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Prodjinoto H, Irakoze W, Gandonou C, Quinet M, Lutts S. Comparison between the impact of osmotic and NaCl treatments on the expression of genes coding for ion transporters in Oryza glaberrima Steud. PLoS One 2023; 18:e0290752. [PMID: 37967065 PMCID: PMC10650995 DOI: 10.1371/journal.pone.0290752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/14/2023] [Indexed: 11/17/2023] Open
Abstract
We analyzed the expression of genes coding for Na+ transporters (OsHKT1.5, OsHKT1.1, OsSOS1, OsSOS2, OsNHX1, OsNHX2), Cl- transporter (OsNRT1, OsCLC, OsCCC1) and gene coding for the transcription factor DREB (OsDREB2) involved in response to desiccation in two cultivars of O. glaberrrima differing in salt-resistance (salt-tolerant cultivar (TOG5307) and salt-sensitive (TOG 5949)) exposed to NaCl, PEG or both agents present simultaneously. Seedlings were grown in iso-osmotic nutrient solution (Ψs = -0.47±0.02 MPa) containing PEG 6,000 12.9% (water stress), NaCl 75 mM (salt stress) and PEG 6.4% + NaCl 37.5 mM (MIX-treatment) during 1 and 7 days. Plants were analyzed for gene expression, mineral nutrients, and photosynthetic-related parameters. Na+ and Cl- accumulations in salt-treated plants were lower in roots and shoots of TOG5307 comparatively to TOG5949 while water content decreased in TOG5307. TOG5307 exhibited tolerance to water stress and maintained higher net photosynthesis and water use efficiency than TOG5949 in response to all treatments, but was less efficient for osmotic adjustment. Dehydration tolerance of TOG5307 involves a higher OsDREB2 expression. TOG5307 also exhibited a higher OsSOS1, OsSOS2, OsNHX1 and OsNHX2 expression than TOG5949 in response to salinity. OsHKT1.5 was slightly induced in the shoot. OsHKT1.1 was recorded in the shoots but remained undetectable in the roots. Chloride and sodium accumulations were strongly reduced in the shoots when PEG was present. Salinity resistance in Oryza glaberrima implies tolerance to dehydration as well as complementary strategies of Na+ exclusion through the SOS system and Na+ tolerance through vacuolar sequestration.
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Affiliation(s)
- Hermann Prodjinoto
- Groupe de Recherche en Physiologie végétale – Earth and Life Institute-Agronomy (ELIA) – Université catholique de Louvain, Louvain-la-Neuve, Belgium
- Laboratoire de Physiologie végétale et d’Etude des Stress environnementaux, Faculté des Sciences et Techniques, Université d’Abomey-Calavi, Cotonou, République du Bénin
| | - Willy Irakoze
- Faculté d’Agronomie et de Bio-ingénierie, Université du Burundi, Bujumbura, Burundi
| | - Christophe Gandonou
- Laboratoire de Physiologie végétale et d’Etude des Stress environnementaux, Faculté des Sciences et Techniques, Université d’Abomey-Calavi, Cotonou, République du Bénin
| | - Muriel Quinet
- Groupe de Recherche en Physiologie végétale – Earth and Life Institute-Agronomy (ELIA) – Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Stanley Lutts
- Groupe de Recherche en Physiologie végétale – Earth and Life Institute-Agronomy (ELIA) – Université catholique de Louvain, Louvain-la-Neuve, Belgium
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Jaganathan D, Rajakani R, Doddamani D, Saravanan D, Pulipati S, Hari Sundar G V, Sellamuthu G, Jayabalan S, Kumari K, Parthasarathy P, S P, Ramalingam S, Shivaprasad PV, Venkataraman G. A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance. Sci Rep 2023; 13:2195. [PMID: 36750679 PMCID: PMC9905475 DOI: 10.1038/s41598-023-28836-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group. The miRNA-miRNA* duplex region is completely conserved across eleven Oryza species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the 'A10234287911' allele may promote better processing vis-à-vis the structure conferred by 'G10234287911' allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression.
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Affiliation(s)
- Deepa Jaganathan
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India.,Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India
| | - Raja Rajakani
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | | | - Divya Saravanan
- Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India
| | - Shalini Pulipati
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | - Vivek Hari Sundar G
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Gothandapani Sellamuthu
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India.,Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Shilpha Jayabalan
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | - Kumkum Kumari
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | - Pavithra Parthasarathy
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | - Punitha S
- GIS and Remote Sensing Laboratory, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India
| | | | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Chennai, Tamil Nadu, 600113, India.
