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Saminadane T, Geddam S, Krishnaswamy P, Jothiganapathy K, Tamilselvan A, Ramadoss BR, Sri Hari Reddy P, Singh US, Singh RK, Platten JD, Gregorio GB, Singh NK, Bisht DS, Kota S, Ponnuvel S, Guntupalli P. Development of early maturing salt-tolerant rice variety KKL(R) 3 using a combination of conventional and molecular breeding approaches. Front Genet 2024; 14:1332691. [PMID: 38371308 PMCID: PMC10869446 DOI: 10.3389/fgene.2023.1332691] [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: 11/03/2023] [Accepted: 12/27/2023] [Indexed: 02/20/2024] Open
Abstract
Introduction: Soil salinity poses a severe threat to rice production, resulting in stunted growth, leaf damage, and substantial yield losses. This study focuses on developing an early maturing seedling stage salinity tolerant rice variety by integrating conventional breeding methods with marker assisted breeding (MAB) approaches. Methods: Seedling-stage salinity tolerance Quantitative Trait Locus (QTL) "Saltol" from the salt-tolerant parent FL478 was introduced into the high-yielding but salt-sensitive rice variety ADT 45. This was achieved through a combination of conventional breeding and MAB. The breeding process involved rigorous selection, screening, and physiological parameter assessments. Results: KKL(R) 3 (KR 15066) identified as the top performing Recombinant Inbred Line (RIL), consistently demonstrating maximum mean grain yields under both salinity (3435.6 kg/ha) and normal (6421.8 kg/ha) conditions. In comparison to the early maturing, salt-tolerant national check variety CSR 10, KKL(R) 3 exhibited a substantial yield increase over 50%. Discussion: The notable improvement observed in KKL(R) 3 positions it as a promising variety for release, offering a reliable solution to maximize yields, ensure food security, and promote agricultural sustainability in both saline and non-saline environments. The study highlights the effectiveness of MAB in developing salt-tolerant rice varieties and emphasizes the significance of the Saltol QTL in enhancing seedling stage salinity tolerance. The potential release of KKL(R) 3 has the capacity to revolutionize rice production in salt affected regions, providing farmers with a reliable solution to maximize yields and contribute to food security while ensuring agricultural sustainability.
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Affiliation(s)
- Thirumeni Saminadane
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
| | - Sathyadevi Geddam
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
| | - Paramasivam Krishnaswamy
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
| | - Karthick Jothiganapathy
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
| | - Anandhan Tamilselvan
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamilnadu, India
| | - Bharathi Raja Ramadoss
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamilnadu, India
| | - Patil Sri Hari Reddy
- Department of Plant Breeding and Genetics, Pandit Jawaharlal Nehru College of Agriculture and Research Institute, Karaikal, Puducherry, India
| | - Uma Shankar Singh
- International Rice Research Institute, Manila, Metro Manila, Philippines
| | - Rakesh Kumar Singh
- International Rice Research Institute, Manila, Metro Manila, Philippines
| | | | - Glenn B. Gregorio
- College of Agriculture and Food Science, University of the Philippines Los Banos (UPLB), Los Baños, Laguna, Philippines
| | - Nagendra Kumar Singh
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR) - National Institute for Plant Biotechnology, New Delhi, India
| | - Deepak Singh Bisht
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR) - National Institute for Plant Biotechnology, New Delhi, India
| | - Suneetha Kota
- ICAR - Indian Institute of Rice Research, Hyderabad, Telangana, India
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Padmavathi G, Bangale U, Rao K, Balakrishnan D, Arun M, Singh RK, Sundaram RM. Progress and prospects in harnessing wild relatives for genetic enhancement of salt tolerance in rice. FRONTIERS IN PLANT SCIENCE 2024; 14:1253726. [PMID: 38371332 PMCID: PMC10870985 DOI: 10.3389/fpls.2023.1253726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/13/2023] [Indexed: 02/20/2024]
Abstract
Salt stress is the second most devastating abiotic stress after drought and limits rice production globally. Genetic enhancement of salinity tolerance is a promising and cost-effective approach to achieve yield gains in salt-affected areas. Breeding for salinity tolerance is challenging because of the genetic complexity of the response of rice plants to salt stress, as it is governed by minor genes with low heritability and high G × E interactions. The involvement of numerous physiological and biochemical factors further complicates this complexity. The intensive selection and breeding efforts targeted towards the improvement of yield in the green-revolution era inadvertently resulted in the gradual disappearance of the loci governing salinity tolerance and a significant reduction in genetic variability among cultivars. The limited utilization of genetic resources and narrow genetic base of improved cultivars have resulted in a plateau in response to salinity tolerance in modern cultivars. Wild species are an excellent genetic resource for broadening the genetic base of domesticated rice. Exploiting novel genes of underutilized wild rice relatives to restore salinity tolerance loci eliminated during domestication can result in significant genetic gain in rice cultivars. Wild species of rice, Oryza rufipogon and Oryza nivara, have been harnessed in the development of a few improved rice varieties like Jarava and Chinsura Nona 2. Furthermore, increased access to sequence information and enhanced knowledge about the genomics of salinity tolerance in wild relatives has provided an opportunity for the deployment of wild rice accessions in breeding programs, while overcoming the cross-incompatibility and linkage drag barriers witnessed in wild hybridization. Pre-breeding is another avenue for building material that are ready for utilization in breeding programs. Efforts should be directed towards systematic collection, evaluation, characterization, and deciphering salt tolerance mechanisms in wild rice introgression lines and deploying untapped novel loci to improve salinity tolerance in rice cultivars. This review highlights the potential of wild relatives of Oryza to enhance tolerance to salinity, track the progress of work, and provide a perspective for future research.
