1
|
Tomar S, Subba A, Chatterjee Y, Singhal NK, Pareek A, Singla-Pareek SL. A cystathionine beta-synthase domain containing protein, OsCBSCBS4, interacts with OsSnRK1A and OsPKG and functions in abiotic stress tolerance in rice. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39073079 DOI: 10.1111/pce.15061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024]
Abstract
The Cystathionine-β-Synthase (CBS) domain-containing proteins (CDCPs) constitute a functionally diverse protein superfamily, sharing an evolutionary conserved CBS domain either in pair or quad. Rice genome (Oryza sativa subsp. indica) encodes 42 CDCPs; their functions remain largely unexplored. This study examines OsCBSCBS4, a quadruple CBS domain containing protein towards its role in regulating the abiotic stress tolerance in rice. Gene expression analyses revealed upregulation of OsCBSCBS4 in response to diverse abiotic stresses. Further, the cytoplasm-localised OsCBSCBS4 showed interaction with two different kinases, a cytoplasmic localised cGMP-dependant protein kinase (OsPKG) and the nucleo-cytoplasmic catalytic subunit of sucrose-nonfermentation 1-related protein kinase 1 (OsSnRK1A). The interaction with the latter assisted in trafficking of OsCBSCBS4 to the nucleus as well. Overexpression of OsCBSCBS4 in rice resulted in enhanced tolerance to drought and salinity stress, via maintaining better physiological parameters and antioxidant activity. Additionally, OsCBSCBS4-overexpressing rice plants exhibited reduced yield penalty under stress conditions. The in silico docking and in vitro binding analyses of OsCBSCBS4 with ATP suggest its involvement in cellular energy balance. Overall, this study provides novel insight into the unexplored functions of OsCBSCBS4 and demonstrates it as a new promising target for augmenting crop resilience.
Collapse
Affiliation(s)
- Surabhi Tomar
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashish Subba
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Yajnaseni Chatterjee
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | | | - Ashwani Pareek
- National Agri-Food Biotechnology Institute, Mohali, India
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| |
Collapse
|
2
|
Xie E, Chen J, Wang B, Shen Y, Tang D, Du G, Li Y, Cheng Z. The transcribed centromeric gene OsMRPL15 is essential for pollen development in rice. PLANT PHYSIOLOGY 2023; 192:1063-1079. [PMID: 36905369 PMCID: PMC10231452 DOI: 10.1093/plphys/kiad153] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/19/2023] [Accepted: 02/15/2023] [Indexed: 06/01/2023]
Abstract
Centromeres consist of highly repetitive sequences that are challenging to map, clone, and sequence. Active genes exist in centromeric regions, but their biological functions are difficult to explore owing to extreme suppression of recombination in these regions. In this study, we used the CRISPR/Cas9 system to knock out the transcribed gene Mitochondrial Ribosomal Protein L15 (OsMRPL15), located in the centromeric region of rice (Oryza sativa) chromosome 8, resulting in gametophyte sterility. Osmrpl15 pollen was completely sterile, with abnormalities appearing at the tricellular stage including the absence of starch granules and disrupted mitochondrial structure. Loss of OsMRPL15 caused abnormal accumulation of mitoribosomal proteins and large subunit rRNA in pollen mitochondria. Moreover, the biosynthesis of several proteins in mitochondria was defective, and expression of mitochondrial genes was upregulated at the mRNA level. Osmrpl15 pollen contained smaller amounts of intermediates related to starch metabolism than wild-type pollen, while biosynthesis of several amino acids was upregulated, possibly to compensate for defective mitochondrial protein biosynthesis and initiate consumption of carbohydrates necessary for starch biosynthesis. These results provide further insight into how defects in mitoribosome development cause gametophyte male sterility.