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Jayabalan S, Rajakani R, Kumari K, Pulipati S, Hariharan RVG, Venkatesan SD, Jaganathan D, Kancharla PK, Raju K, Venkataraman G. Morpho-physiological, biochemical and molecular characterization of coastal rice landraces to identify novel genetic sources of salinity tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 187:50-66. [PMID: 35952550 DOI: 10.1016/j.plaphy.2022.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 07/01/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Soil salinity is a leading cause for yield losses in rice, affecting nearly 6% of global rice cultivable area. India is host to a rich diversity of coastal rice landraces that are naturally tolerant to salinity and an untapped source to identify novel determinants of salinity tolerance. In the present study, we have assessed the relative salinity tolerance of 43 previously genotyped rice landraces at seedling stage, using thirteen morpho-physiological and biochemical parameters using a hydroponics system. Among 43 rice varieties, 25 were tolerant, 15 were moderately tolerant, 1 was moderately susceptible and 2 sensitive checks were found to be highly susceptible based on standard salinity scoring methods. In addition to previously known saline tolerant genotypes (Pokkali, FL478 and Nona Bokra), the present study has novel genotypes such as Katrangi, Orkyma, Aduisen 1, Orumundakan 1, Hoogla, and Talmugur 2 as potential sources of salinity tolerance through measurement of morpho-physiological and biochemical parameters including Na+, K+ estimations and Na+/K+ ratios. Further, Pallipuram Pokkali may be an important source of the tissue tolerance trait under salinity. Four marker trait associations (RM455-root Na+; RM161-shoot and root Na+/K+ ratios; RM237-salinity tolerance index) accounted for phenotypic variations in the range of 20.97-39.82%. A significant increase in root endodermal and exodermal suberization was observed in selected rice landraces under salinity. For the first time, variation in the number of suberized sclerenchymatous layers as well as passage cells is reported, in addition to expression level changes in suberin biosynthetic genes (CYP86A2, CYP81B1, CYP86A8 and PERL).
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Affiliation(s)
- Shilpha Jayabalan
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Taramani, Chennai, 600113, Tamil Nadu, India; Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Raja Rajakani
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Taramani, Chennai, 600113, Tamil Nadu, India
| | - Kumkum Kumari
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Taramani, Chennai, 600113, Tamil Nadu, India
| | - Shalini Pulipati
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Taramani, Chennai, 600113, Tamil Nadu, India
| | - Raj V Ganesh Hariharan
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram, 603203, Tamil Nadu, India
| | - Sowmiya Devi Venkatesan
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram, 603203, Tamil Nadu, India
| | - Deepa Jaganathan
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Taramani, Chennai, 600113, Tamil Nadu, India; Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, Tamil Nadu, India
| | - Pavan Kumar Kancharla
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Kalaimani Raju
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Taramani, Chennai, 600113, Tamil Nadu, India
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Taramani, Chennai, 600113, Tamil Nadu, India.
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Yadav AK, Kumar A, Grover N, Ellur RK, Krishnan SG, Bollinedi H, Bhowmick PK, Vinod KK, Nagarajan M, Krishnamurthy SL, Singh AK. Marker aided introgression of 'Saltol', a major QTL for seedling stage salinity tolerance into an elite Basmati rice variety 'Pusa Basmati 1509'. Sci Rep 2020; 10:13877. [PMID: 32887905 PMCID: PMC7474085 DOI: 10.1038/s41598-020-70664-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 07/31/2020] [Indexed: 11/26/2022] Open
Abstract
Marker assisted backcross breeding was used to transfer Saltol, a major QTL for seedling stage salinity tolerance from the donor FL478 to Pusa Basmati 1509 (PB 1509), a high yielding and early maturing Basmati rice variety. Foreground selection was carried out using three markers namely, AP3206f, RM3412b and RM10793, linked to Saltol. In addition, 105 genome-wide SSR markers polymorphic between FL478 and PB 1509 were used in background selection. Among the BC3F4 near isogenic lines (NILs) developed, recurrent parent genome recovery ranged from 96.67 to 98.57%. Multi-season evaluation identified some of the NILs showing significantly higher yield with grain and cooking quality comparable to PB 1509. All the NILs exhibited tolerance to salinity with significantly higher relative water content, membrane stability index and proline content as compared to PB 1509. The root and shoot concentration of Na+, K+ and Na+/K+ in NILs was at par with FL478 under stress conditions. The gene OsHKT1;5 located in the Saltol region showed higher expression levels under stress indicating its role in conferring salinity tolerance. Salt tolerant NILs of PB 1509 will be useful in stabilizing production in salt affected areas.
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Affiliation(s)
- Ashutosh Kumar Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.,Amity Institute of Biotechnology, Amity University, Noida, 201303, India
| | - Aruna Kumar
- Amity Institute of Biotechnology, Amity University, Noida, 201303, India
| | - Nitasha Grover
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Haritha Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Prolay Kumar Bhowmick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - K K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - M Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR-Indian Agricultural Research Institute, Aduthurai, Tamil Nadu, 612101, India
| | - S L Krishnamurthy
- ICAR-Central Soil Salinity Research Institute, Karnal, 132001, India
| | - Ashok Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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