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Khan WA, Penrose B, Yun P, Zhou M, Shabala S. Exogenous zinc application mitigates negative effects of salinity on barley ( Hordeum vulgare) growth by improving root ionic homeostasis. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23266. [PMID: 38753957 DOI: 10.1071/fp23266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024]
Abstract
Detrimental effects of salinity could be mitigated by exogenous zinc (Zn) application; however, the mechanisms underlying this amelioration are poorly understood. This study demonstrated the interaction between Zn and salinity by measuring plant biomass, photosynthetic performance, ion concentrations, ROS accumulation, antioxidant activity and electrophysiological parameters in barley (Hordeum vulgare L.). Salinity stress (200mM NaCl for 3weeks) resulted in a massive reduction in plant biomass; however, both fresh and dry weight of shoots were increased by ~30% with adequate Zn supply. Zinc supplementation also maintained K+ and Na+ homeostasis and prevented H2 O2 toxicity under salinity stress. Furthermore, exposure to 10mM H2 O2 resulted in massive K+ efflux from root epidermal cells in both the elongation and mature root zones, and pre-treating roots with Zn reduced ROS-induced K+ efflux from the roots by 3-4-fold. Similar results were observed for Ca2+ . The observed effects may be causally related to more efficient regulation of cation-permeable non-selective channels involved in the transport and sequestration of Na+ , K+ and Ca2+ in various cellular compartments and tissues. This study provides valuable insights into Zn protective functions in plants and encourages the use of Zn fertilisers in barley crops grown on salt-affected soils.
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Affiliation(s)
- Waleed Amjad Khan
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas. 7001, Australia
| | - Beth Penrose
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas. 7001, Australia
| | - Ping Yun
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas. 7001, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas. 7001, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas. 7001, Australia; and International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China; and School of Biological Science, University of Western Australia, Crawley, WA 6009, Australia
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Jiang L, Ke D, Sun B, Zhang J, Lyu S, Yu H, Chen P, Mao X, Liu Q, Chen W, Fan Z, Huang L, Yin S, Deng Y, Li C. Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process. Microbiol Spectr 2024; 12:e0333023. [PMID: 38470483 PMCID: PMC10986595 DOI: 10.1128/spectrum.03330-23] [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: 09/10/2023] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.
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Affiliation(s)
- Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Da Ke
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Shuwei Lyu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Pingli Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Li Huang
- Healthtimegene Institute, Shenzhen, China
| | - Sanjun Yin
- Healthtimegene Institute, Shenzhen, China
| | - Yizhen Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
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Khan WA, Penrose B, Shabala S, Zhang X, Cao F, Zhou M. Mapping QTL for Mineral Accumulation and Shoot Dry Biomass in Barley under Different Levels of Zinc Supply. Int J Mol Sci 2023; 24:14333. [PMID: 37762635 PMCID: PMC10532338 DOI: 10.3390/ijms241814333] [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: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Zinc (Zn) deficiency is a common limiting factor in agricultural soils, which leads to significant reduction in both the yield and nutritional quality of agricultural produce. Exploring the quantitative trait loci (QTL) for shoot and grain Zn accumulation would help to develop new barley cultivars with greater Zn accumulation efficiency. In this study, two glasshouse experiments were conducted by growing plants under adequate and low Zn supply. From the preliminary screening of ten barley cultivars, Sahara (0.05 mg/pot) and Yerong (0.06 mg/pot) showed the lowest change in shoot Zn accumulation, while Franklin (0.16 mg/pot) had the highest change due to changes in Zn supply for plant growth. Therefore, the double haploid (DH) population derived from Yerong × Franklin was selected to identify QTL for shoot mineral accumulation and biomass production. A major QTL hotspot was detected on chromosome 2H between 31.91 and 73.12 cM encoding genes for regulating shoot mineral accumulations of Zn, Fe, Ca, K and P, and the biomass. Further investigation demonstrated 16 potential candidate genes for mineral accumulation, in addition to a single candidate gene for shoot biomass in the identified QTL region. This study provides a useful resource for enhancing nutritional quality and yield potential in future barley breeding programs.
