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Kaur S, Seem K, Duhan N, Kumar S, Kaundal R, Mohapatra T. Comparative miRNome and transcriptome analyses reveal the expression of novel miRNAs in the panicle of rice implicated in sustained agronomic performance under terminal drought stress. PLANTA 2024; 259:128. [PMID: 38639776 DOI: 10.1007/s00425-024-04399-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024]
Abstract
MAIN CONCLUSION Differential expression of 128 known and 111 novel miRNAs in the panicle of Nagina 22 under terminal drought stress targeting transcription factors, stress-associated genes, etc., enhances drought tolerance and helps sustain agronomic performance under terminal drought stress. Drought tolerance is a complex multigenic trait, wherein the genes are fine-tuned by coding and non-coding components in mitigating deleterious effects. MicroRNA (miRNA) controls gene expression at post-transcriptional level either by cleaving mRNA (transcript) or by suppressing its translation. miRNAs are known to control developmental processes and abiotic stress tolerance in plants. To identify terminal drought-responsive novel miRNA in contrasting rice cultivars, we constructed small RNA (sRNA) libraries from immature panicles of drought-tolerant rice [Nagina 22 (N 22)] and drought-sensitive (IR 64) cultivars grown under control and terminal drought stress. Our analysis of sRNA-seq data resulted in the identification of 169 known and 148 novel miRNAs in the rice cultivars. Among the novel miRNAs, 68 were up-regulated while 43 were down-regulated in the panicle of N 22 under stress. Interestingly, 31 novel miRNAs up-regulated in N 22 were down-regulated in IR 64, whereas 4 miRNAs down-regulated in N 22 were up-regulated in IR 64 under stress. To detect the effects of miRNA on mRNA expression level, transcriptome analysis was performed, while differential expression of miRNAs and their target genes was validated by RT-qPCR. Targets of the differentially expressed miRNAs include transcription factors and stress-associated genes involved in cellular/metabolic/developmental processes, response to abiotic stress, programmed cell death, photosynthesis, panicle/seed development, and grain yield. Differential expression of the miRNAs could be validated in an independent set of the samples. The findings might be useful in genetic improvement of drought-tolerant rice.
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Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
- ICAR-Research Complex for North Eastern Hill Region (NEH), Umiam, Meghalaya, 793103, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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Singh P, Sundaram KT, Vinukonda VP, Venkateshwarlu C, Paul PJ, Pahi B, Gurjar A, Singh UM, Kalia S, Kumar A, Singh VK, Sinha P. Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties. Commun Biol 2024; 7:89. [PMID: 38216712 PMCID: PMC10786901 DOI: 10.1038/s42003-024-05769-7] [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: 03/24/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Abstract
Haplotype-based breeding is an emerging and innovative concept that enables the development of designer crop varieties by exploiting and exploring superior alleles/haplotypes among target genes to create new traits in breeding programs. In this regard, whole-genome re-sequencing of 399 genotypes (landraces and breeding lines) from the 3000 rice genomes panel (3K-RG) is mined to identify the superior haplotypes for 95 drought-responsive candidate genes. Candidate gene-based association analysis reveals 69 marker-trait associations (MTAs) in 16 genes for single plant yield (SPY) under drought stress. Haplo-pheno analysis of these 16 genes identifies superior haplotypes for seven genes associated with the higher SPY under drought stress. Our study reveals that the performance of lines possessing superior haplotypes is significantly higher (p ≤ 0.05) as measured by single plant yield (SPY), for the OsGSK1-H4, OsDSR2-H3, OsDIL1-H22, OsDREB1C-H3, ASR3-H88, DSM3-H4 and ZFP182-H4 genes as compared to lines without the superior haplotypes. The validation results indicate that a superior haplotype for the DREB transcription factor (OsDREB1C) is present in all the drought-tolerant rice varieties, while it was notably absent in all susceptible varieties. These lines carrying the superior haplotypes can be used as potential donors in haplotype-based breeding to develop high-yielding drought-tolerant rice varieties.
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Affiliation(s)
- Preeti Singh
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | - Krishna T Sundaram
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | | | | | - Pronob J Paul
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | - Bandana Pahi
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | - Anoop Gurjar
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Uma Maheshwar Singh
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Sanjay Kalia
- Department of Biotechnology, CGO Complex, Lodhi Road, New Delhi, India
| | - Arvind Kumar
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India.
| | - Pallavi Sinha
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India.
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3
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Dwivedi AK, Singh V, Anwar K, Pareek A, Jain M. Integrated transcriptome, proteome and metabolome analyses revealed secondary metabolites and auxiliary carbohydrate metabolism augmenting drought tolerance in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107849. [PMID: 37393858 DOI: 10.1016/j.plaphy.2023.107849] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/01/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023]
Abstract
Drought is one of the major consequences of climate change and a serious threat to rice production. Drought stress activates interactions among genes, proteins and metabolites at the molecular level. A comparative multi-omics analysis of drought-tolerant and drought-sensitive rice cultivars can decipher the molecular mechanisms involved in drought tolerance/response. Here, we characterized the global-level transcriptome, proteome, and metabolome profiles, and performed integrated analyses thereof in a drought-sensitive (IR64) and a drought-tolerant (Nagina 22) rice cultivar under control and drought-stress conditions. The transcriptional dynamics and its integration with proteome analysis revealed the role of transporters in regulation of drought stress. The proteome response illustrated the contribution of translational machinery to drought tolerance in N22. The metabolite profiling revealed that aromatic amino acids and soluble sugars contribute majorly to drought tolerance in rice. The integrated transcriptome, proteome and metabolome analysis performed using statistical and knowledge-based methods revealed the preference for auxiliary carbohydrate metabolism through glycolysis and pentose phosphate pathway contributed to drought tolerance in N22. In addition, L-phenylalanine and the genes/proteins responsible for its biosynthesis were also found to contribute to drought tolerance in N22. In conclusion, our study provided mechanistic insights into the drought response/adaptation mechanism and is expected to facilitate engineering of drought tolerance in rice.
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Affiliation(s)
- Anuj Kumar Dwivedi
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Vikram Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Khalid Anwar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Ashwani Pareek
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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4
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Usman B, Derakhshani B, Jung KH. Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2019. [PMID: 37653936 PMCID: PMC10221523 DOI: 10.3390/plants12102019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.
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Affiliation(s)
- Babar Usman
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Behnam Derakhshani
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Ki-Hong Jung
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
- Research Center for Plant Plasticity, Kyung Hee University, Yongin 17104, Republic of Korea
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5
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Rahimi Y, Khahani B, Jamali A, Alipour H, Bihamta MR, Ingvarsson PK. Genome-wide association study to identify genomic loci associated with early vigor in bread wheat under simulated water deficit complemented with quantitative trait loci meta-analysis. G3 (BETHESDA, MD.) 2023; 13:jkac320. [PMID: 36458966 PMCID: PMC10248217 DOI: 10.1093/g3journal/jkac320] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022]
Abstract
A genome-wide association study (GWAS) was used to identify associated loci with early vigor under simulated water deficit and grain yield under field drought in a diverse collection of Iranian bread wheat landraces. In addition, a meta-quantitative trait loci (MQTL) analysis was used to further expand our approach by retrieving already published quantitative trait loci (QTL) from recombinant inbred lines, double haploids, back-crosses, and F2 mapping populations. In the current study, around 16%, 14%, and 16% of SNPs were in significant linkage disequilibrium (LD) in the A, B, and D genomes, respectively, and varied between 5.44% (4A) and 21.85% (6A). Three main subgroups were identified among the landraces with different degrees of admixture, and population structure was further explored through principal component analysis. Our GWAS identified 54 marker-trait associations (MTAs) that were located across the wheat genome but with the highest number found in the B sub-genome. The gene ontology (GO) analysis of MTAs revealed that around 75% were located within or closed to protein-coding genes. In the MQTL analysis, 23 MQTLs, from a total of 215 QTLs, were identified and successfully projected onto the reference map. MQT-YLD4, MQT-YLD9, MQT-YLD13, MQT-YLD17, MQT-YLD18, MQT-YLD19, and MQTL-RL1 contributed to the highest number of projected QTLs and were therefore regarded as the most reliable and stable QTLs under water deficit conditions. These MQTLs greatly facilitate the identification of putative candidate genes underlying at each MQTL interval due to the reduced confidence of intervals associated with MQTLs. These findings provide important information on the genetic basis of early vigor traits and grain yield under water deficit conditions and set the foundation for future investigations into adaptation to water deficit in bread wheat.