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Affiliation(s)
- Guntupalli Padmavathi
- Crop Improvement Section, Plant Breeding, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - Umakanth Bangale
- Crop Improvement Section, Plant Breeding, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - K. Nagendra Rao
- Genetics and Plant Breeding, Sugarcane Research Station, Vuyyuru, India
| | - Divya Balakrishnan
- Crop Improvement Section, Plant Breeding, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - Melekote Nagabhushan Arun
- Crop Production Section, Agronomy, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - Rakesh Kumar Singh
- Crop Diversification and Genetics Section, International Center for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates
| | - Raman Meenakshi Sundaram
- Crop Improvement Section, Plant Breeding, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
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Hanif S, Zia M. Glycine betaine capped ZnO NPs eliminate oxidative stress to coriander plants grown under NaCl presence. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 197:107651. [PMID: 36989991 DOI: 10.1016/j.plaphy.2023.107651] [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: 12/16/2022] [Revised: 01/21/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Salinity is one of the major abiotic stresses for sustainable agriculture. The use of mineral nutrients in form of nanoparticles can be a novel strategy to fight against abiotic stresses. An in vitro study has been conducted to investigate the effect of zinc oxide nanoparticles (ZnO NPs) capped with glycine betaine (ZnOBt) on coriander plants exposed to saline (NaCl) stress. SEM and XRD analysis revealed 14.73 nm and 17.34 nm size of ZnO and ZnOBt NPs, respectively with spherical to hexagonal structures. Coriander plant length and biomass increased by the application of ZnO and ZnOBt NPs. ZnOBt NPs depicted promising results at 100 mg/L where, shoot and root length increased up to 14 cm and 13 cm, respectively as compared to plants grown under saline stress. ZnOBt NPs also increased fresh and dry weight of shoots and roots as compared to other treatments. The results depict that ZnOBt NPs mitigated stress condition. This is evident from concentration of phenolic and flavonoid contents that decreased in both roots and shoots. Free radical scavenging activity, total antioxidant capacity and total reducing power also decreased in plants by ZnOBt NPs when applied with stress. The concentration of superoxide and peroxide dismutase also decreased by application of ZnOBt NPs to salt stress plants. Glycine betaine with ZnO NPs, in conclusion, can be an effective remedy for salinity-exposed plants. These nanoparticles can be encouraged as a viable technique to overcome the detrimental effects of saline stress on plants.
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Affiliation(s)
- Saad Hanif
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Zia
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Kim TH, Kim SM. Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:1401. [PMID: 36987089 PMCID: PMC10056360 DOI: 10.3390/plants12061401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Salt stress is a major constraint in rice production worldwide. Salt stress is estimated to cause annual losses of 30-50% in rice production. Discovering and deploying salt-resistance genes are the most effective ways to control salt stress. We performed a genome-wide association study (GWAS) to detect QTLs related to salt tolerance at the seedling stage using the japonica-multiparent advanced generation intercross (MAGIC) population. Four QTLs (qDTS1-1, qDTS1-2, qDTS2, and qDTS9) associated with salt tolerance were identified on chromosomes 1, 2, and 9. Among these QTLs, a novel QTL, qDTS1-2, was located between flanking SNPs (1354576 and id1028360) on chromosome 1, with the largest -log10(P) value of 5.81 and a total phenotypic variance of 15.2%. RNA-seq analysis revealed that among the seven differentially expressed genes (DEGs) commonly identified in both P6 and JM298 showing salt tolerance, two upregulated genes, Os01g0963600 (ASR transcription factor) and Os01g0975300 (OsMYB48), related to salt and drought tolerance, were also involved in the target region of qDTS1-2. The results of this study can provide insights into further understanding of salt tolerance mechanisms and developing DNA markers for marker-assisted selection (MAS) breeding to improve the salt tolerance of cultivars in rice breeding programs.