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Affiliation(s)
- Waleed Amjad Khan
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (W.A.K.); (B.P.); (S.S.)
| | - Beth Penrose
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (W.A.K.); (B.P.); (S.S.)
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (W.A.K.); (B.P.); (S.S.)
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Xueqing Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Fangbin Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (W.A.K.); (B.P.); (S.S.)
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Loitongbam B, Singh PK, Sah RP, Verma OP, Singh B, Bisen P, Kulhari S, Rathi SR, Upadhyay S, Singh NK, Sahu R, Singh RK. Identification of QTLs for zinc deficiency tolerance in a recombinant inbred population of rice (Oryza sativa L.). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:6309-6319. [PMID: 35531753 DOI: 10.1002/jsfa.11981] [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: 07/06/2021] [Revised: 04/18/2022] [Accepted: 05/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Deficiency of Zn is a major soil constraint in rice plant growth and yield. Edaphic factors such as Zn deficiency in soil in relation to plant performance are still poorly understood. Here, we report promising quantitative trait loci (QTL) conferring tolerance to Zn deficiency, which were identified through biparental mapping. The experiment was conducted using the 236 F7 recombinant inbred line mapping population derived from the cross of Kinandang Patong (Zn deficiency sensitive) and A69-1 (Zn deficiency tolerant). RESULTS A total of six QTLs (qLB-2B, qLB-4B, qPM-4B, qPM-6B, qRZC-4B, qSZC-4B) on chromosomes 2, 4 and 6 were identified for environment 1, whereas five QTLs (qLB-2 N, qLB-4 N, qPM-4 N, qRZC-4 N, qSZC-4 N) on chromosomes 2 and 4 were detected for environment 2. Among these, five major (51.30, 48.70, 28.60, 56.00, 52.00 > 10 R2 ) and one minor (5.40 < 10 R2 ) QTLs for environment 1 and four major (51.48, 50.20, 53.00, 48.00 > 10 R2 ) and one minor (4.44 < 10) QTLs for environment 2 for Zn deficiency tolerance with a logarithm of odd threshold value higher than 3 were identified. The QTLs (qLB-4B, qPM-4B, qRZC-4B, qSZC-4B, qLB-4 N, qPM-4 N, qRZC-4 N, qSZC-4 N) for leaf bronzing, plant mortality root zinc concentration and shoot zinc concentration identified on chromosome 4 were found to be the most promising and highly reproducible across the locations that explained phenotypic variation from 48.00% to 56.00% with the same marker interval RM6748-RM303. CONCLUSION The new QTLs and its linked markers identified in the present study can be utilized for Zn deficiency tolerance in elite cultivars using marker-assisted backcrossing. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Bapsila Loitongbam
- College of Agriculture, Central Agricultural University (Imphal), Pasighat, India
- Institute of Agricultural Science, Banaras Hindu University, Varanasi, India
| | - Pawan Kumar Singh
- Institute of Agricultural Science, Banaras Hindu University, Varanasi, India
| | - Rameswar Prasad Sah
- Division of Crop Improvement, ICAR-National Rice Research Institute, Cuttack, India
| | - Om Prakash Verma
- Acharya Narendra Deva University of Agriculture & Technology (NDUAT), Ayodhya, India
| | - Balwant Singh
- National Research Centre on Plant Biotechnology, New Delhi, (ICAR), New Delhi, India
| | - Prashant Bisen
- Narayan Institute of Agricultural Sciences, Gopa Narayan Singh University, Rohtas-Bihar, India
| | - Sandhya Kulhari
- Agriculture Research Station, Agriculture University, Kota, India
| | - Sanket R Rathi
- Institute of Agricultural Science, Banaras Hindu University, Varanasi, India
| | - Sameer Upadhyay
- Institute of Agricultural Science, Banaras Hindu University, Varanasi, India
| | - Nagendra Kumar Singh
- National Research Centre on Plant Biotechnology, New Delhi, (ICAR), New Delhi, India
| | - Rabin Sahu
- Division of Crop Improvement, ICAR-National Rice Research Institute, Cuttack, India
| | - Rakesh Kumar Singh
- Crop Diversification and Genetics International Center for Biosaline Agriculture, Dubai, United Arab Emirates
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Rakotondramanana M, Tanaka R, Pariasca-Tanaka J, Stangoulis J, Grenier C, Wissuwa M. Genomic prediction of zinc-biofortification potential in rice gene bank accessions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2265-2278. [PMID: 35618915 PMCID: PMC9271118 DOI: 10.1007/s00122-022-04110-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