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Affiliation(s)
- Yousef Rahimi
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Bahman Khahani
- Department of Plant Genetics and Production, College of Agriculture, Shiraz University, 71441-65186 Shiraz, Iran
| | - Ali Jamali
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, 31587-77871 Karaj, Iran
| | - Hadi Alipour
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, 5756151818 Urmia, Iran
| | - Mohammad Reza Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, 31587-77871 Karaj, Iran
| | - Pär K Ingvarsson
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
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Phillippy BQ, Donahue JL, Williams SP, Cridland CA, Perera IY, Gillaspy GE. Regulation of inositol 1,2,4,5,6-pentakisphosphate and inositol hexakisphosphate levels in Gossypium hirsutum by IPK1. PLANTA 2023; 257:46. [PMID: 36695941 DOI: 10.1007/s00425-023-04080-9] [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: 12/30/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
The IPK1 genes, which code for 2-kinases that can synthesize Ins(1,2,4,5,6)P5 from Ins(1,4,5,6)P4, are expressed throughout cotton plants, resulting in the highest Ins(1,2,4,5,6)P5 concentrations in young leaves and flower buds. Cotton leaves contain large amounts of Ins(1,2,4,5,6)P5 and InsP6 compared to plants not in the Malvaceae family. The inositol polyphosphate pathway has been linked to stress tolerance in numerous plant species. Accordingly, we sought to determine why cotton and other Malvaceae have such high levels of these inositol phosphates. We have quantified the levels of InsP5 and InsP6 in different tissues of cotton plants and determined the expression of IPK1 (inositol 1,3,4,5,6-pentakisphosphate 2-kinase gene) in vegetative and reproductive tissues. Gossypium hirsutum was found to contain four IPK1 genes that were grouped into two pair (AB, CD) where each pair consists of very similar sequences that were measured together. More IPK1AB is expressed in leaves than in roots, whereas more IPK1CD is expressed in roots than in leaves. Leaves and flower buds have more InsP5 and InsP6 than stems and roots. Leaves and roots contain more InsP5 than InsP6, whereas flower buds and stems contain more InsP6 than InsP5. Dark-grown seedlings contain more InsP5 and InsP6 than those grown under lights, and the ratio of InsP5 to InsP6 is greater in the light-grown seedlings. During 35 days of the life cycle of the third true leaf, InsP5 and InsP6 gradually decreased by more than 50%. Silencing IPK1AB and IPK1CD with Cotton Leaf Crumple Virus-induced gene silencing (VIGS) resulted in plants with an intense viral phenotype, reduced IPK1AB expression and lowered amounts of InsP5. The results are consistent with Ins(1,2,4,5,6)P5 synthesis from Ins(1,4,5,6)P4 by IPK1. This study detailed the central role of IPK1 in cotton inositol polyphosphate metabolism, which has potential to be harnessed to improve the resistance of plants to different kinds of stress.
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Affiliation(s)
- Brian Q Phillippy
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
| | - Janet L Donahue
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Sarah P Williams
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
- Department of Biology, College of William and Mary, Williamsburg, VA, USA
| | | | - Imara Y Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
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7
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Ju C, Ma X, Han B, Zhang W, Zhao Z, Geng L, Cui D, Han L. Candidate gene discovery for salt tolerance in rice ( Oryza sativa L.) at the germination stage based on genome-wide association study. FRONTIERS IN PLANT SCIENCE 2022; 13:1010654. [PMID: 36388603 PMCID: PMC9664195 DOI: 10.3389/fpls.2022.1010654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Salt stress affects rice seed germination and seedling formation, seriously restricting rice production. Screening salt-tolerant rice varieties and analyzing the genetic mechanisms underlying salt tolerance are therefore very important to ensure rice production. In this study, 313 Oryza sativa ssp. japonica germplasm were used to conduct a genome-wide association study (GWAS) using 1% NaCl as a salt stress treatment during germination stage. The germination potential (GP) on different days and the germination index (GI) under salt stress were used as salt tolerance indicators. The results of population structure analysis showed that the 313 germplasm studied could be divided into two subpopulations, consistent with the geographical origins of the materials. There were 52 loci significantly related to salt tolerance during germination, and the phenotypic contribution rate of 29 loci was > 10%. A region on chromosome 11 (17049672-17249672 bp) was repeatedly located, and the candidate gene LOC_Os11g29490, which encodes a plasma membrane ATPase, was identified in this locus. Further haplotype analysis showed the GP of germplasm with different haplotypes at that locus significantly differed under salt stress (p < 0.05), and germplasm carrying Hap2 displayed strong salt tolerance during the germination stage. Two other promising candidate genes for salt tolerance were identified: LOC_Os01g27170 (OsHAK3), which encodes a potassium transporter, and LOC_Os10g42550 (OsITPK5), which encodes an inositol 1, 3, 4-trisphosphate 5/6-kinase. The results of this study provide a theoretical basis for salt-tolerant gene cloning and molecular design breeding in rice.
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Affiliation(s)
- Chunyan Ju
- Chongqing Engineering Research Center of Specialty Crop Resources, College of Life Sciences, Chongqing Normal University, Chongqing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Zhang
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Tangshan, China
- Tangshan Key Laboratory of Rice Breeding, Tangshan, China
| | - Zhengwu Zhao
- Chongqing Engineering Research Center of Specialty Crop Resources, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Leiyue Geng
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Tangshan, China
- Tangshan Key Laboratory of Rice Breeding, Tangshan, China
| | - Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Ortiz D, Salas-Fernandez MG. Dissecting the genetic control of natural variation in sorghum photosynthetic response to drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3251-3267. [PMID: 34791180 PMCID: PMC9126735 DOI: 10.1093/jxb/erab502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Drought stress causes crop yield losses worldwide. Sorghum is a C4 species tolerant to moderate drought stress, and its extensive natural variation for photosynthetic traits under water-limiting conditions can be exploited for developing cultivars with enhanced stress tolerance. The objective of this study was to discover genes/genomic regions that control the sorghum photosynthetic capacity under pre-anthesis water-limiting conditions. We performed a genome-wide association study for seven photosynthetic gas exchange and chlorophyll fluorescence traits during three periods of contrasting soil volumetric water content (VWC): control (30% VWC), drought (15% VWC), and recovery (30% VWC). Water stress was imposed with an automated irrigation system that generated a controlled dry-down period for all plants, to perform an unbiased genotypic comparison. A total of 60 genomic regions were associated with natural variation in one or more photosynthetic traits in a particular treatment or with derived variables. We identified 33 promising candidate genes with predicted functions related to stress signaling, oxidative stress protection, hormonal response to stress, and dehydration protection. Our results provide new knowledge about the natural variation and genetic control of sorghum photosynthetic response to drought with the ultimate goal of improving its adaptation and productivity under water stress scenarios.
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Affiliation(s)
- Diego Ortiz
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
- Instituto Nacional de Tecnologia Agropecuaria, Manfredi, Cordoba 5988, Argentina
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Wang X, Li J, Sun J, Gu S, Wang J, Su C, Li Y, Ma D, Zhao M, Chen W. Mining Beneficial Genes for Salt Tolerance From a Core Collection of Rice Landraces at the Seedling Stage Through Genome-Wide Association Mapping. FRONTIERS IN PLANT SCIENCE 2022; 13:847863. [PMID: 35557725 PMCID: PMC9087808 DOI: 10.3389/fpls.2022.847863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Rice is a salt-sensitive plant. High concentration of salt will hinder the absorption of water and nutrients and ultimately affect the yield. In this study, eight seedling-stage salt-related traits within a core collection of rice landraces were evaluated under salinity stress (100 mM NaCl) and normal conditions in a growth chamber. Genome-wide association study (GWAS) was performed with the genotypic data including 2,487,353 single-nucleotide polymorphisms (SNPs) detected in the core collection. A total of 65 QTLs significantly associated with salt tolerance (ST) were identified by GWAS. Among them, a co-localization QTL qTL4 associated with the SKC, RN/K, and SNC on chromosome 6, which explained 14.38-17.94% of phenotypic variation, was selected for further analysis. According to haplotype analysis, qRT-PCR analysis, and sequence alignment, it was finally determined that 4 candidate genes (LOC_Os06g47720, LOC_Os06g47820, LOC_Os06g47850, LOC_Os06g47970) were related to ST. The results provide useful candidate genes for marker assisted selection for ST in the rice molecular breeding programs.
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Affiliation(s)
- Xiaoliang Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Jinquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Strube Research GmbH & Co. KG, Söllingen, Germany
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Shuang Gu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Jingbo Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Chang Su
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Yueting Li
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Minghui Zhao
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wenfu Chen
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
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10
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Zeng Z, Zhang S, Li W, Chen B, Li W. Gene-coexpression network analysis identifies specific modules and hub genes related to cold stress in rice. BMC Genomics 2022; 23:251. [PMID: 35365095 PMCID: PMC8974213 DOI: 10.1186/s12864-022-08438-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 03/03/2022] [Indexed: 11/25/2022] Open
Abstract
Background When plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury. Indica cultivars can usually withstand only mild cold stress in a relatively short period. Hormone-mediated defence response plays an important role in cold stress. Weighted gene co-expression network analysis (WGCNA) is a very useful tool for studying the correlation between genes, identifying modules with high phenotype correlation, and identifying Hub genes in different modules. Many studies have elucidated the molecular mechanisms of cold tolerance in different plants, but little information about the recovery process after cold stress is available. Results To understand the molecular mechanism of cold tolerance in rice, we performed comprehensive transcriptome analyses during cold treatment and recovery stage in two cultivars of near-isogenic lines (9311 and DC907). Twelve transcriptomes in two rice cultivars were determined. A total of 2509 new genes were predicted by fragment splicing and assembly, and 7506 differentially expressed genes were identified by pairwise comparison. A total of 26 modules were obtained by expression-network analysis, 12 of which were highly correlated with cold stress or recovery treatment. We further identified candidate Hub genes associated with specific modules and analysed their regulatory relationships based on coexpression data. Results showed that various plant-hormone regulatory genes acted together to protect plants from physiological damage under short-term low-temperature stress. We speculated that this may be common in rice. Under long-term cold stress, rice improved the tolerance to low-temperature stress by promoting autophagy, sugar synthesis, and metabolism. Conclusion Through WGCNA analysis at the transcriptome level, we provided a potential regulatory mechanism for the cold stress and recovery of rice cultivars and identified candidate central genes. Our findings provided an important reference for the future cultivation of rice strains with good tolerance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08438-3.
