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Tong L, Lin M, Zhu L, Liao B, Lu L, Lu Y, Chen J, Shi J, Hao Z. Unraveling the Role of the Liriodendron Thioredoxin (TRX) Gene Family in an Abiotic Stress Response. PLANTS (BASEL, SWITZERLAND) 2024; 13:1674. [PMID: 38931106 PMCID: PMC11207409 DOI: 10.3390/plants13121674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Thioredoxin (TRX) is a small protein with REDOX activity that plays a crucial role in a plant's growth, development, and stress resistance. The TRX family has been extensively studied in Arabidopsis, rice, and wheat, and so it is likely that its members have similar biological functions in Liriodendron that have not been reported in Liriodendron. In this study, we performed the genome-wide identification of the TRX gene family based on the Liriodendron chinense genome, leading to a total of 42 LcTRX gene members. A phylogenetic analysis categorized these 42 LcTRX proteins into 13 subfamilies. We further characterized their chromosome distributions, gene structures, conserved protein motifs, and cis-elements in the promoter regions. In addition, based on the publicly available transcriptome data for Liriodendron hybrid and following RT-qPCR experiments, we explored the expression patterns of LhTRXs to different abiotic stressors, i.e., drought, cold, and heat stress. Notably, we found that several LhTRXs, especially LhTRX-h3, were significantly upregulated in response to abiotic stress. In addition, the subcellular localization assay showed that LhTRX-h3 was mainly distributed in the cytoplasm. Subsequently, we obtained LhTRX-h3 overexpression (OE) and knockout (KO) callus lines in Liriodendron hybrid. Compared to the wild type (WT) and LhTRX-h3-KO callus proliferation of LhTRX-h3-OE lines was significantly enhanced with reduced reactive oxygen species (ROS) accumulation under drought stress. Our findings that LhTRX-h3 is sufficient to improve drought tolerance. and underscore the significance of the TRX gene family in environmental stress responses in Liriodendron.
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Affiliation(s)
- Lu Tong
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (L.T.); (M.L.); (L.Z.); (B.L.); (L.L.); (Y.L.); (J.C.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Mengyuan Lin
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (L.T.); (M.L.); (L.Z.); (B.L.); (L.L.); (Y.L.); (J.C.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Liming Zhu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (L.T.); (M.L.); (L.Z.); (B.L.); (L.L.); (Y.L.); (J.C.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Bojun Liao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (L.T.); (M.L.); (L.Z.); (B.L.); (L.L.); (Y.L.); (J.C.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Lu Lu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (L.T.); (M.L.); (L.Z.); (B.L.); (L.L.); (Y.L.); (J.C.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Ye Lu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (L.T.); (M.L.); (L.Z.); (B.L.); (L.L.); (Y.L.); (J.C.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (L.T.); (M.L.); (L.Z.); (B.L.); (L.L.); (Y.L.); (J.C.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Jisen Shi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (L.T.); (M.L.); (L.Z.); (B.L.); (L.L.); (Y.L.); (J.C.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Zhaodong Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (L.T.); (M.L.); (L.Z.); (B.L.); (L.L.); (Y.L.); (J.C.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
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Kumar D, Ramkumar MK, Dutta B, Kumar A, Pandey R, Jain PK, Gaikwad K, Mishra DC, Chaturvedi KK, Rai A, Solanke AU, Sevanthi AM. Integration of miRNA dynamics and drought tolerant QTLs in rice reveals the role of miR2919 in drought stress response. BMC Genomics 2023; 24:526. [PMID: 37674140 PMCID: PMC10481553 DOI: 10.1186/s12864-023-09609-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/20/2023] [Indexed: 09/08/2023] Open
Abstract
To combat drought stress in rice, a major threat to global food security, three major quantitative trait loci for 'yield under drought stress' (qDTYs) were successfully exploited in the last decade. However, their molecular basis still remains unknown. To understand the role of secondary regulation by miRNA in drought stress response and their relation, if any, with the three qDTYs, the miRNA dynamics under drought stress was studied at booting stage in two drought tolerant (Sahbaghi Dhan and Vandana) and one drought sensitive (IR 20) cultivars. In total, 53 known and 40 novel differentially expressed (DE) miRNAs were identified. The primary drought responsive miRNAs were Osa-MIR2919, Osa-MIR3979, Osa-MIR159f, Osa-MIR156k, Osa-MIR528, Osa-MIR530, Osa-MIR2091, Osa-MIR531a, Osa-MIR531b as well as three novel ones. Sixty-one target genes that corresponded to 11 known and 4 novel DE miRNAs were found to be co-localized with the three qDTYs, out of the 1746 target genes identified. We could validate miRNA-mRNA expression under drought for nine known and three novel miRNAs in eight different rice genotypes showing varying degree of tolerance. From our study, Osa-MIR2919, Osa-MIR3979, Osa-MIR528, Osa-MIR2091-5p and Chr01_11911S14Astr and their target genes LOC_Os01g72000, LOC_Os01g66890, LOC_Os01g57990, LOC_Os01g56780, LOC_Os01g72834, LOC_Os01g61880 and LOC_Os01g72780 were identified as the most promising candidates for drought tolerance at booting stage. Of these, Osa-MIR2919 with 19 target genes in the qDTYs is being reported for the first time. It acts as a negative regulator of drought stress tolerance by modulating the cytokinin and brassinosteroid signalling pathway.