A genomic prediction model successfully predicted grain Zn concentrations in 3000 gene bank accessions and this was verified experimentally with selected potential donors having high on-farm grain-Zn in Madagascar. Increasing zinc (Zn) concentrations in edible parts of food crops, an approach termed Zn-biofortification, is a global breeding objective to alleviate micro-nutrient malnutrition. In particular, infants in countries like Madagascar are at risk of Zn deficiency because their dominant food source, rice, contains insufficient Zn. Biofortified rice varieties with increased grain Zn concentrations would offer a solution and our objective is to explore the genotypic variation present among rice gene bank accessions and to possibly identify underlying genetic factors through genomic prediction and genome-wide association studies (GWAS). A training set of 253 rice accessions was grown at two field sites in Madagascar to determine grain Zn concentrations and grain yield. A multi-locus GWAS analysis identified eight loci. Among these, QTN_11.3 had the largest effect and a rare allele increased grain Zn concentrations by 15%. A genomic prediction model was developed from the above training set to predict Zn concentrations of 3000 sequenced rice accessions. Predicted concentrations ranged from 17.1 to 40.2 ppm with a prediction accuracy of 0.51. An independent confirmation with 61 gene bank seed samples provided high correlations (r = 0.74) between measured and predicted values. Accessions from the aus sub-species had the highest predicted grain Zn concentrations and these were confirmed in additional field experiments, with one potential donor having more than twice the grain Zn compared to a local check variety. We conclude utilizing donors from the aus sub-species and employing genomic selection during the breeding process is the most promising approach to raise grain Zn concentrations in rice.
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Affiliation(s)
- Mbolatantely Rakotondramanana
- Rice Research Department, The National Center for Applied Research on Rural Development (FOFIFA), 101, Antananarivo, Madagascar
| | - Ryokei Tanaka
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Juan Pariasca-Tanaka
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - James Stangoulis
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Cécile Grenier
- CIRAD, INRAE, Institut Agro, UMR AGAP Institut, Univ Montpellier, 34398, Montpellier, France
| | - Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.
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Hamzah Saleem M, Usman K, Rizwan M, Al Jabri H, Alsafran M. Functions and strategies for enhancing zinc availability in plants for sustainable agriculture. FRONTIERS IN PLANT SCIENCE 2022; 13:1033092. [PMID: 36275511 PMCID: PMC9586378 DOI: 10.3389/fpls.2022.1033092] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/21/2022] [Indexed: 05/13/2023]
Abstract
Zinc (Zn), which is regarded as a crucial micronutrient for plants, and is considered to be a vital micronutrient for plants. Zn has a significant role in the biochemistry and metabolism of plants owing to its significance and toxicity for biological systems at specific Zn concentrations, i.e., insufficient or harmful above the optimal range. It contributes to several cellular and physiological activities of plants and promotes plant growth, development, and yield. Zn is an important structural, enzymatic, and regulatory component of many proteins and enzymes. Consequently, it is essential to understand the interplay and chemistry of Zn in soil, its absorption, transport, and the response of plants to Zn deficiency, as well as to develop sustainable strategies for Zn deficiency in plants. Zn deficiency appears to be a widespread and prevalent issue in crops across the world, resulting in severe production losses that compromise nutritional quality. Considering this, enhancing Zn usage efficiency is the most effective strategy, which entails improving the architecture of the root system, absorption of Zn complexes by organic acids, and Zn uptake and translocation mechanisms in plants. Here, we provide an overview of various biotechnological techniques to improve Zn utilization efficiency and ensure the quality of crop. In light of the current status, an effort has been made to further dissect the absorption, transport, assimilation, function, deficiency, and toxicity symptoms caused by Zn in plants. As a result, we have described the potential information on diverse solutions, such as root structure alteration, the use of biostimulators, and nanomaterials, that may be used efficiently for Zn uptake, thereby assuring sustainable agriculture.