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Affiliation(s)
- Zhichi Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Life Science and Technology, Guangxi University, Nanning, China
| | - Sichen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Life Science and Technology, Guangxi University, Nanning, China
| | - Wenyan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,College of Life Science and Technology, Guangxi University, Nanning, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China. .,College of Agriculture, Guangxi University, Nanning, China.
| | - Wenlan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China. .,College of Life Science and Technology, Guangxi University, Nanning, China.
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11
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Cross A, Li JB, Waugh R, Golicz AA, Pourkheirandish M. Grain dispersal mechanism in cereals arose from a genome duplication followed by changes in spatial expression of genes involved in pollen development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1263-1277. [PMID: 35192007 PMCID: PMC9033732 DOI: 10.1007/s00122-022-04029-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/04/2022] [Indexed: 05/31/2023]
Abstract
Grain disarticulation in wild progenitor of wheat and barley evolved through a local duplication event followed by neo-functionalization resulting from changes in location of gene expression. One of the most critical events in the process of cereal domestication was the loss of the natural mode of grain dispersal. Grain dispersal in barley is controlled by two major genes, Btr1 and Btr2, which affect the thickness of cell walls around the disarticulation zone. The barley genome also encodes Btr1-like and Btr2-like genes, which have been shown to be the ancestral copies. While Btr and Btr-like genes are non-redundant, the biological function of Btr-like genes is unknown. We explored the potential biological role of the Btr-like genes by surveying their expression profile across 212 publicly available transcriptome datasets representing diverse organs, developmental stages and stress conditions. We found that Btr1-like and Btr2-like are expressed exclusively in immature anther samples throughout Prophase I of meiosis within the meiocyte. The similar and restricted expression profile of these two genes suggests they are involved in a common biological function. Further analysis revealed 141 genes co-expressed with Btr1-like and 122 genes co-expressed with Btr2-like, with 105 genes in common, supporting Btr-like genes involvement in a shared molecular pathway. We hypothesize that the Btr-like genes play a crucial role in pollen development by facilitating the formation of the callose wall around the meiocyte or in the secretion of callase by the tapetum. Our data suggest that Btr genes retained an ancestral function in cell wall modification and gained a new role in grain dispersal due to changes in their spatial expression becoming spike specific after gene duplication.
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Affiliation(s)
- Arthur Cross
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia
| | - John B Li
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia
| | - Robbie Waugh
- Division of Plant Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Agnieszka A Golicz
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia.
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Gießen, Gießen, Germany.
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12
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Islam MR, Naveed SA, Zhang Y, Li Z, Zhao X, Fiaz S, Zhang F, Wu Z, Hu Z, Fu B, Shi Y, Shah SM, Xu J, Wang W. Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses. Front Genet 2022; 13:822516. [PMID: 35281797 PMCID: PMC8905349 DOI: 10.3389/fgene.2022.822516] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/03/2022] [Indexed: 11/29/2022] Open
Abstract
Multiple stress tolerance at the seed germination stage is crucial for better crop establishment in the direct-seeded rice ecosystem. Therefore, identifying rice genes/quantitative trait loci (QTLs) associated with salinity and anaerobic tolerance at the germination stage is a prerequisite for adaptive breeding. Here, we studied 498 highly diverse rice accessions Xian (Indica) and Geng (Japonica), and six traits that are highly associated with salinity and anaerobic tolerance at germination stage were measured. A high-density 2.8M Single Nucleotide Polymorphisms (SNP) genotype map generated from the 3,000 Rice Genomes Project (3KRGP) was used for mapping through a genome-wide association study. In total, 99 loci harboring 117 QTLs were detected in different populations, 54, 21, and 42 of which were associated with anaerobic, salinity, and combined (anaerobic and salinity) stress tolerance. Nineteen QTLs were close to the reported loci for abiotic stress tolerance, whereas two regions on chromosome 4 (qSGr4a/qCL4c/qRI4d and qAGr4/qSGr4b) and one region on chromosome 10 (qRI10/qCL10/ qSGr10b/qBM10) were associated with anaerobic and salinity related traits. Further haplotype analysis detected 25 promising candidates genes significantly associated with the target traits. Two known genes (OsMT2B and OsTPP7) significantly associated with grain yield and its related traits under saline and anaerobic stress conditions were identified. In this study, we identified the genes involved in auxin efflux (Os09g0491740) and transportation (Os01g0976100), whereas we identified multistress responses gene OsMT2B (Os01g0974200) and a major gene OsTPP7 (Os09g0369400) involved in anaerobic germination and coleoptile elongation on chromosome 9. These promising candidates provide valuable resources for validating potential salt and anaerobic tolerance genes and will facilitate direct-seeded rice breeding for salt and anaerobic tolerance through marker-assisted selection or gene editing.
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Affiliation(s)
- Mohammad Rafiqul Islam
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shahzad Amir Naveed
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Anhui Agricultural University, Hefei, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Zhichao Wu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqing Hu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Shahid Masood Shah
- Department of Biotechnology, COMSATS University Islamabad-Abbottabad Campus, Abbottabad, Pakistan
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Anhui Agricultural University, Hefei, China.,National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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13
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Shukla A, Kaur M, Kanwar S, Kaur G, Sharma S, Ganguli S, Kumari V, Mazumder K, Pandey P, Rouached H, Rishi V, Bhandari R, Pandey AK. Wheat inositol pyrophosphate kinase TaVIH2-3B modulates cell-wall composition and drought tolerance in Arabidopsis. BMC Biol 2021; 19:261. [PMID: 34895221 PMCID: PMC8665518 DOI: 10.1186/s12915-021-01198-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/22/2021] [Indexed: 02/08/2023] Open
Abstract
Background Inositol pyrophosphates (PP-InsPs) are high-energy derivatives of inositol, involved in different signalling and regulatory responses of eukaryotic cells. Distinct PP-InsPs species are characterized by the presence of phosphate at a variable number of the 6-carbon inositol ring backbone, and two distinct classes of inositol phosphate kinases responsible for their synthesis have been identified in Arabidopsis, namely ITPKinase (inositol 1,3,4 trisphosphate 5/6 kinase) and PP-IP5Kinase (diphosphoinositol pentakisphosphate kinases). Plant PP-IP5Ks are capable of synthesizing InsP8 and were previously shown to control defense against pathogens and phosphate response signals. However, other potential roles of plant PP-IP5Ks, especially towards abiotic stress, remain poorly understood. Results Here, we characterized the physiological functions of two Triticum aestivum L. (hexaploid wheat) PPIP5K homologs, TaVIH1 and TaVIH2. We demonstrate that wheat VIH proteins can utilize InsP7 as the substrate to produce InsP8, a process that requires the functional VIH-kinase domains. At the transcriptional level, both TaVIH1 and TaVIH2 are expressed in different wheat tissues, including developing grains, but show selective response to abiotic stresses during drought-mimic experiments. Ectopic overexpression of TaVIH2-3B in Arabidopsis confers tolerance to drought stress and rescues the sensitivity of Atvih2 mutants. RNAseq analysis of TaVIH2-3B-expressing transgenic lines of Arabidopsis shows genome-wide reprogramming with remarkable effects on genes involved in cell-wall biosynthesis, which is supported by the observation of enhanced accumulation of polysaccharides (arabinogalactan, cellulose, and arabinoxylan) in the transgenic plants. Conclusions Overall, this work identifies a novel function of VIH proteins, implicating them in modulation of the expression of cell-wall homeostasis genes, and tolerance to water-deficit stress. This work suggests that plant VIH enzymes may be linked to drought tolerance and opens up the possibility of future research into using plant VIH-derived products to generate drought-resistant plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01198-8.
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Affiliation(s)
- Anuj Shukla
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, S.A.S. Nagar, Mohali-140306, Punjab, India.,Regional Centre for Biotechnology, Faridabad - 121001 Haryana (NCR), Delhi, India
| | - Mandeep Kaur
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, S.A.S. Nagar, Mohali-140306, Punjab, India
| | - Swati Kanwar
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, S.A.S. Nagar, Mohali-140306, Punjab, India
| | - Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, S.A.S. Nagar, Mohali-140306, Punjab, India
| | - Shivani Sharma
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, S.A.S. Nagar, Mohali-140306, Punjab, India
| | - Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Vandana Kumari
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, S.A.S. Nagar, Mohali-140306, Punjab, India
| | - Koushik Mazumder
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, S.A.S. Nagar, Mohali-140306, Punjab, India
| | - Pratima Pandey
- Department of Biological Sciences, Indian Institute of Education and Research, Mohali, 140306, India
| | - Hatem Rouached
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.,Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Vikas Rishi
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, S.A.S. Nagar, Mohali-140306, Punjab, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Ajay Kumar Pandey
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, S.A.S. Nagar, Mohali-140306, Punjab, India.
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14
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Sonsungsan P, Chantanakool P, Suratanee A, Buaboocha T, Comai L, Chadchawan S, Plaimas K. Identification of Key Genes in 'Luang Pratahn', Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks. FRONTIERS IN PLANT SCIENCE 2021; 12:744654. [PMID: 34925399 PMCID: PMC8675607 DOI: 10.3389/fpls.2021.744654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/01/2021] [Indexed: 05/13/2023]
Abstract
Salinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critical genes. The transcriptomes of 'Luang Pratahn' rice, a local Thai rice variety with high salt tolerance, were used as a model for analyzing and identifying the key genes responsible for salt-stress tolerance. Based on 3' Tag-Seq data from the time course of salt-stress treatment, weighted gene co-expression network analysis was used to identify key genes in gene modules. We obtained 1,386 significantly differentially expressed genes in eight modules. Among them, six modules indicated a significant correlation within 6, 12, or 48h after salt stress. Functional and pathway enrichment analysis was performed on the co-expressed genes of interesting modules to reveal which genes were mainly enriched within important functions for salt-stress responses. To identify the key genes in salt-stress responses, we considered the two-state co-expression networks, normal growth conditions, and salt stress to investigate which genes were less important in a normal situation but gained more impact under stress. We identified key genes for the response to biotic and abiotic stimuli and tolerance to salt stress. Thus, these novel genes may play important roles in salinity tolerance and serve as potential biomarkers to improve salt tolerance cultivars.