Collapse
Affiliation(s)
- En Xie
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiawei Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Bingxin Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Guijie Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhukuan Cheng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
3
|
Schierenbeck M, Alqudah AM, Thabet SG, Lohwasser U, Simón MR, Börner A. Association mapping unravels the genetics controlling seedling drought stress tolerance in winter wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1061845. [PMID: 36818842 PMCID: PMC9933780 DOI: 10.3389/fpls.2023.1061845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Drought is a major constraint in wheat (Triticum aestivum L.) grain yield. The present work aimed to identify quantitative trait nucleotides (QTNs)/ candidate genes influencing drought tolerance-related traits at the seedling stage in 261 accessions of a diverse winter wheat panel. Seeds from three consecutive years were exposed to polyethylene glycol 12% (PEG-6000) and a control treatment (distilled water). The Farm-CPU method was used for the association analysis with 17,093 polymorphic SNPs. PEG treatment reduced shoot length (SL) (-36.3%) and root length (RL) (-11.3%) compared with control treatments, while the coleoptile length (CL) was increased by 11% under drought conditions, suggesting that it might be considered as an indicator of stress-tolerance. Interestingly, we revealed 70 stable QTN across 17 chromosomes. Eight QTNs related to more than one trait were detected on chromosomes 1B, 2A (2), 2B, 2D, 4B, 7A, and 7B and located nearby or inside candidate genes within the linkage disequilibrium (LD) interval. For instance, the QTN on chromosome 2D is located inside the gene TraesCS2D02G133900 that controls the variation of CL_S and SL_C. The allelic variation at the candidate genes showed significant influence on the associated traits, demonstrating their role in controlling the natural variation of multi-traits of drought stress tolerance. The gene expression of these candidate genes under different stress conditions validates their biological role in stress tolerance. Our findings offer insight into understanding the genetic factors and diverse mechanisms in response to water shortage conditions that are important for wheat improvement and adaptation at early developmental stages.
Collapse
Affiliation(s)
- Matías Schierenbeck
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Seeland, Germany
- Cereals, Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina
- CONICET CCT La Plata, La Plata, Argentina
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha, Qatar
| | - Samar G. Thabet
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Ulrike Lohwasser
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Seeland, Germany
| | - María Rosa Simón
- Cereals, Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina
- CONICET CCT La Plata, La Plata, Argentina
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Seeland, Germany
| |
Collapse
|
4
|
Liu H, Wang Q, Xie L, Xu K, Zhang F, Ruan X, Li L, Tan G. Genome-wide identification of cystathionine beta synthase genes in wheat and its relationship with anther male sterility under heat stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1061472. [PMID: 36589045 PMCID: PMC9795209 DOI: 10.3389/fpls.2022.1061472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Cystathionine beta synthase (CBS) domains containing proteins (CDCPs) plays an important role in plant development through regulation of the thioredoxin system, as well as its ability to respond to biotic and abiotic stress conditions. Despite this, no systematic study has examined the wheat CBS gene family and its relation to high temperature-induced male sterility. In this study, 66 CBS family members were identified in the wheat genome, and their gene or protein sequences were used for subsequent analysis. The TaCBS gene family was found to be unevenly distributed on 21 chromosomes, and they were classified into four subgroups according to their gene structure and phylogeny. The results of collinearity analysis showed that there were 25 shared orthologous genes between wheat, rice and Brachypodium distachyon, and one shared orthologous gene between wheat, millet and barley. The cis-regulatory elements of the TaCBS were related to JA, IAA, MYB, etc. GO and KEGG pathway analysis identified these TaCBS genes to be associated with pollination, reproduction, and signaling and cellular processes, respectively. A heatmap of wheat plants based on transcriptome data showed that TaCBS genes were expressed to a higher extent in spikelets relative to other tissues. In addition, 29 putative tae-miRNAs were identified, targeting 41 TaCBS genes. Moreover, qRT-PCR validation of six TaCBS genes indicated their critical role in anther development, as five of them were expressed at lower levels in heat-stressed male sterile anthers than in Normal anthers. Together with anther phenotypes, paraffin sections, starch potassium iodide staining, and qRT-PCR data, we hypothesized that the TaCBS gene has a very important connection with the heat-stressed sterility process in wheat, and these data provide a basis for further insight into their relationship.