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Affiliation(s)
| | - Kamal Usman
- Agricultural Research Station, Office of VP for Research and Graduate Studies, Qatar University, Doha, Qatar
| | | | - Hareb Al Jabri
- Center for Sustainable Development (CSD), College of Arts and Sciences, Qatar University, Doha, Qatar
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mohammed Alsafran
- Agricultural Research Station, Office of VP for Research and Graduate Studies, Qatar University, Doha, Qatar
- Central Laboratories Unit (CLU), Office of VP for Research and Graduate Studies, Qatar University, Doha, Qatar
- *Correspondence: Mohammed Alsafran,
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Xu J, Wang X, Zhu H, Yu F. Identification and Analysis of Zinc Efficiency-Associated Loci in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:739282. [PMID: 34868123 PMCID: PMC8634756 DOI: 10.3389/fpls.2021.739282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Zinc (Zn) deficiency, a globally predominant micronutrient disorder in crops and humans, reduces crop yields and adversely impacts human health. Despite numerous studies on the physiological mechanisms underlying Zn deficiency tolerance, its genetic basis of molecular mechanism is still poorly understood. Thus, the Zn efficiency of 20 maize inbred lines was evaluated, and a quantitative trait locus (QTL) analysis was performed in the recombination inbred line population derived from the most Zn-efficient (Ye478) and Zn-inefficient inbred line (Wu312) to identify the candidate genes associated with Zn deficiency tolerance. On this basis, we analyzed the expression of ZmZIP1-ZmZIP8. Thirteen QTLs for the traits associated with Zn deficiency tolerance were detected, explaining 7.6-63.5% of the phenotypic variation. The genes responsible for Zn uptake and transport across membranes (ZmZIP3, ZmHMA3, ZmHMA4) were identified, which probably form a sophisticated network to regulate the uptake, translocation, and redistribution of Zn. Additionally, we identified the genes involved in the indole-3-acetic acid (IAA) biosynthesis (ZmIGPS) and auxin-dependent gene regulation (ZmIAA). Notably, a high upregulation of ZmZIP3 was found in the Zn-deficient root of Ye478, but not in that of Wu312. Additionally, ZmZIP4, ZmZIP5, and ZmZIP7 were up-regulated in the Zn-deficient roots of Ye478 and Wu312. Our findings provide a new insight into the genetic basis of Zn deficiency tolerance.
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Affiliation(s)
| | | | | | - Futong Yu
- Key Laboratory of Plant-Soil Interaction (MOE), Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
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Zeng H, Zhang X, Ding M, Zhu Y. Integrated analyses of miRNAome and transcriptome reveal zinc deficiency responses in rice seedlings. BMC PLANT BIOLOGY 2019; 19:585. [PMID: 31878878 PMCID: PMC6933703 DOI: 10.1186/s12870-019-2203-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/15/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Zinc (Zn) deficiency is one of the most widespread soil constraints affecting rice productivity, but the molecular mechanisms underlying the regulation of Zn deficiency response is still limited. Here, we aim to understand the molecular mechanisms of Zn deficiency response by integrating the analyses of the global miRNA and mRNA expression profiles under Zn deficiency and resupply in rice seedlings by integrating Illumina's high-throughput small RNA sequencing and transcriptome sequencing. RESULTS The transcriptome sequencing identified 360 genes that were differentially expressed in the shoots and roots of Zn-deficient rice seedlings, and 97 of them were recovered after Zn resupply. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply. The integrated analyses of miRNAome and transcriptome data showed that 12 differentially expressed genes are the potential target genes of 10 Zn-responsive miRNAs such as miR171g-5p, miR397b-5p, miR398a-5p and miR528-5p. Some miRNA genes and differentially expressed genes were selected for validation by quantitative RT-PCR, and their expressions were similar to that of the sequencing results. CONCLUSION These results provide insights into miRNA-mediated regulatory pathways in Zn deficiency response, and provide candidate genes for genetic improvement of Zn deficiency tolerance in rice.