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Affiliation(s)
- Pajaree Sonsungsan
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Pheerawat Chantanakool
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok, Thailand
| | - Teerapong Buaboocha
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Luca Comai
- Department of Plant Biology, College of Biological Sciences, College of Biological Sciences, University of California, Davis, Davis, CA, United States
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kitiporn Plaimas
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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15
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Jiang Z, Tu H, Bai B, Yang C, Zhao B, Guo Z, Liu Q, Zhao H, Yang W, Xiong L, Zhang J. Combining UAV-RGB high-throughput field phenotyping and genome-wide association study to reveal genetic variation of rice germplasms in dynamic response to drought stress. THE NEW PHYTOLOGIST 2021; 232:440-455. [PMID: 34165797 DOI: 10.1111/nph.17580] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/17/2021] [Indexed: 05/24/2023]
Abstract
Accurate and high-throughput phenotyping of the dynamic response of a large rice population to drought stress in the field is a bottleneck for genetic dissection and breeding of drought resistance. Here, high-efficiency and high-frequent image acquisition by an unmanned aerial vehicle (UAV) was utilized to quantify the dynamic drought response of a rice population under field conditions. Deep convolutional neural networks (DCNNs) and canopy height models were applied to extract highly correlated phenotypic traits including UAV-based leaf-rolling score (LRS_uav), plant water content (PWC_uav) and a new composite trait, drought resistance index by UAV (DRI_uav). The DCNNs achieved high accuracy (correlation coefficient R = 0.84 for modeling set and R = 0.86 for test set) to replace manual leaf-rolling rating. PWC_uav values were precisely estimated (correlation coefficient R = 0.88) and DRI_uav was modeled to monitor the drought resistance of rice accessions dynamically and comprehensively. A total of 111 significantly associated loci were detected by genome-wide association study for the three dynamic traits, and 30.6% of them were not detected in previous mapping studies using nondynamic drought response traits. Unmanned aerial vehicle and deep learning are confirmed effective phenotyping techniques for more complete genetic dissection of rice dynamic responses to drought and exploration of valuable alleles for drought resistance improvement.
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Affiliation(s)
- Zhao Jiang
- Macro Agriculture Research Institute, College of Resource and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Baowei Bai
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chenghai Yang
- Aerial Application Technology Research Unit, USDA-Agricultural Research Service, College Station, TX, 77845, USA
| | - Biquan Zhao
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, 68583-0988, USA
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68583-0726, USA
| | - Ziyue Guo
- Macro Agriculture Research Institute, College of Resource and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qian Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Zhang
- Macro Agriculture Research Institute, College of Resource and Environment, Huazhong Agricultural University, Wuhan, 430070, China
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16
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Silva VM, Putti FF, White PJ, Reis ARD. Phytic acid accumulation in plants: Biosynthesis pathway regulation and role in human diet. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 164:132-146. [PMID: 33991859 DOI: 10.1016/j.plaphy.2021.04.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Phytate or phytic acid (PA), is a phosphorus (P) containing compound generated by the stepwise phosphorylation of myo-inositol. It forms complexes with some nutrient cations, such as Ca, Fe and Zn, compromising their absorption and thus acting as an anti-nutrient in the digestive tract of humans and monogastric animals. Conversely, PAs are an important form of P storage in seeds, making up to 90% of total seed P. Phytates also play a role in germination and are related to the synthesis of abscisic acid and gibberellins, the hormones involved in seed germination. Decreasing PA content in plants is desirable for human dietary. Therefore, low phytic acid (lpa) mutants might present some negative pleiotropic effects, which could impair germination and seed viability. In the present study, we review current knowledge of the genes encoding enzymes that function in different stages of PA synthesis, from the first phosphorylation of myo-inositol to PA transport into seed reserve tissues, and the application of this knowledge to reduce PA concentrations in edible crops to enhance human diet. Finally, phylogenetic data for PA concentrations in different plant families and distributed across several countries under different environmental conditions are compiled. The results of the present study help explain the importance of PA accumulation in different plant families and the distribution of PA accumulation in different foods.
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Affiliation(s)
| | | | - Philip J White
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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17
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Xu L, Xiao L, Xiao Y, Peng D, Xiao X, Huang W, Gheysen G, Wang G. Plasmodesmata play pivotal role in sucrose supply to Meloidogyne graminicola-caused giant cells in rice. MOLECULAR PLANT PATHOLOGY 2021; 22:539-550. [PMID: 33723908 PMCID: PMC8035636 DOI: 10.1111/mpp.13042] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/24/2021] [Accepted: 01/28/2021] [Indexed: 05/20/2023]
Abstract
On infection, plant-parasitic nematodes establish feeding sites in roots from which they take up carbohydrates among other nutrients. Knowledge on how carbohydrates are supplied to the nematodes' feeding sites is limited. Here, gene expression analyses showed that RNA levels of OsSWEET11 to OsSWEET15 were extremely low in both Meloidogyne graminicola (Mg)-caused galls and noninoculated roots. All the rice sucrose transporter genes, OsSUT1 to OsSUT5, were either down-regulated in Mg-caused galls compared with noninoculated rice roots or had very low transcript abundance. OsSUT1 was the only gene up-regulated in galls, at 14 days postinoculation (dpi), after being highly down-regulated at 3 and 7 dpi. OsSUT4 was down-regulated at 3 dpi. No noticeable OsSUTs promoter activities were detected in Mg-caused galls of pOsSUT1 to -5::GUS rice lines. Loading experiments with carboxyfluorescein diacetate (CFDA) demonstrated that symplastic connections exist between phloem and Mg-caused giant cells (GCs). According to data from OsGNS5- and OsGSL2-overexpressing rice plants that had decreased and increased callose deposition, respectively, callose negatively affected Mg parasitism and sucrose supply to Mg-caused GCs. Our results suggest that plasmodesmata-mediated sucrose transport plays a pivotal role in sucrose supply from rice root phloem to Mg-caused GCs, and OsSWEET11 to -15 and OsSUTs are not major players in it, although further functional analysis is needed for OsSUT1 and OsSUT4.
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Affiliation(s)
- Li‐he Xu
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Li‐ying Xiao
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yan‐nong Xiao
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - De‐liang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural ScienceBeijingChina
| | - Xue‐qiong Xiao
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Wen‐kun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural ScienceBeijingChina
| | - Godelieve Gheysen
- Department of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Gao‐feng Wang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
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18
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Meta-Analysis of Quantitative Traits Loci (QTL) Identified in Drought Response in Rice ( Oryza sativa L.). PLANTS 2021; 10:plants10040716. [PMID: 33917162 PMCID: PMC8067883 DOI: 10.3390/plants10040716] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 11/17/2022]
Abstract
Rice is an important grain that is the staple food for most of the world's population. Drought is one of the major stresses that negatively affects rice yield. The nature of drought tolerance in rice is complex as it is determined by various components and has low heritability. Therefore, to ensure success in breeding programs for drought tolerant rice, QTLs (quantitative trait loci) of interest must be stable in a variety of plant genotypes and environments. This study identified stable QTLs in rice chromosomes in a variety of backgrounds and environments and conducted a meta-QTL analysis of stable QTLs that have been reported by previous research for use in breeding programs. A total of 653 QTLs for drought tolerance in rice from 27 genetic maps were recorded for analysis. The QTLs recorded were related to 13 traits in rice that respond to drought. Through the use of BioMercartor V4.2, a consensus map containing QTLs and molecular markers were generated using 27 genetic maps that were extracted from the previous 20 studies and meta-QTL analysis was conducted on the consensus map. A total of 70 MQTLs were identified and a total of 453 QTLs were mapped into the meta-QTL areas. Five meta-QTLs from chromosome 1 (MQTL 1.5 and MQTL 1.6), chromosome 2 (MQTL2.1 and MQTL 2.2) and chromosome 3 (MQTL 3.1) were selected for functional annotation as these regions have high number of QTLs and include many traits in rice that respond to drought. A number of genes in MQTL1.5 (268 genes), MQTL1.6 (640 genes), MQTL 2.1 (319 genes), MQTL 2.2 (19 genes) and MQTL 3.1 (787 genes) were annotated through Blast2GO. Few major proteins that respond to drought stress were identified in the meta-QTL areas which are Abscisic Acid-Insensitive Protein 5 (ABI5), the G-box binding factor 4 (GBF4), protein kinase PINOID (PID), histidine kinase 2 (AHK2), protein related to autophagy 18A (ATG18A), mitochondrial transcription termination factor (MTERF), aquaporin PIP 1-2, protein detoxification 48 (DTX48) and inositol-tetrakisphosphate 1-kinase 2 (ITPK2). These proteins are regulatory proteins involved in the regulation of signal transduction and gene expression that respond to drought stress. The meta-QTLs derived from this study and the genes that have been identified can be used effectively in molecular breeding and in genetic engineering for drought resistance/tolerance in rice.