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Affiliation(s)
- Tae-Heon Kim
- Institute of Agricultural Science and Technology, Kyungpook National University, Daegu 41566, Republic of Korea;
- Department of Ecological & Environmental System, Kyungpook National University, Sangju 37224, Republic of Korea
| | - Suk-Man Kim
- Department of Ecological & Environmental System, Kyungpook National University, Sangju 37224, Republic of Korea
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Marè C, Zampieri E, Cavallaro V, Frouin J, Grenier C, Courtois B, Brottier L, Tacconi G, Finocchiaro F, Serrat X, Nogués S, Bundó M, San Segundo B, Negrini N, Pesenti M, Sacchi GA, Gavina G, Bovina R, Monaco S, Tondelli A, Cattivelli L, Valè G. Marker-Assisted Introgression of the Salinity Tolerance Locus Saltol in Temperate Japonica Rice. RICE (NEW YORK, N.Y.) 2023; 16:2. [PMID: 36633713 PMCID: PMC9837369 DOI: 10.1186/s12284-023-00619-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Rice is one of the most salt sensitive crops at seedling, early vegetative and reproductive stages. Varieties with salinity tolerance at seedling stage promote an efficient growth at early stages in salt affected soils, leading to healthy vegetative growth that protects crop yield. Saltol major QTL confers capacity to young rice plants growing under salt condition by maintaining a low Na+/K+ molar ratio in the shoots. RESULTS Marker-assisted backcross (MABC) procedure was adopted to transfer Saltol locus conferring salt tolerance at seedling stage from donor indica IR64-Saltol to two temperate japonica varieties, Vialone Nano and Onice. Forward and background selections were accomplished using polymorphic KASP markers and a final evaluation of genetic background recovery of the selected lines was conducted using 15,580 SNP markers obtained from Genotyping by Sequencing. Three MABC generations followed by two selfing, allowed the identification of introgression lines achieving a recovery of the recurrent parent (RP) genome up to 100% (based on KASP markers) or 98.97% (based on GBS). Lines with highest RP genome recovery (RPGR) were evaluated for agronomical-phenological traits in field under non-salinized conditions. VN1, VN4, O1 lines were selected considering the agronomic evaluations and the RPGR% results as the most interesting for commercial exploitation. A physiological characterization was conducted by evaluating salt tolerance under hydroponic conditions. The selected lines showed lower standard evaluation system (SES) scores: 62% of VN4, and 57% of O1 plants reaching SES 3 or SES 5 respectively, while only 40% of Vialone Nano and 25% of Onice plants recorded scores from 3 to 5, respectively. VN1, VN4 and O1 showed a reduced electrolyte leakage values, and limited negative effects on relative water content and shoot/root fresh weight ratio. CONCLUSION The Saltol locus was successfully transferred to two elite varieties by MABC in a time frame of three years. The application of background selection until BC3F3 allowed the selection of lines with a RPGR up to 98.97%. Physiological evaluations for the selected lines indicate an improved salinity tolerance at seedling stage. The results supported the effectiveness of the Saltol locus in temperate japonica and of the MABC procedure for recovering of the RP favorable traits.
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Affiliation(s)
- Caterina Marè
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy.