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Affiliation(s)
- Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121 China
| | - Xin Zhang
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, 417000 China
| | - Ming Ding
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yiyong Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095 China
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Kirk GJ, Boghi A, Affholder M, Keyes SD, Heppell J, Roose T. Soil carbon dioxide venting through rice roots. PLANT, CELL & ENVIRONMENT 2019; 42:3197-3207. [PMID: 31378945 PMCID: PMC6972674 DOI: 10.1111/pce.13638] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 05/12/2023]
Abstract
The growth of rice in submerged soils depends on its ability to form continuous gas channels-aerenchyma-through which oxygen (O2 ) diffuses from the shoots to aerate the roots. Less well understood is the extent to which aerenchyma permits venting of respiratory carbon dioxide (CO2 ) in the opposite direction. Large, potentially toxic concentrations of dissolved CO2 develop in submerged rice soils. We show using X-ray computed tomography and image-based mathematical modelling that CO2 venting through rice roots is far greater than thought hitherto. We found rates of venting equivalent to a third of the daily CO2 fixation in photosynthesis. Without this venting through the roots, the concentrations of CO2 and associated bicarbonate (HCO3- ) in root cells would have been well above levels known to be toxic to roots. Removal of CO2 and hence carbonic acid (H2 CO3 ) from the soil was sufficient to increase the pH in the rhizosphere close to the roots by 0.7 units, which is sufficient to solubilize or immobilize various nutrients and toxicants. A sensitivity analysis of the model showed that such changes are expected for a wide range of plant and soil conditions.
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Affiliation(s)
- Guy J.D. Kirk
- School of Water, Energy and EnvironmentCranfield UniversityCranfieldUK
| | - Andrea Boghi
- School of Water, Energy and EnvironmentCranfield UniversityCranfieldUK
- Faculty of Engineering and EnvironmentUniversity of SouthamptonSouthamptonUK
| | | | - Samuel D. Keyes
- Faculty of Engineering and EnvironmentUniversity of SouthamptonSouthamptonUK
| | - James Heppell
- Faculty of Engineering and EnvironmentUniversity of SouthamptonSouthamptonUK
| | - Tiina Roose
- Faculty of Engineering and EnvironmentUniversity of SouthamptonSouthamptonUK
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Jabeen N, Maqbool Q, Bibi T, Nazar M, Hussain SZ, Hussain T, Jan T, Ahmad I, Maaza M, Anwaar S. Optimised synthesis of ZnO-nano-fertiliser through green chemistry: boosted growth dynamics of economically important L. esculentum. IET Nanobiotechnol 2019; 12:405-411. [PMID: 29768221 DOI: 10.1049/iet-nbt.2017.0094] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mounting-up economic losses to annual crops yield due to micronutrient deficiency, fertiliser inefficiency and increasing microbial invasions (e.g. Xanthomonas cempestri attack on tomatoes) are needed to be solved via nano-biotechnology. So keeping this in view, the authors' current study presents the new horizon in the field of nano-fertiliser with highly nutritive and preservative effect of green fabricated zinc oxide-nanostructures (ZnO-NSs) during Lycopersicum esculentum (tomato) growth dynamics. ZnO-NS prepared via green chemistry possesses highly homogenous crystalline structures well-characterised through ultraviolet and visible spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction and scanning electron microscope. The ZnO-NS average size was found as small as 18 nm having a crystallite size of 5 nm. L. esculentum were grown in different concentrations of ZnO-NS to examine the different morphological parameters includes time of seed germination, germination percentage, the number of plant leaves, the height of the plant, average number of branches, days count for flowering and fruiting time period along with fruit quantity. Promising results clearly predict that bio-fabricated ZnO-NS at optimum concentration resulted as growth booster and dramatically triggered the plant yield.