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19
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RNAi-mediated down-regulation of ITPK-2 enhanced inorganic phosphorus and minerals in the transgenic rice. J Biosci 2021. [DOI: 10.1007/s12038-021-00154-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Jiang M, Liu Y, Li R, Li S, Tan Y, Huang J, Shu Q. An Inositol 1, 3, 4, 5, 6-Pentakisphosphate 2-Kinase 1 Mutant with a 33-nt Deletion Showed Enhanced Tolerance to Salt and Drought Stress in Rice. PLANTS 2020; 10:plants10010023. [PMID: 33374298 PMCID: PMC7824669 DOI: 10.3390/plants10010023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 01/24/2023]
Abstract
OsIPK1 encodes inositol 1,3,4,5,6-pentakisphosphate 2-kinase, which catalyzes the conversion of myo-inositol-1,3,4,5,6-pentakisphosphate to myo-inositol-1,2,3,4,5,6-hexakisphosphate (IP6) in rice. By clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas9)-mediated mutagenesis in the 3rd exon of the gene, three OsIPK1 mutations, i.e., osipk1_1 (a 33-nt deletion), osipk1_2 (a 1-nt deletion), and osipk1_3 (a 2-nt deletion) were identified in T0 plants of the rice line Xidao #1 (wild type, WT). A transfer DNA free line with the homozygous osipk1_1 mutation was developed; however, no homozygous mutant lines could be developed for the other two mutations. The comparative assay showed that the osipk1_1 mutant line had a significantly lower level of phytic acid (PA, IP6; −19.5%) in rice grain and agronomic traits comparable to the WT. However, the osipk1_1 mutant was more tolerant to salt and drought stresses than the WT, with significantly lower levels of inositol triphosphate (IP3), reactive oxygen species (ROS) and induced IP6, and higher activities of antioxidant enzymes in seedlings subjected to these stresses. Further analyses showed that the transcription of stress response genes was significantly upregulated in the osipk1_1 mutant under stress. Thus, the low phytic acid mutant osipk1_1 should have potential applications in rice breeding and production.
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Affiliation(s)
- Meng Jiang
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China; (M.J.); (Y.L.); (S.L.); (Y.T.); (J.H.)
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China
| | - Yanhua Liu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China; (M.J.); (Y.L.); (S.L.); (Y.T.); (J.H.)
| | - Ruiqing Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China;
| | - Shan Li
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China; (M.J.); (Y.L.); (S.L.); (Y.T.); (J.H.)
| | - Yuanyuan Tan
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China; (M.J.); (Y.L.); (S.L.); (Y.T.); (J.H.)
| | - Jianzhong Huang
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China; (M.J.); (Y.L.); (S.L.); (Y.T.); (J.H.)
- Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qingyao Shu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China; (M.J.); (Y.L.); (S.L.); (Y.T.); (J.H.)
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China
- Correspondence:
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Li Q, Ma C, Tai H, Qiu H, Yang A. Comparative transcriptome analysis of two rice genotypes differing in their tolerance to saline-alkaline stress. PLoS One 2020; 15:e0243112. [PMID: 33259539 PMCID: PMC7707490 DOI: 10.1371/journal.pone.0243112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/14/2020] [Indexed: 11/18/2022] Open
Abstract
Saline-alkaline stress is an abiotic stress that suppresses rice plant growth and reduces yield. However, few studies have investigated the mechanism by which rice plants respond to saline-alkaline stress at a global transcriptional level. Dongdao-4 and Jigeng-88, which differ in their tolerance to saline-alkaline stress, were used to explore gene expression differences under saline-alkaline stress by RNA-seq technology. In seedlings of Dongdao-4 and Jigeng-88, 3523 and 4066 genes with differential levels of expression were detected, respectively. A total of 799 genes were upregulated in the shoots of both Dongdao-4 and Jigeng-88, while 411 genes were upregulated in the roots of both genotypes. Among the downregulated genes in Dongdao-4 and Jigeng-88, a total of 453 and 372 genes were found in shoots and roots, respectively. Gene ontology (GO) analysis showed that upregulated genes were enriched in several GO terms such as response to stress, response to jasmonic acid, organic acid metabolic process, nicotianamine biosynthetic process, and iron homeostasis. The downregulated genes were enriched in several GO terms, such as photosynthesis and response to reactive oxygen species. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that Dongdao-4 seedlings were specifically enriched in the biosynthesis of secondary metabolites such as diterpenoids and phenylpropanoids. The upregulated genes that were involved in secondary metabolite biosynthesis, amino acid biosynthesis, betalain biosynthesis, organic acid metabolic process, and iron homeostasis pathways may be central to saline-alkaline tolerance in both rice genotypes. In contrast, the genes involved in the diterpenoid and phenylpropanoid biosynthesis pathways may contribute to the greater tolerance to saline-alkaline stress in Dongdao-4 seedlings than in Jigeng-88. These results suggest that Dongdao-4 was equipped with a more efficient mechanism involved in multiple biological processes to adapt to saline-alkaline stress.
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Affiliation(s)
- Qian Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (AY); (QL)
| | - Changkun Ma
- State Key Laboratory of Eco-hydraulic Engineering in Arid Area, Xi’an University of Technology, Xi’an, China
| | - Huanhuan Tai
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Huan Qiu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - An Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- * E-mail: (AY); (QL)
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Sashidhar N, Harloff HJ, Potgieter L, Jung C. Gene editing of three BnITPK genes in tetraploid oilseed rape leads to significant reduction of phytic acid in seeds. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2241-2250. [PMID: 32191373 PMCID: PMC7589381 DOI: 10.1111/pbi.13380] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/07/2020] [Accepted: 02/28/2020] [Indexed: 05/20/2023]
Abstract
Commercialization of Brassica napus. L (oilseed rape) meal as protein diet is gaining more attention due to its well-balanced amino acid and protein contents. Phytic acid (PA) is a major source of phosphorus in plants but is considered as anti-nutritive for monogastric animals including humans due to its adverse effects on essential mineral absorption. The undigested PA causes eutrophication, which potentially threatens aquatic life. PA accounts to 2-5% in mature seeds of oilseed rape and is synthesized by complex pathways involving multiple enzymes. Breeding polyploids for recessive traits is challenging as gene functions are encoded by several paralogs. Gene redundancy often requires to knock out several gene copies to study their underlying effects. Therefore, we adopted CRISPR-Cas9 mutagenesis to knock out three functional paralogs of BnITPK. We obtained low PA mutants with an increase of free phosphorus in the canola grade spring cultivar Haydn. These mutants could mark an important milestone in rapeseed breeding with an increase in protein value and no adverse effects on oil contents.
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Affiliation(s)
- Niharika Sashidhar
- Plant Breeding InstituteChristian‐Albrechts‐University of KielKielGermany
| | - Hans J. Harloff
- Plant Breeding InstituteChristian‐Albrechts‐University of KielKielGermany
| | - Lizel Potgieter
- Environmental GenomicsBotanical InstituteChristian‐Albrechts‐University of KielKielGermany
- Environmental GenomicsMax‐Planck‐Institute for Evolutionary BiologyPlönGermany
| | - Christian Jung
- Plant Breeding InstituteChristian‐Albrechts‐University of KielKielGermany
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Yang L, Lei L, Liu H, Wang J, Zheng H, Zou D. Whole-genome mining of abiotic stress gene loci in rice. PLANTA 2020; 252:85. [PMID: 33052473 DOI: 10.1007/s00425-020-03488-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
We projected meta-QTL (MQTL) for drought, salinity, cold state, and high metal ion tolerance in rice using a meta-analysis based on high-density consensus maps. In addition, a genome-wide association analysis was used to validate the results of the meta-analysis, and four new chromosome intervals for mining abiotic stress candidate genes were obtained. Drought, severe cold, high salinity, and high metallic ion concentrations severely restrict rice production. Consequently, the breeding of abiotic stress-tolerant variety is being paid increasingly more attention. This study aimed to identify meta-quantitative trait loci (MQTL) for abiotic stress tolerance in rice, as well as the molecular markers and potential candidate genes of the MQTL regions. We summarized 2785 rice QTL and conducted a meta-analysis of 159 studies. We found 82 drought tolerance (DT), 70 cold tolerance (CT), 70 salt tolerance (ST), and 51 heavy metal ion tolerance (IT) meta-QTL, as well as 20 DT, 11 CT, 22 ST, and 5 IT candidate genes in the MQTL interval. Thirty-one multiple-tolerance related MQTL regions, which were highly enriched, were also detected, and 13 candidate genes related to multiple-tolerance were obtained. In addition, the correlation between DT, CT, and ST was significant in the rice genome. Four candidate genes and four MM-QTL regions were detected simultaneously by GWAS and meta-analysis. The four candidate genes showed distinct genetic differentiation and substantial genetic distance between indica and japonica rice, and the four MM-QTL are potential intervals for mining abiotic stress-related candidate genes. The candidate genes identified in this study will not only be useful for marker-assisted selection and pyramiding but will also accelerate the fine mapping and cloning of the candidate genes associated with abiotic stress-tolerance mechanisms in rice.
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Affiliation(s)
- Luomiao Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Lei Lei
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - HuaLong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China.
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Zhao C, Zhang H, Song C, Zhu JK, Shabala S. Mechanisms of Plant Responses and Adaptation to Soil Salinity. Innovation (N Y) 2020; 1:100017. [PMID: 34557705 PMCID: PMC8454569 DOI: 10.1016/j.xinn.2020.100017] [Citation(s) in RCA: 268] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Soil salinity is a major environmental stress that restricts the growth and yield of crops. Understanding the physiological, metabolic, and biochemical responses of plants to salt stress and mining the salt tolerance-associated genetic resource in nature will be extremely important for us to cultivate salt-tolerant crops. In this review, we provide a comprehensive summary of the mechanisms of salt stress responses in plants, including salt stress-triggered physiological responses, oxidative stress, salt stress sensing and signaling pathways, organellar stress, ion homeostasis, hormonal and gene expression regulation, metabolic changes, as well as salt tolerance mechanisms in halophytes. Important questions regarding salt tolerance that need to be addressed in the future are discussed.