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Affiliation(s)
- Deepesh Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, Indian Agricultural Research Institute, Pusa Campus New Delhi, New Delhi, 110012, India
| | - M K Ramkumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Bipratip Dutta
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, Indian Agricultural Research Institute, Pusa Campus New Delhi, New Delhi, 110012, India
| | - Ajay Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Rakesh Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Pradeep Kumar Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Dwijesh C Mishra
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - K K Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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Saini MR, Chandran LP, Barbadikar KM, Sevanthi AMV, Chawla G, Kaushik M, Mulani E, Phule AS, Govindannagari R, Sonth B, Sinha SK, Sundaram RM, Mandal PK. Understanding plant-microbe interaction of rice and soybean with two contrasting diazotrophic bacteria through comparative transcriptome analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:939395. [PMID: 36483966 PMCID: PMC9724235 DOI: 10.3389/fpls.2022.939395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Understanding the beneficial plant-microbe interactions is becoming extremely critical for deploying microbes imparting plant fitness and achieving sustainability in agriculture. Diazotrophic bacteria have the unique ability to survive without external sources of nitrogen and simultaneously promote host plant growth, but the mechanisms of endophytic interaction in cereals and legumes have not been studied extensively. We have studied the early interaction of two diazotrophic bacteria, Gluconacetobacter diazotrophicus (GAB) and Bradyrhizobium japonicum (BRH), in 15-day-old seedlings of rice and soybean up to 120 h after inoculation (hai) under low-nitrogen medium. Root colonization of GAB in rice was higher than that of BRH, and BRH colonization was higher in soybean roots as observed from the scanning electron microscopy at 120 hai. Peroxidase enzyme was significantly higher at 24 hai but thereafter was reduced sharply in soybean and gradually in rice. The roots of rice and soybean inoculated with GAB and BRH harvested from five time points were pooled, and transcriptome analysis was executed along with control. Two pathways, "Plant pathogen interaction" and "MAPK signaling," were specific to Rice-Gluconacetobacter (RG), whereas the pathways related to nitrogen metabolism and plant hormone signaling were specific to Rice-Bradyrhizobium (RB) in rice. Comparative transcriptome analysis of the root tissues revealed that several plant-diazotroph-specific differentially expressed genes (DEGs) and metabolic pathways of plant-diazotroph-specific transcripts, viz., chitinase, brassinosteroid, auxin, Myeloblastosis (MYB), nodulin, and nitrate transporter (NRT), were common in all plant-diazotroph combinations; three transcripts, viz., nitrate transport accessory protein (NAR), thaumatin, and thionin, were exclusive in rice and another three transcripts, viz., NAC (NAM: no apical meristem, ATAF: Arabidopsis thaliana activating factor, and CUC: cup-shaped cotyledon), ABA (abscisic acid), and ammonium transporter, were exclusive in soybean. Differential expression of these transcripts and reduction in pathogenesis-related (PR) protein expression show the early interaction. Based on the interaction, it can be inferred that the compatibility of rice and soybean is more with GAB and BRH, respectively. We propose that rice is unable to identify the diazotroph as a beneficial microorganism or a pathogen from an early response. So, it expressed the hypersensitivity-related transcripts along with PR proteins. The molecular mechanism of diazotrophic associations of GAB and BRH with rice vis-à-vis soybean will shed light on the basic understanding of host responses to beneficial microorganisms.