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Affiliation(s)
- Nyla Jabeen
- Applied Biotechnology and Genetic Engineering Lab, Department of Bioinformatics and Biotechnology, International Islamic University Islamabad (IIUI), Islamabad 44000, Pakistan.
| | - Qaisar Maqbool
- National Institute of Vacuum Science and Technology (NINVAST), Islamabad 44000, Pakistan
| | - Tahira Bibi
- Applied Biotechnology and Genetic Engineering Lab, Department of Bioinformatics and Biotechnology, International Islamic University Islamabad (IIUI), Islamabad 44000, Pakistan
| | - Mudassar Nazar
- National Institute of Vacuum Science and Technology (NINVAST), Islamabad 44000, Pakistan
| | - Syed Z Hussain
- Department of Biological Sciences, Quaid-i-Azam University, Islamabad 44000, Pakistan
| | - Talib Hussain
- National Institute of Vacuum Science and Technology (NINVAST), Islamabad 44000, Pakistan
| | - Tariq Jan
- Department of Applied Sciences, National Textile University (NTU), Faisalabad, Pakistan
| | - Ishaq Ahmad
- Experimental Physics Directorate (EPD), National Center for Physics, Islamabad 44000, Pakistan
| | - Malik Maaza
- UNESCO-UNISA Africa Chair in Nanosciences/Nanotechnology, College of Graduate Studies, University of South Africa, Pretoria, South Africa
| | - Sadaf Anwaar
- Applied Biotechnology and Genetic Engineering Lab, Department of Bioinformatics and Biotechnology, International Islamic University Islamabad (IIUI), Islamabad 44000, Pakistan
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Noulas C, Tziouvalekas M, Karyotis T. Zinc in soils, water and food crops. J Trace Elem Med Biol 2018; 49:252-260. [PMID: 29472130 DOI: 10.1016/j.jtemb.2018.02.009] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 12/11/2022]
Abstract
A basic knowledge of the dynamics of zinc (Zn) in soils, water and plants are important steps in achieving sustainable solutions to the problem of Zn deficiency in crops and humans. This paper aims at reviewing and discussing the relevant aspects of the role of Zn in the soil-water-plant agro biological system: from the origins of Zn in soils and water to soil Zn deficiency distribution and the factors affecting soil Zn availability to plants, therefore to elucidate the strategies potentially help combating Zn deficiency problems in soil-plant-human continuum. This necessitates identifying the main areas of Zn-deficient soils and food crops and treating them with Zn amendments, mainly fertilizers in order to increase Zn uptake and Zn use efficiency to crops. In surface and groundwater, Zn enters the environment from various sources but predominately from the erosion of soil particles containing Zn. In plants is involved in several key physiological functions (membrane structure, photosynthesis, protein synthesis, and drought and disease tolerance) and is required in small but nevertheless critical contents. Several high revenue food crops such as beans, citrus, corn, rice etc are highly susceptible to Zn deficiency and biofortification is considered as a promising method to accumulate high content of Zn especially in grains. With the world population continuing to rise and the problems of producing extra food rich in Zn to provide an adequate standard of nutrition to increase, it is very important that any losses in production easily corrected so as Zn deficiencies are prevented.
