapse
Affiliation(s)
- Gourav Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Heena Ambreen
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Priyanka Jain
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Anirban Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Baljinder Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Abinaya Manivannan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| |
Collapse
|
4
|
Hua YP, Zhang YF, Zhang TY, Chen JF, Song HL, Wu PJ, Yue CP, Huang JY, Feng YN, Zhou T. Low iron ameliorates the salinity-induced growth cessation of seminal roots in wheat seedlings. PLANT, CELL & ENVIRONMENT 2023; 46:567-591. [PMID: 36358019 DOI: 10.1111/pce.14486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/21/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Wheat plants are ubiquitously simultaneously exposed to salinity and limited iron availability caused by soil saline-alkalisation. Through this study, we found that both low Fe and NaCl severely inhibited the growth of seminal roots in wheat seedlings; however, sufficient Fe caused greater growth cessation of seminal roots than low Fe under salt stress. Low Fe improved the root meristematic division activity, not altering the mature cell sizes compared with sufficient Fe under salt stress. Foliar Fe spray and split-root experiments showed that low Fe-alleviating the salinity-induced growth cessation of seminal roots was dependent on local low Fe signals in the roots. Ionomics combined with TEM/X-ray few differences in the root Na+ uptake and vacuolar Na+ sequestration between two Fe levels under salt stress. Phytohormone profiling and metabolomics revealed salinity-induced overaccumulation of ACC/ethylene and tryptophan/auxin in the roots under sufficient Fe than under low Fe. Differential gene expression, pharmacological inhibitor addition and the root growth performance of transgenic wheat plants revealed that the rootward auxin efflux and was responsible for the low Fe-mediated amelioration of the salinity-induced growth cessation of seminal roots. Our findings will provide novel insights into the modulation of crop root growth under salt stress.
Collapse
Affiliation(s)
- Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yi-Fan Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Tian-Yu Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jun-Fan Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Hai-Li Song
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Peng-Jia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Cai-Peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jin-Yong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying-Na Feng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
5
|
Xu W, Ren H, Qi X, Zhang S, Yu Z, Xie J. Conserved hierarchical gene regulatory networks for drought and cold stress response in Myrica rubra. FRONTIERS IN PLANT SCIENCE 2023; 14:1155504. [PMID: 37123838 PMCID: PMC10140524 DOI: 10.3389/fpls.2023.1155504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Stress response in plant is regulated by a large number of genes co-operating in diverse networks that serve multiple adaptive process. To understand how gene regulatory networks (GRNs) modulating abiotic stress responses, we compare the GRNs underlying drought and cold stresses using samples collected at 4 or 6 h intervals within 48 h in Chinese bayberry (Myrica rubra). We detected 7,583 and 8,840 differentially expressed genes (DEGs) under drought and cold stress respectively, which might be responsive to environmental stresses. Drought- and cold-responsive GRNs, which have been built according to the timing of transcription under both abiotic stresses, have a conserved trans-regulator and a common regulatory network. In both GRNs, basic helix-loop-helix family transcription factor (bHLH) serve as central nodes. MrbHLHp10 transcripts exhibited continuous increase in the two abiotic stresses and acts upstream regulator of ASCORBATE PEROXIDASE (APX) gene. To examine the potential biological functions of MrbHLH10, we generated a transgenic Arabidopsis plant that constitutively overexpresses the MrbHLH10 gene. Compared to wild-type (WT) plants, overexpressing transgenic Arabidopsis plants maintained higher APX activity and biomass accumulation under drought and cold stress. Consistently, RNAi plants had elevated susceptibility to both stresses. Taken together, these results suggested that MrbHLH10 mitigates abiotic stresses through the modulation of ROS scavenging.