Collapse
Affiliation(s)
- Hongzhan Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Qi Wang
- School of Network Engineering, Zhoukou Normal University, Zhoukou, Henan, China
| | - Liuyong Xie
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Kedong Xu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Fuli Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- Institute of Plant Protection and Edible Mushrooms, Zhoukou Academy of Agricultural Sciences, Zhoukou, Henan, China
| | - Xianle Ruan
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Lili Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Guangxuan Tan
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| |
Collapse
|
5
|
Zhou JR, Li J, Lin JX, Xu HM, Chu N, Wang QN, Gao SJ. Genome-wide characterization of cys-tathionine-β-synthase domain-containing proteins in sugarcane reveals their role in defense responses under multiple stressors. FRONTIERS IN PLANT SCIENCE 2022; 13:985653. [PMID: 36092401 PMCID: PMC9453547 DOI: 10.3389/fpls.2022.985653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Cys-tathionine-β-synthase (CBS) domain-containing proteins (CDCPs) are essential for regulating plant responses to various biotic and abiotic stressors. This study describes the systematic identification and characterization of CDCP family genes in Saccharum spontaneum. A total of 95 SsCDCP genes and eight phylogenetic groups were identified that were distributed over 29 chromosomes of the AP85-441 genome. Most (78/95) SsCDCPs underwent fragment duplication events, and 64 gene pairs were located in synteny blocks. Expression profiling of nine ShCDCPs was also carried out in the Saccharum spp. cultivars ROC22 and MT11-611 that are resistant and susceptible to red stripe, respectively, in response to: (i) Infection by the bacterial pathogen Acidovorax avenue subsp. avenae (Aaa); (ii) abiotic stressors (drought and salinity); and (iii) exogenous salicylic acid (SA) treatment. Members of one gene pair (ShCBSD-PB1-5A and ShCBSD-PB1-7A-1) with a fragment duplication event acted as negative regulators in sugarcane under four stresses, as supported by the significantly decreased expression levels of ShCBSD-PB1-5A (23-83%) and ShCBSD-PB1-7A-1 (15-75%) at all-time points, suggesting that they have functional redundancy. Genes in another pair, ShCBS-4C and ShCBS-4D-1, which have a fragment duplication event, play opposing regulatory roles in sugarcane exposed to multiple stresses, particularly Aaa and NaCl treatments. ShCBS-4C expression was significantly decreased by 32-77%, but ShCBS-4D-1 expression was dramatically upregulated by 1.2-6.2-fold in response to Aaa treatment of both cultivars across all-time points. This result suggested that both genes exhibited functional divergence. Meanwhile, the expression of SsCBSDCBS-5A was significantly upregulated in ROC22 by 1.4-4.6-fold in response to the four stressors. These findings provide important clues for further elucidating the function of ShCDCP genes in sugarcane responding to a diverse range of stresses.
Collapse
Affiliation(s)
- Jing-Ru Zhou
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juan Li
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jia-Xin Lin
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hui-Mei Xu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Na Chu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qin-Nan Wang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Nanfan and Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
6
|
Tomar S, Subba A, Bala M, Singh AK, Pareek A, Singla-Pareek SL. Genetic Conservation of CBS Domain Containing Protein Family in Oryza Species and Their Association with Abiotic Stress Responses. Int J Mol Sci 2022; 23:ijms23031687. [PMID: 35163610 PMCID: PMC8836131 DOI: 10.3390/ijms23031687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 01/27/2023] Open
Abstract
Crop Wild Relatives (CWRs) form a comprehensive gene pool that can answer the queries related to plant domestication, speciation, and ecological adaptation. The genus ‘Oryza’ comprises about 27 species, of which two are cultivated, while the remaining are wild. Here, we have attempted to understand the conservation and diversification of the genes encoding Cystathionine β-synthase (CBS) domain-containing proteins (CDCPs) in domesticated and CWRs of rice. Few members of CDCPs were previously identified to be stress-responsive and associated with multiple stress tolerance in rice. Through genome-wide analysis of eleven rice genomes, we identified a total of 36 genes encoding CDCPs in O. longistaminata, 38 in O. glaberrima, 39 each in O. rufipogon, O. glumaepatula, O. brachyantha, O. punctata, and O. sativa subsp. japonica, 40 each in O. barthii and O. meridionalis, 41 in O. nivara, and 42 in O. sativa subsp. indica. Gene duplication analysis as well as non-synonymous and synonymous substitutions in the duplicated gene pairs indicated that this family is shaped majorly by the negative or purifying selection pressure through the long-term evolution process. We identified the presence of two additional hetero-domains, namely TerCH and CoatomerE (specifically in O. sativa subsp. indica), which were not reported previously in plant CDCPs. The in silico expression analysis revealed some of the members to be responsive to various abiotic stresses. Furthermore, the qRT-PCR based analysis identified some members to be highly inducive specifically in salt-tolerant genotype in response to salinity. The cis-regulatory element analysis predicted the presence of numerous stress as well as a few phytohormone-responsive elements in their promoter region. The data presented in this study would be helpful in the characterization of these CDCPs from rice, particularly in relation to abiotic stress tolerance.