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Affiliation(s)
- Manish Ranjan Saini
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
- Kalinga Institute of Industrial Technology (KIIT) School of Biotechnology, KIIT University, Bhubaneswar, India
| | | | | | - Amitha Mithra V. Sevanthi
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | - Gautam Chawla
- Division of Nematology, ICAR- Indian Agriculture Research Institute, New Delhi, India
| | - Megha Kaushik
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | - Ekta Mulani
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | | | | | - Bandeppa Sonth
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Subodh Kumar Sinha
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | | | - Pranab Kumar Mandal
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
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Sevanthi AM, Sinha SK, V S, Rani M, Saini MR, Kumari S, Kaushik M, Prakash C, K V, Singh GP, Mohapatra T, Mandal PK. Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice. RICE (NEW YORK, N.Y.) 2021; 14:49. [PMID: 34089405 PMCID: PMC8179884 DOI: 10.1186/s12284-021-00487-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/05/2021] [Indexed: 05/19/2023]
Abstract
We report here the genome-wide changes resulting from low N (N-W+), low water (N+W-)) and dual stresses (N-W-) in root and shoot tissues of two rice genotypes, namely, IR 64 (IR64) and Nagina 22 (N22), and their association with the QTLs for nitrogen use efficiency. For all the root parameters, except for root length under N-W+, N22 performed better than IR64. Chlorophyll a, b and carotenoid content were higher in IR64 under N+W+ treatment and N-W+ and N+W- stresses; however, under dual stress, N22 had higher chlorophyll b content. While nitrite reductase, glutamate synthase (GS) and citrate synthase assays showed better specific activity in IR64, glutamate dehydrogenase showed better specific activity in N22 under dual stress (N-W-); the other N and C assimilating enzymes showed similar but low specific activities in both the genotypes. A total of 8926 differentially expressed genes (DEGs) were identified compared to optimal (N+W+) condition from across all treatments. While 1174, 698 and 903 DEGs in IR64 roots and 1197, 187 and 781 in N22 roots were identified, nearly double the number of DEGs were found in the shoot tissues; 3357, 1006 and 4005 in IR64 and 4004, 990 and 2143 in N22, under N-W+, N+W- and N-W- treatments, respectively. IR64 and N22 showed differential expression in 15 and 11 N-transporter genes respectively, under one or more stress treatments, out of which four showed differential expression also in N+W- condition. The negative regulators of N- stress, e.g., NIGT1, OsACTPK1 and OsBT were downregulated in IR64 while in N22, OsBT was not downregulated. Overall, N22 performed better under dual stress conditions owing to its better root architecture, chlorophyll and porphyrin synthesis and oxidative stress management. We identified 12 QTLs for seed and straw N content using 253 recombinant inbred lines derived from IR64 and N22 and a 5K SNP array. The QTL hotspot region on chromosome 6 comprised of 61 genes, of which, five were DEGs encoding for UDP-glucuronosyltransferase, serine threonine kinase, anthocyanidin 3-O-glucosyltransferase, and nitrate induced proteins. The DEGs, QTLs and candidate genes reported in this study can serve as a major resource for both rice improvement and functional biology.