| | - Elisa Zampieri
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy
- Institute for Sustainable Plant Protection, National Research Council, Strada Delle Cacce 73, 10135, Turin, Italy
| | - Viviana Cavallaro
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy - DiSAA, University of Milan, Milan, Italy
| | - Julien Frouin
- CIRAD, UMR AGAP, 34398, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Cécile Grenier
- CIRAD, UMR AGAP, 34398, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Brigitte Courtois
- CIRAD, UMR AGAP, 34398, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Laurent Brottier
- CIRAD, UMR AGAP, 34398, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Gianni Tacconi
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Franca Finocchiaro
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Xavier Serrat
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Secció de Fisiologia Vegetal, Universitat de Barcelona, Barcelona, Spain
| | - Salvador Nogués
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Secció de Fisiologia Vegetal, Universitat de Barcelona, Barcelona, Spain
| | - Mireia Bundó
- Centre for Research in Agricultural Genomics (CRAG)-CSIC-IRTA-UAB-UB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics (CRAG)-CSIC-IRTA-UAB-UB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Noemi Negrini
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy - DiSAA, University of Milan, Milan, Italy
| | - Michele Pesenti
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy - DiSAA, University of Milan, Milan, Italy
| | - Gian Attilio Sacchi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy - DiSAA, University of Milan, Milan, Italy
| | - Giacomo Gavina
- SIS Società Italiana Sementi, Via Mirandola, 5, 40068, San Lazzaro di Savena, Bologna, Italy
| | - Riccardo Bovina
- SIS Società Italiana Sementi, Via Mirandola, 5, 40068, San Lazzaro di Savena, Bologna, Italy
| | - Stefano Monaco
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy
- Council for Agricultural Research and Economics, Research Centre for Engineering and Agro-Food Processing, Strada Delle Cacce 73, 10135, Turin, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, Piacenza, Italy
| | - Giampiero Valè
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, University of Piemonte Orientale, Piazza S. Eusebio 5, 13100, Vercelli, Italy.
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Rekha G, Abhilash Kumar V, Gokulan CG, Koushik MBVN, Laxmi Prasanna B, Kulkarni S, Aleena D, Harika G, Hajira SK, Pranathi K, Punniakoti E, Kale RR, Dilip Kumar T, Ayyappa D, Anila M, Sinha P, Manohara KK, Padmavathi G, Subba Rao LV, Laha GS, Srinivas Prasad MS, Fiyaz RA, Suneetha K, Balachandran SM, Patel HK, Sonti RV, Senguttuvel P, Sundaram RM. DRR Dhan 58, a Seedling Stage Salinity Tolerant NIL of Improved Samba Mahsuri Shows Superior Performance in Multi-location Trials. RICE (NEW YORK, N.Y.) 2022; 15:45. [PMID: 35976520 PMCID: PMC9385912 DOI: 10.1186/s12284-022-00591-3] [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: 11/17/2020] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Improved Samba Mahsuri (ISM) is an elite, high-yielding, bacterial blight resistant, fine-grained rice variety with low glycaemic index. It is highly sensitive to salt stress, particularly at seedling stage, which significantly reduces its yield potential in coastal areas. A salinity tolerant QTL, Saltol, associated with seedling stage tolerance was previously mapped on chromosome 1 (10.6-11.5 Mb) from the Indian landrace, Pokkali and is effective in different genetic backgrounds. The objective of this study was to enhance salinity tolerance of ISM by incorporating the Saltol QTL through marker-assisted backcross breeding using the breeding line, FL478 (Pokkali/IR29). RESULTS Foreground selection was carried out at each generation using five Saltol-specific markers and three bacterial blight resistance genes, Xa21, xa13 and xa5. Background selection was conducted using 66 well distributed polymorphic SSR markers and at the BC3F2 generation, a single plant with maximum recurrent parent genome recovery (95.3%) was identified and advanced to the BC3F4 generation. Based on bacterial blight resistance, seedling stage salinity tolerance and resemblance to ISM, four advanced breeding lines were selected for testing in replicated experiments near Hyderabad, India. A promising near-isogenic line, DRR Dhan 58, was evaluated in multi-location trials-coastal salinity and it showed significant salinity tolerance, resistance to bacterial blight disease, high yield and excellent grain quality during the 2019 and 2020 trials. DRR Dhan 58 was 95.1% similar to ISM based on genotyping with the 90 K SNP chip. Whole genome resequencing analysis of Pokkali and FL478 which were salinity tolerant checks, ISM and DRR Dhan 58 showed a high degree of relatedness with respect to the candidate gene loci for Saltol and OsSKC1 (Shoot K+ Concentration 1). CONCLUSION DRR Dhan 58, possessing Saltol and three bacterial blight resistance genes (Xa21, xa13 and xa5) in the genetic background of the Indian mega-variety of rice, Samba Mahsuri, was developed for potential cultivation in areas prone to seedling stage salinity, as well as areas with endemic bacterial blight disease. This entry had a 24% yield advantage over the recurrent parent ISM under coastal saline conditions in multi-location trials and was recently released for commercial cultivation in India.