Collapse
Affiliation(s)
- Surabhi Tomar
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Ashish Subba
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Meenu Bala
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India;
- National Agri-Food Biotechnology Institute, Mohali 140306, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
- Correspondence:
| |
Collapse
|
7
|
Kumar G, Arya M, Padma R, Puthusseri B, Giridhar P. Distinct GmASMTs are involved in regulating transcription factors and signalling cross-talk across embryo development, biotic, and abiotic stress in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:948901. [PMID: 36035712 PMCID: PMC9403468 DOI: 10.3389/fpls.2022.948901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/15/2022] [Indexed: 05/08/2023]
Abstract
N-Acetylserotonin O-methyltransferase (ASMT) is the final enzyme involved in melatonin biosynthesis. Identifying the expression of ASMT will reveal the regulatory role in the development and stress conditions in soybean. To identify and characterize ASMT in soybean (GmASMT), we employed genome-wide analysis, gene structure, cis-acting elements, gene expression, co-expression network analysis, and enzyme assay. We found seven pairs of segmental and tandem duplication pairs among the 44 identified GmASMTs by genome-wide analysis. Notably, co-expression network analysis reported that distinct GmASMTs are involved in various stress response. For example, GmASMT3, GmASMT44, GmASMT17, and GmASMT7 are involved in embryo development, heat, drought, aphid, and soybean cyst nematode infections, respectively. These distinct networks of GmASMTs were associated with transcription factors (NAC, MYB, WRKY, and ERF), stress signalling, isoflavone and secondary metabolites, calcium, and calmodulin proteins involved in stress regulation. Further, GmASMTs demonstrated auxin-like activities by regulating the genes involved in auxin transporter (WAT1 and NRT1/PTR) and auxin-responsive protein during developmental and biotic stress. The current study identified the key regulatory role of GmASMTs during development and stress. Hence GmASMT could be the primary target in genetic engineering for crop improvement under changing environmental conditions.
Collapse
Affiliation(s)
- Gyanendra Kumar
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
| | - Monisha Arya
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
| | - Radhika Padma
- Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Bijesh Puthusseri
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
| | - Parvatam Giridhar
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
- *Correspondence: Parvatam Giridhar,
| |
Collapse
|
8
|
Satrio RD, Fendiyanto MH, Supena EDJ, Suharsono S, Miftahudin M. Genome-wide SNP discovery, linkage mapping, and analysis of QTL for morpho-physiological traits in rice during vegetative stage under drought stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2635-2650. [PMID: 34924715 PMCID: PMC8639969 DOI: 10.1007/s12298-021-01095-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 06/14/2023]
Abstract
Drought tolerance in rice is controlled by several genes and is inherited quantitatively. Low genetic map density and the use of phenotypic traits that do not reflect the corresponding tolerance level have been obstacles in genetic analyses performed to identify genes that control drought-tolerant traits in rice. The current study aimed to construct a genetic map from high-density single-nucleotide polymorphism (SNP) markers generated from genome sequences of recombinant inbred lines (RILs), derived from IR64 × Hawara Bunar. Moreover, it sought to analyze the quantitative trait loci (QTL) and identify the drought tolerance candidate genes. A linkage map along 1980 cM on the 12 rice chromosomes was constructed employing 55,205 SNP markers resulting from the RIL genome sequences. A total of 175 morpho-physiological traits pertaining to drought stress were determined. A total of 41 QTLs were detected in 13 regions on rice chromosomes 1, 3, 6, 8, 9, and 12. Moreover, three hotspot QTL regions were found on chromosomes 6 and 8, along with two major QTL on chromosome 9. Differential gene expression for the loci within the QTL physical map intervals revealed many potential candidate genes. The markers tightly linked to the QTL and their candidate genes can potentially be used for pyramiding in marker-assisted breeding in order to achieve genetic improvement concerning the tolerance of rice to drought stress. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01095-y.