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Affiliation(s)
- Chunzhao Zhao
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Heng Zhang
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chunpeng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
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Vlcko T, Ohnoutkova L. Allelic Variants of CRISPR/Cas9 Induced Mutation in an Inositol Trisphosphate 5/6 Kinase Gene Manifest Different Phenotypes in Barley. PLANTS (BASEL, SWITZERLAND) 2020; 9:E195. [PMID: 32033421 PMCID: PMC7076722 DOI: 10.3390/plants9020195] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/03/2020] [Indexed: 02/04/2023]
Abstract
Inositol trisphosphate 5/6 kinases (ITPK) constitute a small group of enzymes participating in the sequential phosphorylation of inositol phosphate to inositol hexakisphosphate (IP6), which is a major storage form of phosphate in cereal grains. The development of lines with reduced IP6 content could enhance phosphate and mineral bioavailability. Moreover, plant ITPKs participate in abiotic stress signaling. To elucidate the role of HvITPK1 in IP6 synthesis and stress signaling, a barley itpk1 mutant was created using programmable nuclease Cas9. Homozygous single bp insertion and deletion mutant lines were obtained. The mutants contained altered levels of phosphate in the mature grains, ranging from 65% to 174% of the wild type (WT) content. Homozygous mutant lines were tested for their response to salinity during germination. Interestingly, insertion mutant lines revealed a higher tolerance to salinity stress than deletion mutants. Mature embryos of an insertion mutant itpk1-2 and deletion mutant itpk1-33 were cultivated in vitro on MS medium supplemented with NaCl at 50, 100, and 200 mM. While both mutants grew less well than WT on no or low salt concentrations, the itpk1-2 mutant was affected less than the WT and itpk33 when grown on the highest NaCl concentration. The expression of all ITPKs was induced in roots in response to salt stress. In shoots, the differential effect of high salt on IPTK expression in the two iptk1 mutants was consistent with their different sensitivities to salt stress. The results extend the evidence for the involvement of ITPK genes in phosphate storage and abiotic stress signaling.
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Affiliation(s)
| | - Ludmila Ohnoutkova
- Laboratory of Growth Regulators, Palacký University & Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 241/27, Olomouc 78371, Czech Republic;
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26
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Liu S, Hu ZM, Zhang Q, Yang X, Critchley AT, Duan D. PI signal transduction and ubiquitination respond to dehydration stress in the red seaweed Gloiopeltis furcata under successive tidal cycles. BMC PLANT BIOLOGY 2019; 19:516. [PMID: 31771523 PMCID: PMC6880600 DOI: 10.1186/s12870-019-2125-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 11/08/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND Intermittent dehydration caused by tidal changes is one of the most important abiotic factors that intertidal seaweeds must cope with in order to retain normal growth and reproduction. However, the underlying molecular mechanisms for the adaptation of red seaweeds to repeated dehydration-rehydration cycles remain poorly understood. RESULTS We chose the red seaweed Gloiopeltis furcata as a model and simulated natural tidal changes with two consecutive dehydration-rehydration cycles occurring over 24 h in order to gain insight into key molecular pathways and regulation of genes which are associated with dehydration tolerance. Transcription sequencing assembled 32,681 uni-genes (GC content = 55.32%), of which 12,813 were annotated. Weighted gene co-expression network analysis (WGCNA) divided all transcripts into 20 modules, with Coral2 identified as the key module anchoring dehydration-induced genes. Pathways enriched analysis indicated that the ubiquitin-mediated proteolysis pathway (UPP) and phosphatidylinositol (PI) signaling system were crucial for a successful response in G. furcata. Network-establishing and quantitative reverse transcription PCR (qRT-PCR) suggested that genes encoding ubiquitin-protein ligase E3 (E3-1), SUMO-activating enzyme sub-unit 2 (SAE2), calmodulin (CaM) and inositol-1,3,4-trisphosphate 5/6-kinase (ITPK) were the hub genes which responded positively to two successive dehydration treatments. Network-based interactions with hub genes indicated that transcription factor (e.g. TFIID), RNA modification (e.g. DEAH) and osmotic adjustment (e.g. MIP, ABC1, Bam1) were related to these two pathways. CONCLUSIONS RNA sequencing-based evidence from G. furcata enriched the informational database for intertidal red seaweeds which face periodic dehydration stress during the low tide period. This provided insights into an increased understanding of how ubiquitin-mediated proteolysis and the phosphatidylinositol signaling system help seaweeds responding to dehydration-rehydration cycles.
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Affiliation(s)
- Shun Liu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Zi-Min Hu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 People’s Republic of China
| | - Quansheng Zhang
- Ocean School, Yantai University, Yantai, 264005 People’s Republic of China
| | - Xiaoqi Yang
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Alan T. Critchley
- Verschuren Centre for Sustainability in Energy and Environment, University of Cape Breton, Sydney, Nova Scotia Canada
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 People’s Republic of China
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Bisht N, Mishra SK, Chauhan PS. Bacillus amyloliquefaciens inoculation alters physiology of rice (Oryza sativa L. var. IR-36) through modulating carbohydrate metabolism to mitigate stress induced by nutrient starvation. Int J Biol Macromol 2019; 143:937-951. [PMID: 31739073 DOI: 10.1016/j.ijbiomac.2019.09.154] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/11/2019] [Accepted: 09/22/2019] [Indexed: 12/14/2022]
Abstract
To avoid disproportionate usage of chemicals in agriculture, an alternative eco-friendly strategy is required to improve soil fertility, and enhance crop productivity. Therefore, the present study demonstrates the role of plant beneficial rhizobacteria viz., Paenibacillus lentimorbus B-30488 (B-30488), Bacillus amyloliquefaciens SN13 (SN13), and their consortium in rice (Oryza sativa L. var. IR-36) facing nutrient deprivation. Parameters such as proline, total soluble sugar, relative water content, electrolytic leakage and malondialdehyde content were modulated in control rice seedlings as compared to treated under nutrient starved conditions. Bacterial inoculation not only significantly improved the agronomic parameters but also concentrations, uptake and partitioning of macro-micro nutrients. To disclose PGPR induced mechanisms to low nutrient stress tolerance, GC-MS analysis was performed. Overall 43 differential metabolites were characterized. Proline, glutamine, linolenic acid, malic acid, ribitol, propanoic acid and serine were accumulated in seedlings exposed to nutrient starvation. In PGPR inoculated rice glucose, fructose, mannose, glucitol, oleic acid, gulonic acid, raffinose, inositol were accumulated that induce metabolic and physiological parameters to reduce the impact of stress. Based on results SN13 was selected for gene expression analysis of metabolism-related genes that further affirmed the ability of PGPR to modulate carbohydrate metabolism in rice seedlings under suboptimum nutrient level.
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Affiliation(s)
- Nikita Bisht
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shashank Kumar Mishra
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, India
| | - Puneet Singh Chauhan
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Pang X, Xue M, Ren M, Nan D, Wu Y, Guo H. Ammopiptanthus mongolicus stress-responsive NAC gene enhances the tolerance of transgenic Arabidopsis thaliana to drought and cold stresses. Genet Mol Biol 2019; 42:624-634. [PMID: 31424071 PMCID: PMC6905445 DOI: 10.1590/1678-4685-gmb-2018-0101] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 02/11/2019] [Indexed: 12/02/2022] Open
Abstract
Drought and cold are the primary factors limiting plant growth worldwide. The Ammopiptanthus mongolicus NAC11 (AmNAC11) gene encodes a stress-responsive transcription factor. Expression of the AmNAC11 gene was induced by drought, cold and high salinity. The AmNAC11 protein was localized in the nucleus and plays an important role in tolerance to drought, cold and salt stresses. We also found that differential expression of AmNAC11 was induced in the early stages of seed germination and was related to root growth. When the AmNAC11 gene was introduced into Arabidopsis thaliana by an Agrobacterium-mediated method, the transgenic lines expressing AmNAC11 displayed significantly enhanced tolerance to drought and freezing stresses compared to wild-type Arabidopsis thaliana plants. These results indicated that over-expression of the AmNAC11 gene in Arabidopsis could significantly enhance its tolerance to drought and freezing stresses. Our study provides a promising approach to improve the tolerance of crop cultivars to abiotic stresses through genetic engineering.