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Affiliation(s)
- G Rekha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - V Abhilash Kumar
- Rallis India Limited, Seeds/Biotech R&D Division, Bangalore, India
| | - C G Gokulan
- Crop Improvement Section, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - M B V N Koushik
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | | | - Swapnil Kulkarni
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - D Aleena
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - G Harika
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - S K Hajira
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - K Pranathi
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - E Punniakoti
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - R R Kale
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - T Dilip Kumar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - D Ayyappa
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - M Anila
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - Pragya Sinha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - K K Manohara
- Genetics and Plant Breeding, ICAR- Central Coastal Agricultural Research Institute, Ella, Goa, India
| | - G Padmavathi
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - L V Subba Rao
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - G S Laha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - M S Srinivas Prasad
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - R A Fiyaz
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - K Suneetha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - S M Balachandran
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - Hitendra Kumar Patel
- Crop Improvement Section, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ramesh V Sonti
- Crop Improvement Section, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - P Senguttuvel
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - R M Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India.
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Golpour M, Alimohammadi M, Sohbatzadeh F, Fattahi S, Bekeschus S, Rafiei A. Cold atmospheric pressure plasma treatment combined with starvation increases autophagy and apoptosis in melanoma in vitro and in vivo. Exp Dermatol 2022; 31:1016-1028. [PMID: 35181947 DOI: 10.1111/exd.14544] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 12/01/2022]
Abstract
Despite advances in therapy, malignant melanoma remains a fatal disease. Among several emerging approaches to combat cancer, cold atmospheric pressure plasma (CAP) has shown promising results as a novel antitumor agent in preclinical models so far. The technology mainly relies on the emittance of various reactive oxygen and nitrogen species (ROS/RNS) that are tumor-toxic at high concentrations. Moreover, malignant melanoma has a metabolic dimension that can be targeted by mild starvation. To this end, we investigated the combined effect of starvation and CAP treatment on melanoma in vitro and in vivo. In vitro, starvation+CAP led to cell morphology changes, decreased metabolic activity and increased lipid peroxidation accompanied by apoptosis and DNA fragmentation in murine B16 melanoma cells but not murine non-malignant L929 fibroblasts. This was paralleled by increased apoptosis (Bax, Bcl-2 and Caspase-3) and autophagy (Lc3 and Atg5)-related gene expression. In vivo, starvation reduced tumor burden. Combination with CAP treatment augmented this effect significantly, albeit there was no difference of combination treatment to CAP exposure alone. Interestingly, there was an overall greater increase of Lc3 and Atg5 in the tumor tissue compared to CAP exposure alone, while starvation-induced autophagy-related gene expression was similar to in the combination group. These data collectively suggest that CAP-derived ROS/RNS treatment and autophagy-induction augment antitumor effects in malignant melanoma in vitro and in vivo.
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Affiliation(s)
- Monireh Golpour
- Molecular and Cell Biology Research Center, Student Research Committee, Faculty of Medicine, Mazandaran University of Medical Science, Sari, Iran
| | - Mina Alimohammadi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farshad Sohbatzadeh
- Department of Atomic and Molecular Physics, Faculty of Science, University of Mazandaran, Babolsar, Iran
| | | | - Sander Bekeschus
- ZIK Plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Greifswald, Germany
| | - Alireza Rafiei
- Department of Immunology, Molecular and Cell Biology Research Center, School of Medicine, Mazandaran University of Medical Science, Sari, Iran
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Kaur N, Prashanth KH, Bhatti MS, Pati PK. OsSalT gene cloned from rice provides evidence of its role in salinity and drought stress tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 320:111306. [PMID: 35643601 DOI: 10.1016/j.plantsci.2022.111306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/31/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stresses impose a huge threat to agricultural productivity and global food security. To counter this challenge, the precise identification of the right candidate gene (s) for conferring abiotic stress tolerance without compromising the growth and yield is crucial. OsSalT is identified as a salt stress responsive gene located on SalTol QTL of chromosome 1 of rice, however, there is no genetic evidence of its function and probable pathway of its regulation. To get better insights into its functioning, earlier we elucidated the structure of SALT protein at atomic scale {PDB ID (5GVY)} and solution state that provided key clues on the probable mode of its action. Herein, we report the modulation of OsSalT gene in response to various factors and its functional characterization. Results indicate that OsSalT operates through both abscisic acid and gibberellic acid-dependent pathways and is linked to the adaptive stress mechanisms of plants. Its overexpression in a model plant resulted in improved salinity and drought stress tolerance. The OsSalT transformed plants also showed vigorous root growth, early flowering, and better seed germination. The triggering of multiple responses by OsSalT suggested that modulation of such mannose-binding lectin could be a potential game-changer for the improvement of many crops in future.