Collapse
Affiliation(s)
- Rizky Dwi Satrio
- Plant Biology Graduate Program, Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Kampus IPB Dramaga, Bogor, 16680 Indonesia
- Department of Biology, Faculty of Military Mathematics and Natural Sciences, The Republic of Indonesia Defense University (Unhan RI), Komplek Indonesia Peace and Security Center (IPSC) Sentul, Bogor, 16810 Indonesia
| | - Miftahul Huda Fendiyanto
- Plant Biology Graduate Program, Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Kampus IPB Dramaga, Bogor, 16680 Indonesia
- Department of Biology, Faculty of Military Mathematics and Natural Sciences, The Republic of Indonesia Defense University (Unhan RI), Komplek Indonesia Peace and Security Center (IPSC) Sentul, Bogor, 16810 Indonesia
| | - Ence Darmo Jaya Supena
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Kampus IPB Dramaga, Bogor, 16680 Indonesia
- Faculty of Military Mathematics and Natural Sciences, The Republic of Indonesia Defense University (Unhan RI), Komplek Indonesia Peace and Security Center (IPSC) Sentul, Bogor, 16810 Indonesia
| | - Sony Suharsono
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Kampus IPB Dramaga, Bogor, 16680 Indonesia
| | - Miftahudin Miftahudin
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Kampus IPB Dramaga, Bogor, 16680 Indonesia
| |
Collapse
|
9
|
Karthikaichamy A, Beardall J, Coppel R, Noronha S, Bulach D, Schittenhelm RB, Srivastava S. Data-Independent-Acquisition-Based Proteomic Approach towards Understanding the Acclimation Strategy of Oleaginous Microalga Microchloropsis gaditana CCMP526 in Hypersaline Conditions. ACS OMEGA 2021; 6:22151-22164. [PMID: 34497906 PMCID: PMC8412934 DOI: 10.1021/acsomega.1c02786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Salinity is one of the significant factors that affect growth and cellular metabolism, including photosynthesis and lipid accumulation, in microalgae and higher plants. Microchloropsis gaditana CCMP526 can acclimatize to different salinity levels by accumulating compatible solutes, carbohydrates, and lipids as energy storage molecules. We used proteomics to understand the molecular basis for acclimation of M. gaditana to increased salinity levels [55 and 100 PSU (practical salinity unit)]. Correspondence analysis was used for the identification of salinity-responsive proteins (SRPs). The highest number of salinity-induced proteins was observed in 100 PSU. Gene ontology enrichment analysis revealed a separate path of acclimation for cells exposed to 55 and 100 PSU. Osmolyte and lipid biosynthesis were upregulated in hypersaline conditions. Concomitantly, lipid oxidation pathways were also upregulated in hypersaline conditions, providing acetyl-CoA for energy metabolism through the tricarboxylic acid cycle. Carbon fixation and photosynthesis were tightly regulated, while chlorophyll biosynthesis was affected in hypersaline conditions. Importantly, temporal proteome analysis of salinity-induced M. gaditana revealed vital SRPs which could be used for engineering salinity resilient microalgal strains for improved productivity in hypersaline culture conditions.