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Affiliation(s)
- Christos Noulas
- Hellenic Agricultural Organization 'DEMETER', Agricultural Research General Directorate (N.AG.RE.F.), Institute of Industrial and Forage Crops, Department of Soil and Water Resources, 1, Theophrastou Str., 41335, Larissa, Greece.
| | - Miltiadis Tziouvalekas
- Hellenic Agricultural Organization 'DEMETER', Agricultural Research General Directorate (N.AG.RE.F.), Institute of Industrial and Forage Crops, Department of Soil and Water Resources, 1, Theophrastou Str., 41335, Larissa, Greece
| | - Theodore Karyotis
- Hellenic Agricultural Organization 'DEMETER', Agricultural Research General Directorate (N.AG.RE.F.), Institute of Industrial and Forage Crops, Department of Soil and Water Resources, 1, Theophrastou Str., 41335, Larissa, Greece
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Neeraja CN, Kulkarni KS, Madhu Babu P, Sanjeeva Rao D, Surekha K, Ravindra Babu V. Transporter genes identified in landraces associated with high zinc in polished rice through panicle transcriptome for biofortification. PLoS One 2018; 13:e0192362. [PMID: 29394277 PMCID: PMC5796704 DOI: 10.1371/journal.pone.0192362] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/21/2018] [Indexed: 11/27/2022] Open
Abstract
Polished rice is poor source of micronutrients, however wide genotypic variability exists for zinc uptake and remobilization and zinc content in brown and polished grains in rice. Two landraces (Chittimutyalu and Kala Jeera Joha) and one popular improved variety (BPT 5204) were grown under zinc sufficient soil and their analyses showed high zinc in straw of improved variety, but high zinc in polished rice in landraces suggesting better translocation ability of zinc into the grain in landraces. Transcriptome analyses of the panicle tissue showed 41182 novel transcripts across three samples. Out of 1011 differentially expressed exclusive transcripts by two landraces, 311 were up regulated and 534 were down regulated. Phosphate transporter-exporter (PHO), proton-coupled peptide transporters (POT) and vacuolar iron transporter (VIT) showed enhanced and significant differential expression in landraces. Out of 24 genes subjected to quantitative real time analyses for confirmation, eight genes showed significant differential expression in landraces. Through mapping, six rice microsatellite markers spanning the genomic regions of six differentially expressed genes were validated for their association with zinc in brown and polished rice using recombinant inbred lines (RIL) of BPT 5204/Chittimutyalu. Thus, this study reports repertoire of genes associated with high zinc in polished rice and a proof concept for deployment of transcriptome information for validation in mapping population and its use in marker assisted selection for biofortification of rice with zinc.
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Affiliation(s)
- C. N. Neeraja
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
| | - Kalyani S. Kulkarni
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
| | - P. Madhu Babu
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
| | - D. Sanjeeva Rao
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
| | - K. Surekha
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
| | - V Ravindra Babu
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Rajendranagar, Telangana, Hyderabad, India
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Affholder MC, Weiss DJ, Wissuwa M, Johnson-Beebout SE, Kirk GJD. Soil CO 2 venting as one of the mechanisms for tolerance of Zn deficiency by rice in flooded soils. PLANT, CELL & ENVIRONMENT 2017; 40:3018-3030. [PMID: 28898428 DOI: 10.1111/pce.13069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/25/2017] [Indexed: 05/26/2023]
Abstract
We sought to explain rice (Oryza sativa) genotype differences in tolerance of zinc (Zn) deficiency in flooded paddy soils and the counter-intuitive observation, made in earlier field experiments, that Zn uptake per plant increases with increasing planting density. We grew tolerant and intolerant genotypes in a Zn-deficient flooded soil at high and low planting densities and found (a) plant Zn concentrations and growth increased with planting density and more so in the tolerant genotype, whereas the concentrations of other nutrients decreased, indicating a specific effect on Zn uptake; (b) the effects of planting density and genotype on Zn uptake could only be explained if the plants induced changes in the soil to make Zn more soluble; and (c) the genotype and planting density effects were both associated with decreases in dissolved CO2 in the rhizosphere soil solution and resulting increases in pH. We suggest that the increases in pH caused solubilization of soil Zn by dissolution of alkali-soluble, Zn-complexing organic ligands from soil organic matter. We conclude that differences in venting of soil CO2 through root aerenchyma were responsible for the genotype and planting density effects.