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Affiliation(s)
| | - Subodh Kumar Sinha
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Sureshkumar V
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Manju Rani
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Manish Ranjan Saini
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Sapna Kumari
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Megha Kaushik
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Chandra Prakash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Venkatesh K
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Trilochan Mohapatra
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India
| | - Pranab Kumar Mandal
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
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Singh BK, Ramkumar MK, Dalal M, Singh A, Solanke AU, Singh NK, Sevanthi AM. Allele mining for a drought responsive gene DRO1 determining root growth angle in donors of drought tolerance in rice ( Oryza sativa L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:523-534. [PMID: 33854281 PMCID: PMC7981370 DOI: 10.1007/s12298-021-00950-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/05/2020] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Deeper Rooting 1 (DRO1) gene identified from a major QTL on chromosome 9 increases the root growth angle (RGA) and thus facilitates survival under drought and hence is an excellent candidate for rice improvement. Twenty-four major Indian upland and lowland genotypes including the 'yield under drought' (DTY) QTL donors were subjected to allele mining of DRO1 (3058 bp) using four pairs of overlapping primers. A total of 216 and 52 SNPs were identified across all genotypes in the gene and coding region (756 bp) respectively with transversions 3.6 fold more common than transitions in the gene and 2.5 times in the CDS. In 251 amino acid long protein, substitutions were found in 19 positions, wherein change in position 92 was the most frequent. Based on allele mining, the 24 genotypes can be classified into 16 primary structure variants ranging from complete functional allele (Satti, IR36 and DTY 3.1 donor, IR81896-B-B-195) to truncated non-functional alleles in PMK2, IR64, IR20 and Swarna. All the DTY donors, other than IR81896-B-B-195, and most of the upland drought tolerant cultivars (Nagina 22, Vandana and Dhagaddeshi) had accumulated 6-19 SNPs and 4-8 amino acid substitutions resulting in substantial differences in their protein structure. The expression analysis revealed that all the genotypes showed upregulation under drought stress though the degree of upregulation varied among genotypes. The information on structural variations in DRO1 gene will be very useful for the breeders, especially in the light of recent breeding programmes on improving drought tolerance using several DTY donors and upland accessions. SUPPLEMENTARY INFORMATION The online version of this article (10.1007/s12298-021-00950-2).
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Affiliation(s)
- Bablee Kumari Singh
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
| | - M. K. Ramkumar
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
| | - Monika Dalal
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
| | - Archana Singh
- Division of Biochemistry, Indian Agricultural Research Institute, Pusa campus, New Delhi, India
| | - Amolkumar U. Solanke
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
| | - Nagendra K. Singh
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
| | - Amitha Mithra Sevanthi
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
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Nadarajah KK. ROS Homeostasis in Abiotic Stress Tolerance in Plants. Int J Mol Sci 2020; 21:E5208. [PMID: 32717820 PMCID: PMC7432042 DOI: 10.3390/ijms21155208] [Citation(s) in RCA: 220] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/21/2022] Open
Abstract
Climate change-induced abiotic stress results in crop yield and production losses. These stresses result in changes at the physiological and molecular level that affect the development and growth of the plant. Reactive oxygen species (ROS) is formed at high levels due to abiotic stress within different organelles, leading to cellular damage. Plants have evolved mechanisms to control the production and scavenging of ROS through enzymatic and non-enzymatic antioxidative processes. However, ROS has a dual function in abiotic stresses where, at high levels, they are toxic to cells while the same molecule can function as a signal transducer that activates a local and systemic plant defense response against stress. The effects, perception, signaling, and activation of ROS and their antioxidative responses are elaborated in this review. This review aims to provide a purview of processes involved in ROS homeostasis in plants and to identify genes that are triggered in response to abiotic-induced oxidative stress. This review articulates the importance of these genes and pathways in understanding the mechanism of resistance in plants and the importance of this information in breeding and genetically developing crops for resistance against abiotic stress in plants.
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Affiliation(s)
- Kalaivani K Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM BANGI, Malaysia
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Abstract
This article comments on:Melandri G, AbdElgawad H, Riewe D, Hageman JA, Asard H, Beemster GTS, Kadam N, Jagadish K, Altmann T, Ruyter-Spira1 C, Bouwmeester H. 2019. Biomarkers for grain yield stability in rice under drought stress. Journal of Experimental Botany 71, 669–683.