Collapse
Affiliation(s)
- Anbarasu Karthikaichamy
- IITB-Monash
Research Academy, Mumbai 400076, India
- Department
of Microbiology, Monash University, Clayton, 3800 Victoria, Australia
- Department
of Chemical Engineering, IIT Bombay, Mumbai 400076, India
| | - John Beardall
- School
of Biological Sciences, Monash University, Clayton, 3800 Victoria, Australia
| | - Ross Coppel
- Department
of Microbiology, Monash University, Clayton, 3800 Victoria, Australia
| | - Santosh Noronha
- Department
of Chemical Engineering, IIT Bombay, Mumbai 400076, India
| | - Dieter Bulach
- Medicine,
Dentistry and Health Sciences, University
of Melbourne, Melbourne 3010, Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics
& Metabolomics Facility, Monash University, Clayton, 3800 Victoria, Australia
| | - Sanjeeva Srivastava
- Department
of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India
| |
Collapse
|
10
|
Buffon G, Blasi ÉADR, Lamb TI, Adamski JM, Schwambach J, Ricachenevsky FK, Bertolazi A, Silveira V, Lopes MCB, Sperotto RA. Oryza sativa cv. Nipponbare and Oryza barthii as Unexpected Tolerance and Susceptibility Sources Against Schizotetranychus oryzae (Acari: Tetranychidae) Mite Infestation. FRONTIERS IN PLANT SCIENCE 2021; 12:613568. [PMID: 33643348 PMCID: PMC7902502 DOI: 10.3389/fpls.2021.613568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
Cultivated rice (Oryza sativa L.) is frequently exposed to multiple stresses, including Schizotetranychus oryzae mite infestation. Rice domestication has narrowed the genetic diversity of the species, leading to a wide susceptibility. This work aimed to analyze the response of two African rice species (Oryza barthii and Oryza glaberrima), weedy rice (O. sativa f. spontanea), and O. sativa cv. Nipponbare to S. oryzae infestation. Surprisingly, leaf damage, histochemistry, and chlorophyll concentration/fluorescence indicated that the African species present a higher level of leaf damage, increased accumulation of H2O2, and lower photosynthetic capacity when compared to O. sativa plants under infested conditions. Infestation decreased tiller number, except in Nipponbare, and caused the death of O. barthii and O. glaberrima plants during the reproductive stage. While infestation did not affect the weight of 1,000 grains in both O. sativa, the number of panicles per plant was affected only in O. sativa f. spontanea, and the percentage of full seeds per panicle and seed length were increased only in Nipponbare. Using proteomic analysis, we identified 195 differentially abundant proteins when comparing susceptible (O. barthii) and tolerant (Nipponbare) plants under control and infested conditions. O. barthii presents a less abundant antioxidant arsenal and is unable to modulate proteins involved in general metabolism and energy production under infested condition. Nipponbare presents high abundance of detoxification-related proteins, general metabolic processes, and energy production, suggesting that the primary metabolism is maintained more active compared to O. barthii under infested condition. Also, under infested conditions, Nipponbare presents higher levels of proline and a greater abundance of defense-related proteins, such as osmotin, ricin B-like lectin, and protease inhibitors (PIs). These differentially abundant proteins can be used as biotechnological tools in breeding programs aiming at increased tolerance to mite infestation.
Collapse
Affiliation(s)
- Giseli Buffon
- Graduate Program in Biotechnology, University of Taquari Valley-Univates, Lajeado, Brazil
| | | | - Thainá Inês Lamb
- Biological Sciences and Health Center, University of Taquari Valley-Univates, Lajeado, Brazil
| | - Janete Mariza Adamski
- Graduate Program in Botany, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Joséli Schwambach
- Graduate Program in Biotechnology, University of Caxias do Sul, Caxias do Sul, Brazil
| | - Felipe Klein Ricachenevsky
- Graduate Program in Molecular and Cellular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Amanda Bertolazi
- Laboratory of Biotechnology, Bioscience and Biotechnology Center, State University of Northern Rio de Janeiro Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Vanildo Silveira
- Laboratory of Biotechnology, Bioscience and Biotechnology Center, State University of Northern Rio de Janeiro Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | | | - Raul Antonio Sperotto
- Graduate Program in Biotechnology, University of Taquari Valley-Univates, Lajeado, Brazil
- Biological Sciences and Health Center, University of Taquari Valley-Univates, Lajeado, Brazil
| |
Collapse
|