Collapse
Affiliation(s)
- Weijie Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Haiying Ren
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Hangzhou, China
- Xianghu Lab., Hangzhou, China
- *Correspondence: Haiying Ren, ; Jianbo Xie,
| | - Xingjiang Qi
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Hangzhou, China
- Xianghu Lab., Hangzhou, China
| | - Shuwen Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Hangzhou, China
| | - Zheping Yu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Hangzhou, China
| | - Jianbo Xie
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- *Correspondence: Haiying Ren, ; Jianbo Xie,
| |
Collapse
|
6
|
Genetic dissection of grain iron and zinc, and thousand kernel weight in wheat (Triticum aestivum L.) using genome-wide association study. Sci Rep 2022; 12:12444. [PMID: 35858934 PMCID: PMC9300641 DOI: 10.1038/s41598-022-15992-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023] Open
Abstract
Genetic biofortification is recognized as a cost-effective and sustainable strategy to reduce micronutrient malnutrition. Genomic regions governing grain iron concentration (GFeC), grain zinc concentration (GZnC), and thousand kernel weight (TKW) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using 35 K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 17 Bonferroni-corrected marker-trait associations (MTAs) in nine chromosomes representing all the three wheat subgenomes. The TKW showed the highest MTAs (7), followed by GZnC (5) and GFeC (5). Furthermore, 14 MTAs were identified with more than 10% phenotypic variation. One stable MTA i.e. AX-95025823 was identified for TKW in both E4 and E5 environments along with pooled data, which is located at 68.9 Mb on 6A chromosome. In silico analysis revealed that the SNPs were located on important putative candidate genes such as Multi antimicrobial extrusion protein, F-box domain, Late embryogenesis abundant protein, LEA-18, Leucine-rich repeat domain superfamily, and C3H4 type zinc finger protein, involved in iron translocation, iron and zinc homeostasis, and grain size modifications. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection. The identified SNPs will be valuable in the rapid development of biofortified wheat varieties to ameliorate the malnutrition problems.
Collapse
|
7
|
Liang X, Li Y, Yao A, Liu W, Yang T, Zhao M, Zhang B, Han D. Overexpression of MxbHLH18 Increased Iron and High Salinity Stress Tolerance in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23148007. [PMID: 35887354 PMCID: PMC9319408 DOI: 10.3390/ijms23148007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 01/21/2023] Open
Abstract
In the life cycle of apple, it will suffer a variety of abiotic stresses, such as iron stress and salt stress. bHLH transcription factors (TFs) play an indispensable role in the response of plants to stress. In this study, a new bHLH gene named MxbHLH18 was separated from Malus xiaojinensis. According to the results of subcellular localization, MxbHLH18 was localized in the nucleus. Salt stress and iron stress affected the expression of MxbHLH18 in Malus xiaojinensis seedlings to a large extent. Due to the introduction of MxbHLH18, the resistance of Arabidopsis thaliana to salt, high iron and low iron was significantly enhanced. Under the environmental conditions of high iron and low iron, the overexpression of MxbHLH18 increased many physiological indexes of transgenic Arabidopsis compared to wild type (WT), such as root length, fresh weight and iron content. The high level expression of MxbHLH18 in transformed Arabidopsis thaliana can not only increased the content of chlorophyll and proline, as well as increasing the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT); it also reduced the content of malondialdehyde (MDA), which was more obvious under high salt conditions. In addition, the relative conductivity, H2O2 content and O2− content in transgenic Arabidopsis decreased under salt stress. Meanwhile, MxbHLH18 can also regulate the expression of downstream genes associated with salt stress (AtCBF1/2/3, AtKIN1 and AtCOR15a/b) and iron stress (AtIRT1, AtFRO2, AtNAS2, ATACT2, AtZIF1 and AtOPT3). Therefore, MxbHLH18 can actively promote the adaptability of plants to the growth environment of salt and low and/or iron.
Collapse
Affiliation(s)
- Xiaoqi Liang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions/College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.L.); (Y.L.); (A.Y.); (T.Y.); (M.Z.)
| | - Yingmei Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions/College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.L.); (Y.L.); (A.Y.); (T.Y.); (M.Z.)
| | - Anqi Yao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions/College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.L.); (Y.L.); (A.Y.); (T.Y.); (M.Z.)
| | - Wanda Liu
- Horticulture Branch of Heilongjiang Academy of Agricultural Sciences, Harbin 150040, China;
| | - Tianyu Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions/College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.L.); (Y.L.); (A.Y.); (T.Y.); (M.Z.)
| | - Mengfei Zhao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions/College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.L.); (Y.L.); (A.Y.); (T.Y.); (M.Z.)
| | - Bingxiu Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions/College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.L.); (Y.L.); (A.Y.); (T.Y.); (M.Z.)
- Correspondence: (B.Z.); (D.H.); Tel.: +86-451-55190781 (D.H.)
| | - Deguo Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions/College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.L.); (Y.L.); (A.Y.); (T.Y.); (M.Z.)