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Affiliation(s)
| | - Dominik J Weiss
- Department of Earth Science and Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Matthias Wissuwa
- Crop Production and Environment Division, Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Sarah E Johnson-Beebout
- Crop and Environmental Sciences Division, International Rice Research Institute, DAPO BOX 7777, Metro Manila, Philippines
| | - Guy J D Kirk
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
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Lee JS, Wissuwa M, Zamora OB, Ismail AM. Biochemical indicators of root damage in rice (Oryza sativa) genotypes under zinc deficiency stress. JOURNAL OF PLANT RESEARCH 2017; 130:1071-1077. [PMID: 28667406 DOI: 10.1007/s10265-017-0962-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Zn deficiency is one of the major soil constraints currently limiting rice production. Although recent studies demonstrated that higher antioxidant activity in leaf tissue effectively protects against Zn deficiency stress, little is known about whether similar tolerance mechanisms operate in root tissue. In this study we explored root-specific responses of different rice genotypes to Zn deficiency. Root solute leakage and biomass reduction, antioxidant activity, and metabolic changes were measured using plants grown in Zn-deficient soil and hydroponics. Solute leakage from roots was higher in sensitive genotypes and linked to membrane damage caused by Zn deficiency-induced oxidative stress. However, total root antioxidant activity was four-fold lower than in leaves and did not differ between sensitive and tolerant genotypes. Root metabolite analysis using gas chromatography-mass spectrometry and high performance liquid chromatography indicated that Zn deficiency triggered the accumulation of glycerol-3-phosphate and acetate in sensitive genotypes, while less or no accumulation was seen in tolerant genotypes. We suggest that these metabolites may serve as biochemical indicators of root damage under Zn deficiency.
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Affiliation(s)
- Jae-Sung Lee
- College of Agriculture, University of the Philippines Los Baños College, 4031, Laguna, Philippines
- Crop and Environmental Sciences Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.
| | - Oscar B Zamora
- College of Agriculture, University of the Philippines Los Baños College, 4031, Laguna, Philippines
| | - Abdelbagi M Ismail
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Nanda AK, Wissuwa M. Rapid Crown Root Development Confers Tolerance to Zinc Deficiency in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:428. [PMID: 27066060 PMCID: PMC4815024 DOI: 10.3389/fpls.2016.00428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/18/2016] [Indexed: 05/15/2023]
Abstract
Zinc (Zn) deficiency is one of the leading nutrient disorders in rice (Oryza sativa). Many studies have identified Zn-efficient rice genotypes, but causal mechanisms for Zn deficiency tolerance remain poorly understood. Here, we report a detailed study of the impact of Zn deficiency on crown root development of rice genotypes, differing in their tolerance to this stress. Zn deficiency delayed crown root development and plant biomass accumulation in both Zn-efficient and inefficient genotypes, with the effects being much stronger in the latter. Zn-efficient genotypes had developed new crown roots as early as 3 days after transplanting (DAT) to a Zn deficient field and that was followed by a significant increase in total biomass by 7 DAT. Zn-inefficient genotypes developed few new crown roots and did not increase biomass during the first 7 days following transplanting. This correlated with Zn-efficient genotypes retranslocating a higher proportion of shoot-Zn to their roots, compared to Zn-inefficient genotypes. These latter genotypes were furthermore not efficient in utilizing the limited Zn for root development. Histological analyses indicated no anomalies in crown tissue of Zn-efficient or inefficient genotypes that would have suggested crown root emergence was impeded. We therefore conclude that the rate of crown root initiation was differentially affected by Zn deficiency between genotypes. Rapid crown root development, following transplanting, was identified as a main causative trait for tolerance to Zn deficiency and better Zn retranslocation from shoot to root was a key attribute of Zn-efficient genotypes.
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