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Affiliation(s)
- Ronan Sulpice
- National University Ireland Galway, Plant Systems Biology Laboratory, Ryan Institute, School of Natural Sciences, Galway, Ireland
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A Novel Stay-Green Mutant of Rice with Delayed Leaf Senescence and Better Harvest Index Confers Drought Tolerance. PLANTS 2019; 8:plants8100375. [PMID: 31561513 PMCID: PMC6843539 DOI: 10.3390/plants8100375] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022]
Abstract
Three Ethyl methansulphonate (EMS)-induced stay-green mutants (SGM-1, SGM-2 and SGM-3) and their wild-type (WT), were tested for their Stay-Green (SG) and drought tolerance nature as the relation between these two attributes is not yet established in rice. In the dark induced senescence assay, SGM-3 showed delayed senescence while SGM-1 and SGM-2 showed complete lack of senescence. Mutants showed stable transcript abundance over time, for 15 candidate genes (CGs) associated with senescence, compared to the WT. SGM-3 however showed moderately increasing transcript abundance over time for ATG6a, ATG4a, NYC1, NOL and NYC3. Only SGM-3 performed better than the WT for yield and harvest index under well irrigated as well as drought conditions, though all the mutants showed better performance for other agronomic traits under both the conditions and ascorbate peroxidase activity under drought. Thus, SG trait showed positive correlation with drought tolerance though only SGM-3 could convert this into higher harvest index. Sequence analysis of 80 senescence-associated genes including the 15 CGs showed non-synonymous mutations in four and six genes in SGM-1 and SGM-2 respectively, while no SNPs were found in SGM-3. Analysis of the earlier reported Quantitative Trait Loci (QTL) regions in SGM-3 revealed negligible variations from WT, suggesting it to be a novel SG mutant.
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Yugandhar P, Sun Y, Liu L, Negi M, Nallamothu V, Sun S, Neelamraju S, Rai V, Jain A. Characterization of the loss-of-function mutant NH101 for yield under phosphate deficiency from EMS-induced mutants of rice variety Nagina22. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:1-13. [PMID: 29957570 DOI: 10.1016/j.plaphy.2018.06.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/28/2018] [Accepted: 06/14/2018] [Indexed: 05/09/2023]
Abstract
In earlier studies at IIRR, Hyderabad, screening of ∼2000 EMS mutants of the rice variety Nagina22 (N22) resulted in the identification of 11 loss-of-function mutants with zero grain yield in Pi-deprived soil under field condition. Among these mutants, NH101 was selected for comparative analyses with N22 for various morphophysiological and/or molecular traits during growth in a hydroponic system (7 d) and in a pot soil (50% flowering) under different Pi regime. The total length of the seminal and adventitious roots, agronomic traits (panicle length and unfilled spikelet/panicle), activities of the antioxidant enzymes (SOD, POD, and APX), and the relative expression levels of the genes involved in the maintenance of Pi homeostasis (MPH) i.e., OsPHR2, SPX1/2 OsPT4, 6, and 8 showed significant increase in the Pi-deprived mutant compared with N22. Whereas, some of the traits showed significant reduction in NH101 than N22 such as number of tillers and filled spikelets/panicle, yield, contents of Pi and externally secreted APase, activity of CAT, and the relative expression levels of MPH genes i.e., OsmiR399a, OsPHO1;2, OsIPS1, OsPAP10a, OsPT2, 9, and 10. The study highlighted wide spectrum differential effects of the mutation in NH101 on various traits that play important roles governing the maintenance of Pi homeostasis. This mutant thus provides a rich repository of genetic material amenable for the identification of the genes that are pivotal for Pi use efficiency.
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Affiliation(s)
- Poli Yugandhar
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Yafei Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Lu Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Manisha Negi
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi, 110012, India
| | | | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Sarla Neelamraju
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India.
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi, 110012, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India.
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PS S, SV AM, Prakash C, MK R, Tiwari R, Mohapatra T, Singh NK. High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array. RICE (NEW YORK, N.Y.) 2017; 10:28. [PMID: 28584974 PMCID: PMC5459777 DOI: 10.1186/s12284-017-0167-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 05/30/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set and poor grain quality. Identification of QTLs and causal genes for heat stress tolerance at flowering will facilitate breeding for improved heat tolerance in rice. In the present study, we used 272 F8 recombinant inbred lines derived from a cross between Nagina22, a well-known heat tolerant Aus cultivar and IR64, a heat sensitive popular Indica rice variety to map the QTLs for heat tolerance. RESULTS To enable precise phenotyping for heat stress tolerance, we used a controlled phenotyping facility available at ICAR-Indian Institute of Wheat and Barley Research, Karnal, India. Based on 'days to 50% flowering' data of the RILs, we followed staggered sowing to synchronize flowering to impose heat stress at uniform stage. Using the Illumina infinium 5K SNP array for genotyping the parents and the RILs, and stress susceptibility and stress tolerance indices (SSI and STI) of percent spikelet sterility and yield per plant (g), we identified five QTLs on chromosomes 3, 5, 9 and 12. The identified QTLs explained phenotypic variation in the range of 6.27 to 21. 29%. Of these five QTLs, two high effect QTLs, one novel (qSTIPSS9.1) and one known (qSTIY5.1/qSSIY5.2), were mapped in less than 400 Kbp genomic regions, comprising of 65 and 54 genes, respectively. CONCLUSIONS The present study identified two major QTLs for heat tolerance in rice in narrow physical intervals, which can be employed for crop improvement by marker assisted selection (MAS) after development of suitable scorable markers for breeding of high yielding heat tolerant rice varieties. This is the first report of a major QTL for heat tolerance on chromosome 9 of rice. Further, a known QTL for heat tolerance on chromosome 5 was narrowed down from 23 Mb to 331 Kbp in this study.