- Correspondence: (B.Z.); (D.H.); Tel.: +86-451-55190781 (D.H.)
| |
Collapse
|
8
|
Kumar J, Mishra A, Kumar A, Kaur G, Sharma H, Kaur S, Sharma S, Devi K, Garg M, Pandey AK, Bishnoi M, Pareek A, Roy J. Whole genome re-sequencing of indian wheat genotypes for identification of genomic variants for grain iron and zinc content. Mol Biol Rep 2022; 49:7123-7133. [PMID: 35717473 DOI: 10.1007/s11033-022-07593-w] [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: 10/30/2021] [Revised: 04/16/2022] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Whole-genome sequencing information which is of abundant significance for genetic evolution, and breeding of crops. Wheat (Triticum spp) is most widely grown and consumed crops globally. Micronutrients are very essential for healthy development of human being and their sufficient consumption in diet is essential for various metabolic functions. Biofortification of wheat grains with iron (Fe) and zinc (Zn) has proved the most reliable and effective way to combat micronutrient associated deficiency. Genetic variability for grain micronutrient could provide insight to dissect the traits. METHODS AND RESULTS In the current study, 1300 wheat lines were screened for grain Fe and Zn content, out of which only five important Indian wheat genotypes were selected on the basis of Fe and Zn contents. These lines were multiplied during at the National Agri-Food Biotechnology Institute (NABI) and re-sequenced to identify genomic variants in candidate genes for Fe and Zn between the genotypes. Whole genome sequencing generated ̴ 12 Gb clean data. Comparative genome analysis identified 254 genomic variants in the candidate genes associated with deleterious effect on protein function. CONCLUSIONS The present study demonstrated the fundamental in understanding the genomic variations for Fe and Zn enrichment to generate healthier wheat grains.
Collapse
Affiliation(s)
- Jitendra Kumar
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Ankita Mishra
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Ashish Kumar
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Satveer Kaur
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Shivani Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Kirti Devi
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Monika Garg
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India.
| | - Ajay K Pandey
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India. .,School of Life Sciences, Jawaharlal Nehru University, Delhi, India.
| | - Mahendra Bishnoi
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Ashwani Pareek
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Sector-81, 140306, Mohali, Punjab, India.
| |
Collapse
|
9
|
Wani SH, Gaikwad K, Razzaq A, Samantara K, Kumar M, Govindan V. Improving Zinc and Iron Biofortification in Wheat through Genomics Approaches. Mol Biol Rep 2022; 49:8007-8023. [PMID: 35661970 PMCID: PMC9165711 DOI: 10.1007/s11033-022-07326-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 02/09/2022] [Accepted: 03/02/2022] [Indexed: 11/27/2022]
Abstract
Globally, about 20% of calories (energy) come from wheat. In some countries, it is more than 70%. More than 2 billion people are at risk for zinc deficiency and even more, people are at risk of iron deficiency, nearly a quarter of all children underage group of 5 are physically and cognitively stunted, and lack of dietary zinc is a major contributing factor. Biofortified wheat with elevated levels of zinc and iron has several potential advantages as a delivery vehicle for micronutrients in the diets of resource-poor consumers who depend on cereal-based diets. The conventional breeding strategies have been successful in the introduction of novel alleles for grain Zn and Fe that led to the release of competitive Zn enriched wheat varieties in South Asia. The major challenge over the next few decades will be to maintain the rates of genetic gains for grain yield along with increased grain Zn/Fe concentration to meet the food and nutritional security challenges. Therefore, to remain competitive, the performance of Zn-enhanced lines/varieties must be equal or superior to that of current non-biofortified elite lines/varieties. Since both yield and Zn content are invisible and quantitatively inherited traits except few intermediate effect QTL regions identified for grain Zn, increased breeding efforts and new approaches are required to combine them at high frequency, ensuring that Zn levels are steadily increased to the required levels across the breeding pipelines. The current review article provides a comprehensive list of genomic regions for enhancing grain Zn and Fe concentrations in wheat including key candidate gene families such NAS, ZIP, VLT, ZIFL, and YSL. Implementing forward breeding by taking advantage of the rapid cycling trait pipeline approaches would simultaneously introgress high Zn and Fe QTL into the high Zn and normal elite lines, further increasing Zn and Fe concentrations.