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Affiliation(s)
- Navdeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | | | - Manpreet Singh Bhatti
- Department of Botanical & Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005, India.
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Zhang B, Ma L, Wu B, Xing Y, Qiu X. Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:863789. [PMID: 35557720 PMCID: PMC9087921 DOI: 10.3389/fpls.2022.863789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 05/14/2023]
Abstract
The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.
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Affiliation(s)
- Bo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, China
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10
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Krishnamurthy SL, Sharma PC, Dewan D, Lokeshkumar BM, Rathor S, Warraich AS, Vinaykumar NM, Leung H, Singh RK. Genome wide association study of MAGIC population reveals a novel QTL for salinity and sodicity tolerance in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:819-835. [PMID: 35592486 PMCID: PMC9110595 DOI: 10.1007/s12298-022-01174-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/27/2022] [Accepted: 04/06/2022] [Indexed: 05/24/2023]
Abstract
UNLABELLED The present study was conducted to identify the novel QTLs controlling salinity and sodicity tolerance using indica MAGIC rice population. Phenotyping was carried out in salinity (EC ~ 10 dS/m) and sodicity (pH ~ 9.8) at the seedling stage. Among 391 lines, 43 and 98 lines were found tolerant and moderately tolerant to salinity. For sodicity condition, 2 and 45 lines were showed tolerance and moderately tolerance at seedling stage. MAGIC population was genotyped with the help of genotyping by sequencing (GBS) and filtered 27041SNPs were used for genome wide marker trait association studies. With respect to salinity tolerance, 25 SNPs were distributed on chromosomes 1, 5, 11 and 12, whereas 18 SNPs were mapped on chromosomes 6, 4 and 11 with LOD value of > 3.25 to sodicity tolerance in rice. The candidate gene analysis detected twelve causal genes including SKC1 gene at Saltol region for salinity and six associated genes for sodic stress tolerance. The significant haplotypes responsible for core histone protein coding gene (LOC_Os12g25120) and three uncharacterized protein coding genes (LOC_Os01g20710, LOC_Os01g20870 and LOC_Os12g22020) were identified under saline stress. Likewise, five significant haplotypes coding for ribose 5-phosphate isomerise (LOC_Os04g24140), aspartyl protease (LOC_Os06g15760), aluminum-activated malate transporter (LOC_Os06g15779), OsFBX421-Fbox domain containing protein (LOC_Os11g32940) and one uncharacterized protein (LOC_Os11g32930) were detected for sodic stress tolerance. The identified novel SNPs could be the potential candidates for functional characterization. These candidate genes aid to further understanding of genetic mechanism on salinity and sodicity stress tolerance in rice. The tolerant line could be used in future breeding programme to enhance the salinity and sodicity tolerance in rice. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01174-8.
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Affiliation(s)
| | - P. C. Sharma
- Central Soil Salinity Research Institute, Karnal, India
| | - D. Dewan
- Central Soil Salinity Research Institute, Karnal, India
| | | | - Suman Rathor
- Central Soil Salinity Research Institute, Karnal, India
| | | | | | - Hei Leung
- Division of Genetics and Biotechnology, IRRI, Los Baños, Philippines
| | - R. K. Singh
- Division of Plant Breeding, IRRI, Los Baños, Philippines
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11
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Habila S, Khunpolwattana N, Chantarachot T, Buaboocha T, Comai L, Chadchawan S, Pongpanich M. Salt stress responses and SNP-based phylogenetic analysis of Thai rice cultivars. THE PLANT GENOME 2022; 15:e20189. [PMID: 34994516 DOI: 10.1002/tpg2.20189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/30/2021] [Indexed: 05/24/2023]
Abstract
Genetic diversity is important for developing salt-tolerant rice (Oryza sativa L.) cultivars. Certain Thai rice accessions display salt tolerance at the adult or reproductive stage, but their response to salinity at the seedling stage is unknown. In this study, a total of 10 rice cultivars/line, including eight Thai cultivars and standard salt-tolerant cultivar and susceptible line, were screened using a hydroponic system to identify salt-tolerant genotypes at the seedling stage. Different morphophysiological indicators were used to classify tolerant and susceptible genotypes. Phylogenetic analyses were performed to determine the evolutionary relationships between the cultivars. Results showed that 'Lai Mahk', 'Jao Khao', 'Luang Pratahn', and 'Ma Gawk' exhibited salt stress tolerance comparable with the standard salt-tolerance check 'Pokkali'. Whole-exome single-nucleotide polymorphism (SNP)-based phylogenetic analysis showed that the Thai rice cultivars were monophyletic and distantly related to Pokkali and IR29. Lai Mahk and Luang Pratahn were found closely related when using the whole-exome SNPs for the analysis. This is also the case for the analysis of SNPs from 164 salt-tolerance genes and transcription regulatory genes. The tolerant cultivars shared the same haplotype for 16 genes. Overall, the findings of this study identified four salt-stress-tolerant Thai rice cultivars, which could be used in rice breeding programs for salinity tolerance.