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Affiliation(s)
- Xinyue Pang
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
- State Key Laboratory of Cotton Biology, Anyang, China
- Key Laboratory of Desert and Desertification, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Min Xue
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Meiyan Ren
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Dina Nan
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Yaqi Wu
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Huiqin Guo
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
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Mutation of Inositol 1,3,4-trisphosphate 5/6-kinase6 Impairs Plant Growth and Phytic Acid Synthesis in Rice. PLANTS 2019; 8:plants8050114. [PMID: 31035443 PMCID: PMC6572258 DOI: 10.3390/plants8050114] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/21/2019] [Accepted: 04/24/2019] [Indexed: 01/07/2023]
Abstract
Inositol 1,3,4-trisphosphate 5/6-kinase (ITPK) is encoded by six genes in rice (OsITPK1-6). A previous study had shown that nucleotide substitutions of OsITPK6 could significantly lower the phytic acid content in rice grains. In the present study, the possibility of establishing a genome editing-based method for breeding low-phytic acid cultivars in rice was explored, in conjunction with the functional determination of OsITPK6. Four OsITPK6 mutant lines were generated by targeted mutagenesis of the gene’s first exon using the CRISPR/Cas9 method, one (ositpk6_1) with a 6-bp in-frame deletion, and other three with frameshift mutations (ositpk6_2, _3, and _4). The frameshift mutations severely impaired plant growth and reproduction, while the effect of ositpk6_1 was relatively limited. The mutant lines ositpk6_1 and _2 had significantly lower levels (−10.1% and −32.1%) of phytic acid and higher levels (4.12- and 5.18-fold) of inorganic phosphorus compared with the wild-type (WT) line. The line ositpk6_1 also showed less tolerance to osmotic stresses. Our research demonstrates that mutations of OsITPK6, while effectively reducing phytic acid biosynthesis in rice grain, could significantly impair plant growth and reproduction.
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Yuenyong W, Chinpongpanich A, Comai L, Chadchawan S, Buaboocha T. Downstream components of the calmodulin signaling pathway in the rice salt stress response revealed by transcriptome profiling and target identification. BMC PLANT BIOLOGY 2018; 18:335. [PMID: 30518322 PMCID: PMC6282272 DOI: 10.1186/s12870-018-1538-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/20/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Calmodulin (CaM) is an important calcium sensor protein that transduces Ca2+ signals in plant stress signaling pathways. A previous study has revealed that transgenic rice over-expressing the calmodulin gene OsCam1-1 (LOC_Os03g20370) is more tolerant to salt stress than wild type. To elucidate the role of OsCam1-1 in the salt stress response mechanism, downstream components of the OsCam1-1-mediated response were identified and investigated by transcriptome profiling and target identification. RESULTS Transcriptome profiling of transgenic 'Khao Dawk Mali 105' rice over-expressing OsCam1-1 and wild type rice showed that overexpression of OsCam1-1 widely affected the expression of genes involved in several cellular processes under salt stress, including signaling, hormone-mediated regulation, transcription, lipid metabolism, carbohydrate metabolism, secondary metabolism, photosynthesis, glycolysis, tricarboxylic acid (TCA) cycle and glyoxylate cycle. Under salt stress, the photosynthesis rate in the transgenic rice was slightly lower than in wild type, while sucrose and starch contents were higher, suggesting that energy and carbon metabolism were affected by OsCam1-1 overexpression. Additionally, four known and six novel CaM-interacting proteins were identified by cDNA expression library screening with the recombinant OsCaM1. GO terms enriched in their associated proteins that matched those of the differentially expressed genes affected by OsCam1-1 overexpression revealed various downstream cellular processes that could potentially be regulated by OsCaM1 through their actions. CONCLUSIONS The diverse cellular processes affected by OsCam1-1 overexpression and possessed by the identified CaM1-interacting proteins corroborate the notion that CaM signal transduction pathways compose a complex network of downstream components involved in several cellular processes. These findings suggest that under salt stress, CaM activity elevates metabolic enzymes involved in central energy pathways, which promote or at least maintain the production of energy under the limitation of photosynthesis.
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Affiliation(s)
- Worawat Yuenyong
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Aumnart Chinpongpanich
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 795616 USA
| | - Supachitra Chadchawan
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Teerapong Buaboocha
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Moin M, Bakshi A, Madhav MS, Kirti PB. Cas9/sgRNA-based genome editing and other reverse genetic approaches for functional genomic studies in rice. Brief Funct Genomics 2018; 17:339-351. [PMID: 29579147 DOI: 10.1093/bfgp/ely010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
One of the important and direct ways of investigating the function of a gene is to characterize the phenotypic consequences associated with loss or gain-of-function of the corresponding gene. These mutagenesis strategies have been successfully deployed in Arabidopsis, and subsequently extended to crop species including rice. Researchers have made vast advancements in the area of rice genomics and functional genomics, as it is a diploid plant with a relatively smaller genome size unlike other cereals. The advent of rice genome research and the annotation of high-quality genome sequencing along with the developments in databases and computer searches have enabled the functional characterization of unknown genes in rice. Further, with the improvements in the efficiency of regeneration and transformation protocols, it has now become feasible to produce sizable mutant populations in indica rice varieties also. In this review, various mutagenesis methods, the current status of the mutant resources, limitations and strengths of insertional mutagenesis approaches and also results obtained with suitable screens for stress tolerance in rice are discussed. In addition, targeted genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) or Cas9/single-guide RNA system and its potential applications in generating transgene-free rice plants through genome engineering as an efficient alternative to classical transgenic technology are also discussed.
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Affiliation(s)
- Mazahar Moin
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), India
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Achala Bakshi
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - M S Madhav
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Identification of QTN and candidate genes for Salinity Tolerance at the Germination and Seedling Stages in Rice by Genome-Wide Association Analyses. Sci Rep 2018; 8:6505. [PMID: 29695843 PMCID: PMC5916932 DOI: 10.1038/s41598-018-24946-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 04/13/2018] [Indexed: 12/31/2022] Open
Abstract
To facilitate developing rice varieties tolerant to salt stress, a panel of 208 rice mini-core accessions collected from 25 countries were evaluated for 13 traits associated with salt tolerance (ST) at the germination and seedling stages. The rice panel showed tremendous variation for all measured ST traits and eight accessions showing high levels of ST at either and/or both the germination and seedling stages. Using 395,553 SNP markers covering ~372 Mb of the rice genome and multi-locus mixed linear models, 20 QTN associated with 11 ST traits were identified by GWAS, including 6 QTN affecting ST at the germination stage and 14 QTN for ST at the seedling stage. The integration of bioinformatic with haplotype analyses for the ST QTN lets us identify 22 candidate genes for nine important ST QTN (qGR3, qSNK1, qSNK12, qSNC1, qSNC6, qRNK2, qSDW9a, qSST5 and qSST9). These candidate genes included three known ST genes (SKC1, OsTZF1 and OsEATB) for QTN qSNK1 qSST5 and qSST9. Candidate genes showed significant phenotypic differences in ST traits were detected between or among 2-4 major haplotypes. Thus, our results provided useful materials and genetic information for improving rice ST in future breeding and for molecular dissection of ST in rice.
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Marathe A, Krishnan V, Vinutha T, Dahuja A, Jolly M, Sachdev A. Exploring the role of Inositol 1,3,4-trisphosphate 5/6 kinase-2 (GmITPK2) as a dehydration and salinity stress regulator in Glycine max (L.) Merr. through heterologous expression in E. coli. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 123:331-341. [PMID: 29289899 DOI: 10.1016/j.plaphy.2017.12.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 05/26/2023]
Abstract
Phytic acid (PA) is implicative in a spectrum of biochemical and physiological processes involved in plant stress response. Inositol 1,3,4, Tris phosphate 5/6 kinase (ITPK), a polyphosphate kinase that converts Inositol 1,3,4 trisphosphate to Inositol 1,3,4,5/6 tetra phosphate, averting the inositol phosphate pool towards PA biosynthesis, is a key regulator that exists in four different isoforms in soybean. In the present study, in-silico analysis of the promoter region of ITPKs was done and among the four isoforms, promoter region of GmITPK2 showed the presence of two MYB binding elements for drought inducibility and one for ABA response. Expression profiling through qRT-PCR under drought and salinity stress showed higher expression of GmITPK2 isoform compared to the other members of the family. The study revealed GmITPK2 as an early dehydration responsive gene which is also induced by dehydration and exogenous treatment with ABA. To evaluate the osmo-protective role of GmITPK2, attempts were made to assess the bacterial growth on Luria Broth media containing 200 mM NaCl, 16% PEG and 100 μM ABA, individually. The transformed E. coli BL21 (DE3) cells harbouring the GmITPK2 gene depicted better growth on the media compared to the bacterial cells containing the vector alone. Similarly, the growth of the transformed cells in the liquid media containing 200 mM NaCl, 16% PEG and 100 μM ABA showed higher absorbance at 600 nm compared to control, at different time intervals. The GmITPK2 recombinant E. coli cells showing tolerance to drought and salinity thus demonstrated the functional redundancy of the gene across taxa. The purity and specificity of the recombinant protein was assessed and confirmed through PAGE showing a band of ∼35 kDa on western blotting using Anti- Penta His- HRP conjugate antibody. To the best of our knowledge, the present study is the first report exemplifying the role of GmITPK2 isoform in drought and salinity tolerance in soybean.