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Affiliation(s)
- Shanmugavadivel PS
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
- Present address, Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, 208 024 India
| | - Amitha Mithra SV
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ramkumar MK
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132 001 India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110 001 India
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Ps S, Sv AM, Prakash C, Mk R, Tiwari R, Mohapatra T, Singh NK. High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array. RICE (NEW YORK, N.Y.) 2017. [PMID: 28584974 DOI: 10.1186/s12284-017-0167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
BACKGROUND Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set and poor grain quality. Identification of QTLs and causal genes for heat stress tolerance at flowering will facilitate breeding for improved heat tolerance in rice. In the present study, we used 272 F8 recombinant inbred lines derived from a cross between Nagina22, a well-known heat tolerant Aus cultivar and IR64, a heat sensitive popular Indica rice variety to map the QTLs for heat tolerance. RESULTS To enable precise phenotyping for heat stress tolerance, we used a controlled phenotyping facility available at ICAR-Indian Institute of Wheat and Barley Research, Karnal, India. Based on 'days to 50% flowering' data of the RILs, we followed staggered sowing to synchronize flowering to impose heat stress at uniform stage. Using the Illumina infinium 5K SNP array for genotyping the parents and the RILs, and stress susceptibility and stress tolerance indices (SSI and STI) of percent spikelet sterility and yield per plant (g), we identified five QTLs on chromosomes 3, 5, 9 and 12. The identified QTLs explained phenotypic variation in the range of 6.27 to 21. 29%. Of these five QTLs, two high effect QTLs, one novel (qSTIPSS9.1) and one known (qSTIY5.1/qSSIY5.2), were mapped in less than 400 Kbp genomic regions, comprising of 65 and 54 genes, respectively. CONCLUSIONS The present study identified two major QTLs for heat tolerance in rice in narrow physical intervals, which can be employed for crop improvement by marker assisted selection (MAS) after development of suitable scorable markers for breeding of high yielding heat tolerant rice varieties. This is the first report of a major QTL for heat tolerance on chromosome 9 of rice. Further, a known QTL for heat tolerance on chromosome 5 was narrowed down from 23 Mb to 331 Kbp in this study.
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Affiliation(s)
- Shanmugavadivel Ps
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
- Present address, Division of Plant Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, 208 024, India
| | - Amitha Mithra Sv
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ramkumar Mk
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132 001, India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110 001, India
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Sandhu M, Sureshkumar V, Prakash C, Dixit R, Solanke AU, Sharma TR, Mohapatra T, S V AM. RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement. BMC Bioinformatics 2017; 18:432. [PMID: 28964253 PMCID: PMC5622590 DOI: 10.1186/s12859-017-1846-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Background Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. Results RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. ‘Physical position search’ is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the ‘common genes across varieties’ search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. Conclusions The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201 Electronic supplementary material The online version of this article (10.1186/s12859-017-1846-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maninder Sandhu
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India
| | - V Sureshkumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.,Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Rekha Dixit
- Shobhit University, Modipuram, Meerut, 250110, Uttar Pradesh, India.,Current address: Department of biotechnology, Keralverma faculty of science, Swami Vivekanand Subharti University, Meerut, 250005, Uttar Pradesh, India
| | - Amolkumar U Solanke
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001, India
| | - Amitha Mithra S V
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.
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