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Affiliation(s)
- Susinya Habila
- Center of Excellence in Environment and Plant Physiology, Dep. of Botany, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
- Dep. of Plant Science and Biotechnology, Faculty of Natural Science, Univ. of Jos, Jos Plateau State, Nigeria
| | - Nopphakhun Khunpolwattana
- Center of Excellence in Environment and Plant Physiology, Dep. of Botany, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
| | - Thanin Chantarachot
- Center of Excellence in Environment and Plant Physiology, Dep. of Botany, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
| | - Teerapong Buaboocha
- Molecular Crop Research Unit, Dep. of Biochemistry, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
- Omics Sciences Center, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
| | - Luca Comai
- Genome Center and Dep. of Plant Biology, UC Davis Genome Center, Univ. of California-Davis, Davis, CA, 95616, USA
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology, Dep. of Botany, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
- Omics Sciences Center, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
| | - Monnat Pongpanich
- Omics Sciences Center, Faculty of Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
- Dep. of Mathematics and Computer Science, Faculty Science, Chulalongkorn Univ., Pathum Wan District, Bangkok, 10330, Thailand
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12
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Bundó M, Martín-Cardoso H, Pesenti M, Gómez-Ariza J, Castillo L, Frouin J, Serrat X, Nogués S, Courtois B, Grenier C, Sacchi GA, San Segundo B. Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines. FRONTIERS IN PLANT SCIENCE 2022; 12:797141. [PMID: 35126422 PMCID: PMC8813771 DOI: 10.3389/fpls.2021.797141] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/13/2021] [Indexed: 05/24/2023]
Abstract
Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress, which is currently worsened due to climate change. This study reports the development of salt tolerant introgression lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol quantitative trait loci (QTL), and the salt-sensitive japonica elite cultivar OLESA. Genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASPar) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL (IL22). A total of 1,595 genes were identified in indica regions of IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes were identified in the introgressed indica segments of IL22 whose expression was confirmed [e.g., genes involved in ion transport, callose synthesis, transcriptional regulation of gene expression, hormone signaling and reactive oxygen species (ROS) accumulation]. These genes might well contribute to salt stress tolerance in IL22 plants. Furthermore, comparative transcript profiling revealed that indica introgressions caused important alterations in the background gene expression of IL22 plants (japonica cultivar) compared with its salt-sensitive parent, both under non-stress and salt-stress conditions. In response to salt treatment, only 8.6% of the salt-responsive genes were found to be commonly up- or down-regulated in IL22 and OLESA plants, supporting massive transcriptional reprogramming of gene expression caused by indica introgressions into the recipient genome. Interactions among indica and japonica genes might provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines. Collectively, this study illustrates the usefulness of transcriptomics in the characterization of new rice lines obtained in breeding programs in rice.