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Affiliation(s)
| | - Veda Krishnan
- Division of Biochemistry, ICAR - IARI, New Delhi, India
| | - T Vinutha
- Division of Biochemistry, ICAR - IARI, New Delhi, India
| | - Anil Dahuja
- Division of Biochemistry, ICAR - IARI, New Delhi, India
| | - Monica Jolly
- Division of Biochemistry, ICAR - IARI, New Delhi, India
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Wang X, Komatsu S. Proteomic Analysis of Calcium Effects on Soybean Root Tip under Flooding and Drought Stresses. PLANT & CELL PHYSIOLOGY 2017; 58:1405-1420. [PMID: 28586431 DOI: 10.1093/pcp/pcx078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
Flooding and drought are disadvantageous environmental conditions that induce cytosolic calcium in soybean. To explore the effects of flooding- and drought-induced increases in calcium, a gel-free/label-free proteomic analysis was performed. Cytosolic calcium was decreased by blocking calcium channels in the endoplasmic reticulum (ER) and plasma membrane under both stresses. Calnexin, protein disulfide isomerase, heat shock proteins and thioredoxin were predominantly affected as the ER proteins in response to calcium, and ER-associated degradation-related proteins of HCP-like superfamily protein were up-regulated under stress exposure and then down-regulated. Glycolysis, fermentation, the tricarboxylic acid cycle and amino acid metabolism were mainly induced as the types of cellular metabolism in response to calcium under both stresses. Pyruvate decarboxylase was increased and decreased under flooding and drought, respectively, and was further decreased by the reduction of cytosolic calcium; however, it was recovered by exogenous calcium under both stresses. Furthermore, pyruvate decarboxylase activity was increased under flooding, but decreased under drought. These results suggest that calcium is involved in protein folding in the ER, and ER-associated degradation might alleviate ER stress during the early stage of both stresses. Furthermore, calcium appears to modify energy metabolism, and pyruvate decarboxylase may be a key enzyme in this process under flooding and drought.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
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Liu F, Li ZF, Wang ZY, Wang L. Role of subcellular calcium redistribution in regulating apoptosis and autophagy in cadmium-exposed primary rat proximal tubular cells. J Inorg Biochem 2016; 164:99-109. [DOI: 10.1016/j.jinorgbio.2016.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/30/2016] [Accepted: 09/13/2016] [Indexed: 12/22/2022]
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Lo SF, Fan MJ, Hsing YI, Chen LJ, Chen S, Wen IC, Liu YL, Chen KT, Jiang MJ, Lin MK, Rao MY, Yu LC, Ho THD, Yu SM. Genetic resources offer efficient tools for rice functional genomics research. PLANT, CELL & ENVIRONMENT 2016; 39:998-1013. [PMID: 26301381 DOI: 10.1111/pce.12632] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/13/2015] [Accepted: 08/16/2015] [Indexed: 05/07/2023]
Abstract
Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T-DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene-rich regions, resulting in direct gene knockout or activation of genes within 20-30 kb up- and downstream of the T-DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T-DNA-tagged rice mutant population. We also discuss important features of T-DNA activation- and knockout-tagging and promoter-trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high-throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.
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Affiliation(s)
- Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Ming-Jen Fan
- Department of Biotechnology, Asia University, Lioufeng Road, Wufeng, Taichung, 413, Taiwan, ROC
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Liang-Jwu Chen
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Shu Chen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, Wufeng, Taichung, 413, Taiwan, ROC
| | - Ien-Chie Wen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, Wufeng, Taichung, 413, Taiwan, ROC
| | - Yi-Lun Liu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Ku-Ting Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
| | - Mirng-Jier Jiang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Ming-Kuang Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Meng-Yen Rao
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
| | - Lin-Chih Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
| | - Tuan-Hua David Ho
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115, Taiwan, ROC
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan, ROC
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Aggarwal S, Shukla V, Bhati KK, Kaur M, Sharma S, Singh A, Mantri S, Pandey AK. Hormonal Regulation and Expression Profiles of Wheat Genes Involved during Phytic Acid Biosynthesis Pathway. PLANTS 2015; 4:298-319. [PMID: 27135330 PMCID: PMC4844322 DOI: 10.3390/plants4020298] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 05/26/2015] [Accepted: 06/01/2015] [Indexed: 11/16/2022]
Abstract
Phytic acid (PA) biosynthesis pathway genes were reported from multiple crop species. PA accumulation was enhanced during grain filling and at that time, hormones like Abscisic acid (ABA) and Gibberellic acid (GA3) interplay to control the process of seed development. Regulation of wheat PA pathway genes has not yet been reported in seeds. In an attempt to find the clues for the regulation by hormones, the promoter region of wheat PA pathway genes was analyzed for the presence of cis-elements. Multiple cis-elements of those known to be involved for ABA, GA3, salicylic acid (SA), and cAMP sensing were identified in the promoters of PA pathway genes. Eight genes (TaIMP, TaITPK1-4, TaPLC1, TaIPK2 and TaIPK1) involved in the wheat PA biosynthesis pathway were selected for the expression studies. The temporal expression response was studied in seeds treated with ABA and GA3 using quantitative real time PCR. Our results suggested that exogenous application of ABA induces few PA pathway genes in wheat grains. Comparison of expression profiles for PA pathway for GA3 and ABA suggested the antagonistic regulation of certain genes. Additionally, to reveal stress responses of wheat PA pathway genes, expression was also studied in the presence of SA and cAMP. Results suggested SA specific differential expression of few genes, whereas, overall repression of genes was observed in cAMP treated samples. This study is an effort to understand the regulation of PA biosynthesis genes in wheat.
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Affiliation(s)
- Sipla Aggarwal
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Vishnu Shukla
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Kaushal Kumar Bhati
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Mandeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Shivani Sharma
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Anuradha Singh
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Shrikant Mantri
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Ajay Kumar Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
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Zhou Y, Liu L, Huang W, Yuan M, Zhou F, Li X, Lin Y. Overexpression of OsSWEET5 in rice causes growth retardation and precocious senescence. PLoS One 2014; 9:e94210. [PMID: 24709840 PMCID: PMC3978035 DOI: 10.1371/journal.pone.0094210] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 03/13/2014] [Indexed: 01/07/2023] Open
Abstract
As a novel sugar transporter family, SWEETs play important roles in plant growth and development. Here, we characterized a SWEET gene named OsSWEET5 through its overexpression in rice. Heterologous expression assay indicated that OsSWEET5 encoded a galactose transporter in yeast. OsSWEET5-overexpressing plants displayed the phenotypes of growth retardation and precocious senescence at seedling stage. GC-MS analysis showed that the sugar levels were largely altered in the leaves of the OsSWEET5-overexpressing plants. Molecular analysis revealed that these phenotypes might be due to the transcriptional changes of the genes involved in sugar metabolism and transport. In addition, the transgenic plants showed a lower level of auxin with altered transcription of genes involved in auxin signaling and translocation pathways. However, no obvious phenotype was observed between the amiRNA-OsSWEET5 transgenic lines and WT plants, which could be a result of the functional redundancy of the galactose transporters in rice. Taken together, our findings suggest that OsSWEET5 plays a crucial role in regulating the crosstalk between sugar and auxin in rice.
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Affiliation(s)
- Yong Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Li Liu
- Plant Reproductive Biology, University of California Davis, Davis, California, United States of America
| | - Weifeng Huang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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Zhou Y, Huang W, Liu L, Chen T, Zhou F, Lin Y. Identification and functional characterization of a rice NAC gene involved in the regulation of leaf senescence. BMC PLANT BIOLOGY 2013; 13:132. [PMID: 24028154 PMCID: PMC3847160 DOI: 10.1186/1471-2229-13-132] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/13/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND As the final stage of leaf development, leaf senescence may cause the decline of photosynthesis and gradual reduction of carbon assimilation, which makes it a possible limiting factor for crop yield. NACs are plant-specific transcription factors and some NACs have been confirmed to play important roles in regulating leaf senescence. RESULTS In this study, we reported a member of the NAC transcription factor family named OsNAP whose expression is associated with leaf senescence, and investigated its preliminary function during the process of leaf senescence. The results of qRT-PCR showed that the OsNAP transcripts were accumulated gradually in response to leaf senescence and treatment with methyl jasmonic acid (MeJA). A subcellular localization assay indicated that OsNAP is a nuclear-localized protein. Yeast one-hybrid experiments indicated that OsNAP can bind the NAC recognition site (NACRS)-like sequence. OsNAP-overexpressing transgenic plants displayed an accelerated leaf senescence phenotype at the grain-filling stage, which might be caused by the elevated JA levels and the increased expression of the JA biosynthesis-related genes LOX2 and AOC1, and showed enhanced tolerance ability to MeJA treatment at the seedling stage. Nevertheless, the leaf senescence process was delayed in OsNAP RNAi transgenic plants with a dramatic drop in JA levels and with decreased expression levels of the JA biosynthesis-related genes AOS2, AOC1 and OPR7. CONCLUSIONS These results suggest that OsNAP acts as a positive regulator of leaf senescence and this regulation may occur via the JA pathway.
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Affiliation(s)
- Yong Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weifeng Huang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Liu
- Plant Reproductive Biology, Mail Stop 5, University of California, 1 Shields Avenue, Davis, CA 95616-8780, USA
| | - Taiyu Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
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Chang Y, Long T, Wu C. Effort and contribution of T-DNA Insertion mutant library for rice functional genomics research in China: review and perspective. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:953-966. [PMID: 23020748 DOI: 10.1111/j.1744-7909.2012.01171.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
With the completion of the rice (Oryza sativa L.) genome-sequencing project, the rice research community proposed to characterize the function of every predicted gene in rice by 2020. One of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as T-DNA or transposons. Since 1999, with support from the Ministry of Science and Technology of China for Rice Functional Genomics Programs, large-scale T-DNA insertion mutant populations have been generated in Huazhong Agricultural University, the Chinese Academy of Sciences and the Chinese Academy of Agricultural Sciences. Currently, a total of 372,346 mutant lines have been generated, and 58,226 T-DNA or Tos17 flanking sequence tags have been isolated. Using these mutant resources, more than 40 genes with potential applications in rice breeding have already been identified. These include genes involved in biotic or abiotic stress responses, nutrient metabolism, pollen development, and plant architecture. The functional analysis of these genes will not only deepen our understanding of the fundamental biological questions in rice, but will also offer valuable gene resources for developing Green Super Rice that is high-yielding with few inputs even under the poor growth conditions of many regions of Africa and Asia.
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Affiliation(s)
- Yuxiao Chang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research-Wuhan, Huazhong Agricultural University, Wuhan 430070, China
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