Collapse
Affiliation(s)
- Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, 192102 Khudwani, J&K India
| | - Kiran Gaikwad
- ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, India
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, 38040 Faisalabad, Pakistan
| | - Kajal Samantara
- Department of Genetics and Plant Breeding, Centurion University of Technology and Management, 761211 Odisha, India
| | - Manjeet Kumar
- ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, India
| | - Velu Govindan
- Global Wheat Program International Maize and Wheat Improvement Center Texcoco Mexico, Texcoco, Mexico
| |
Collapse
|
10
|
Zhang L, He J, He H, Wu J, Li M. Genome-wide unbalanced expression bias and expression level dominance toward Brassica oleracea in artificially synthesized intergeneric hybrids of Raphanobrassica. HORTICULTURE RESEARCH 2021; 8:246. [PMID: 34848691 PMCID: PMC8633066 DOI: 10.1038/s41438-021-00672-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 05/04/2023]
Abstract
Raphanobrassica (RrRrCrCr, 2n = 4x = 36), which is generated by distant hybridization between the maternal parent Raphanus sativus (RsRs, 2n = 2x = 18) and the paternal parent Brassica oleracea (C°C°, 2n = 2x = 18), displays intermediate silique phenotypes compared to diploid progenitors. However, the hybrid shares much more similarities in silique phenotypes with those of B. oleracea than those of R. sativus. Strikingly, the silique of Raphanobrassica is obviously split into two parts. To investigate the gene expression patterns behind these phenomena, transcriptome analysis was performed on the upper, middle, and lower sections of pods (RCsiu, RCsim, and RCsil), seeds in the upper and lower sections of siliques (RCseu and RCsel) from Raphanobrassica, whole pods (Rsi and Csi) and all seeds in the siliques (Rse and Cse) from R. sativus and B. oleracea. Transcriptome shock was observed in all five aforementioned tissues of Raphanobrassica. Genome-wide unbalanced biased expression and expression level dominance were also discovered, and both of them were toward B. oleracea in Raphanobrassica, which is consistent with the observed phenotypes. The present results reveal the global gene expression patterns of different sections of siliques of Raphanobrassica, pods, and seeds of B. oleracea and R. sativus, unraveling the tight correlation between global gene expression patterns and phenotypes of the hybrid and its parents.
Collapse
Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jianjie He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongsheng He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jiangsheng Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| |
Collapse
|
11
|
Current Understanding of bHLH Transcription Factors in Plant Abiotic Stress Tolerance. Int J Mol Sci 2021; 22:ijms22094921. [PMID: 34066424 PMCID: PMC8125693 DOI: 10.3390/ijms22094921] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 01/20/2023] Open
Abstract
Named for the characteristic basic helix-loop-helix (bHLH) region in their protein structure, bHLH proteins are a widespread transcription factor class in eukaryotes. bHLHs transcriptionally regulate their target genes by binding to specific positions on their promoters and thereby direct a variety of plant developmental and metabolic processes, such as photomorphogenesis, flowering induction, shade avoidance, and secondary metabolite biosynthesis, which are important for promoting plant tolerance or adaptation to adverse environments. In this review, we discuss the vital roles of bHLHs in plant responses to abiotic stresses, such as drought, salinity, cold, and iron deficiency. We suggest directions for future studies into the roles of bHLH genes in plant and discuss their potential applications in crop breeding.
Collapse
|
12
|
Annotation and Molecular Characterisation of the TaIRO3 and TaHRZ Iron Homeostasis Genes in Bread Wheat ( Triticum aestivum L.). Genes (Basel) 2021; 12:genes12050653. [PMID: 33925484 PMCID: PMC8146704 DOI: 10.3390/genes12050653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 01/30/2023] Open
Abstract
Effective maintenance of plant iron (Fe) homoeostasis relies on a network of transcription factors (TFs) that respond to environmental conditions and regulate Fe uptake, translocation, and storage. The iron-related transcription factor 3 (IRO3), as well as haemerythrin motif-containing really interesting new gene (RING) protein and zinc finger protein (HRZ), are major regulators of Fe homeostasis in diploid species like Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L.), but remain uncharacterised in hexaploid bread wheat (Triticum aestivum L.). In this study, we have identified, annotated, and characterised three TaIRO3 homoeologs and six TaHRZ1 and TaHRZ2 homoeologs in the bread wheat genome. Protein analysis revealed that TaIRO3 and TaHRZ proteins contain functionally conserved domains for DNA-binding, dimerisation, Fe binding, or polyubiquitination, and phylogenetic analysis revealed clustering of TaIRO3 and TaHRZ proteins with other monocot IRO3 and HRZ proteins, respectively. Quantitative reverse-transcription PCR analysis revealed that all TaIRO3 and TaHRZ homoeologs have unique tissue expression profiles and are upregulated in shoot tissues in response to Fe deficiency. After 24 h of Fe deficiency, the expression of TaHRZ homoeologs was upregulated, while the expression of TaIRO3 homoeologs was unchanged, suggesting that TaHRZ functions upstream of TaIRO3 in the wheat Fe homeostasis TF network.
Collapse
|