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Affiliation(s)
- Mireia Bundó
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, Spain
| | | | - Michele Pesenti
- Department of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy – DiSAA, University of Milan, Milan, Italy
| | - Jorge Gómez-Ariza
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, Spain
| | - Laia Castillo
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, Spain
| | - Julien Frouin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Xavier Serrat
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Secció de Fisiologia Vegetal, Universitat de Barcelona, Barcelona, Spain
| | - Salvador Nogués
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Secció de Fisiologia Vegetal, Universitat de Barcelona, Barcelona, Spain
| | - Brigitte Courtois
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Cécile Grenier
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, France
| | - Gian Attilio Sacchi
- Department of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy – DiSAA, University of Milan, Milan, Italy
| | - Blanca San Segundo
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, Spain
- Consejo Superior de Investigaciones Científicas, Barcelona, Spain
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13
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Prakash NR, Lokeshkumar BM, Rathor S, Warraich AS, Yadav S, Vinaykumar NM, Dushynthkumar BM, Krishnamurthy SL, Sharma PC. Meta-analysis and validation of genomic loci governing seedling and reproductive stage salinity tolerance in rice. PHYSIOLOGIA PLANTARUM 2022; 174:e13629. [PMID: 35040153 DOI: 10.1111/ppl.13629] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/29/2021] [Accepted: 01/13/2022] [Indexed: 05/24/2023]
Abstract
Identification of concurrent genomic regions contributing tolerance to salinity at the seedling and reproductive stages were done using 45 quantitative trait loci (QTL) mapping studies reporting 915 individual QTLs. The QTL-data were used to perform a meta-analysis to predict, validate and analyze the Meta-QTLs governing component traits contributing to salinity tolerance. We predicted a total of 65 and 49 Meta-QTLs distributed across the genome governing seedling and reproductive stage salinity tolerance, respectively. Salinity stress (EC ~10.0 dSm-1 ) was evaluated in a set of 32 genotypes grown hydroponically, from these eight extreme (highly tolerant and highly susceptible) genotypes were selected for validation of significant Meta-QTLs. Another set of eight previously known and reported (highly tolerant and highly susceptible) genotypes were evaluated under saline micro plot conditions (EC ~8.0 dSm-1 ) and used for validation of significant Meta-QTLs for reproductive stage salinity tolerance. The microsatellite marker "RM5635" linked to MSQTL4.2 (~295.43 kb) was able to clearly differentiate contrasting genotypes for seedling stage salinity tolerance, whereas at the reproductive stage, none of the markers were able to validate the predicted Meta-QTL for salinity tolerance. Earlier reported, gene expression studies were used for candidate gene analysis of validated MSQTL4.2, which indicated the down regulation of Os04g0423100, a gene encoding Mono-oxygenase-FAD binding domain containing protein. The traits associated with this Meta-QTL were root and shoot sodium and potassium concentration and leaf chlorophyll content. The identified and validated genomic region assumes a great significant role in seedling stage salinity tolerance in rice, and it can be used for marker-assisted backcross breeding programs.
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Affiliation(s)
| | | | - Suman Rathor
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India
| | | | - Satyendra Yadav
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India
| | | | | | | | - Parbodh C Sharma
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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15
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Molecular Breeding for Improving Productivity of Oryza sativa L. cv. Pusa 44 under Reproductive Stage Drought Stress through Introgression of a Major QTL, qDTY12.1. Genes (Basel) 2021; 12:genes12070967. [PMID: 34202818 PMCID: PMC8303740 DOI: 10.3390/genes12070967] [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: 02/11/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 11/24/2022] Open
Abstract
Increasing rice production is quintessential to the task of sustaining global food security, as a majority of the global population is dependent on rice as its staple dietary cereal. Among the various constraints affecting rice production, reproductive stage drought stress (RSDS) is a major challenge, due to its direct impact on grain yield. Several quantitative trait loci (QTLs) conferring RSDS tolerance have been identified in rice, and qDTY12.1 is one of the major QTLs reported. We report the successful introgression of qDTY12.1 into Pusa 44, a drought sensitive mega rice variety of the northwestern Indian plains. Marker-assisted backcross breeding (MABB) was adopted to transfer qDTY12.1 into Pusa 44 in three backcrosses followed by four generations of pedigree selection, leading to development of improved near isogenic lines (NILs). Having a recurrent parent genome (RPG) recovery ranging from 94.7–98.7%, the improved NILs performed 6.5 times better than Pusa 44 under RSDS, coupled with high yield under normal irrigated conditions. The MABB program has been modified so as to defer background selection until BC3F4 to accelerate generational advancements. Deploying phenotypic selection alone in the early backcross generations could help in the successful recovery of RPG. In addition, the grain quality could be recovered in the improved NILs, leading to superior selections. Owing to their improved adaptation to drought, the release of improved NILs for regions prone to intermittent drought can help enhance rice productivity and production.
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Yadav AK, Kumar A, Grover N, Ellur RK, Bollinedi H, Krishnan SG, Bhowmick PK, Vinod KK, Nagarajan M, Singh AK. Genome-Wide Association Study Reveals Marker-Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice. PLANTS (BASEL, SWITZERLAND) 2021; 10:559. [PMID: 33809618 PMCID: PMC8000697 DOI: 10.3390/plants10030559] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 11/16/2022]
Abstract
Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker-trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.
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Affiliation(s)
- Ashutosh Kumar Yadav
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
- 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; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Haritha Bollinedi
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Subbaiyan Gopala Krishnan
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Prolay Kumar Bhowmick
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Kunnummal Kurungara Vinod
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Mariappan Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR—Indian Agricultural Research Institute, Aduthurai 612101, Tamil Nadu, India;
| | - Ashok Kumar Singh
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
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