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Tiwari K, Tiwari S, Kumar N, Sinha S, Krishnamurthy SL, Singh R, Kalia S, Singh NK, Rai V. QTLs and Genes for Salt Stress Tolerance: A Journey from Seed to Seed Continued. PLANTS (BASEL, SWITZERLAND) 2024; 13:1099. [PMID: 38674508 PMCID: PMC11054697 DOI: 10.3390/plants13081099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 04/28/2024]
Abstract
Rice (Oryza sativa L.) is a crucial crop contributing to global food security; however, its production is susceptible to salinity, a significant abiotic stressor that negatively impacts plant germination, vigour, and yield, degrading crop production. Due to the presence of exchangeable sodium ions (Na+), the affected plants sustain two-way damage resulting in initial osmotic stress and subsequent ion toxicity in the plants, which alters the cell's ionic homeostasis and physiological status. To adapt to salt stress, plants sense and transfer osmotic and ionic signals into their respective cells, which results in alterations of their cellular properties. No specific Na+ sensor or receptor has been identified in plants for salt stress other than the SOS pathway. Increasing productivity under salt-affected soils necessitates conventional breeding supplemented with biotechnological interventions. However, knowledge of the genetic basis of salinity stress tolerance in the breeding pool is somewhat limited because of the complicated architecture of salinity stress tolerance, which needs to be expanded to create salt-tolerant variants with better adaptability. A comprehensive study that emphasizes the QTLs, genes and governing mechanisms for salt stress tolerance is discussed in the present study for future research in crop improvement.
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Affiliation(s)
- Keshav Tiwari
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Sushma Tiwari
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Nivesh Kumar
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Shikha Sinha
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | | | - Renu Singh
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, New Delhi 110003, India
| | - Nagendra Kumar Singh
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Vandna Rai
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
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Satasiya P, Patel S, Patel R, Raigar OP, Modha K, Parekh V, Joshi H, Patel V, Chaudhary A, Sharma D, Prajapati M. Meta-analysis of identified genomic regions and candidate genes underlying salinity tolerance in rice (Oryza sativa L.). Sci Rep 2024; 14:5730. [PMID: 38459066 PMCID: PMC10923909 DOI: 10.1038/s41598-024-54764-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/16/2024] [Indexed: 03/10/2024] Open
Abstract
Rice output has grown globally, yet abiotic factors are still a key cause for worry. Salinity stress seems to have the more impact on crop production out of all abiotic stresses. Currently one of the most significant challenges in paddy breeding for salinity tolerance with the help of QTLs, is to determine the QTLs having the best chance of improving salinity tolerance with the least amount of background noise from the tolerant parent. Minimizing the size of the QTL confidence interval (CI) is essential in order to primarily include the genes responsible for salinity stress tolerance. By considering that, a genome-wide meta-QTL analysis on 768 QTLs from 35 rice populations published from 2001 to 2022 was conducted to identify consensus regions and the candidate genes underlying those regions responsible for the salinity tolerance, as it reduces the confidence interval (CI) to many folds from the initial QTL studies. In the present investigation, a total of 65 MQTLs were extracted with an average CI reduced from 17.35 to 1.66 cM including the smallest of 0.01 cM. Identification of the MQTLs for individual traits and then classifying the target traits into correlated morphological, physiological and biochemical aspects, resulted in more efficient interpretation of the salinity tolerance, identifying the candidate genes and to understand the salinity tolerance mechanism as a whole. The results of this study have a huge potential to improve the rice genotypes for salinity tolerance with the help of MAS and MABC.
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Affiliation(s)
- Pratik Satasiya
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Sanyam Patel
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Ritesh Patel
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Om Prakash Raigar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Kaushal Modha
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Vipul Parekh
- Department of Biotechnology, College of Forestry, Navsari Agricultural University, Navsari, Gujarat, India
| | - Haimil Joshi
- Coastal Soil Salinity Research Station Danti-Umbharat, Navsari Agricultural University, Navsari, Gujarat, India
| | - Vipul Patel
- Regional Rice Research Station, Vyara, Navsari Agricultural University, Navsari, Gujarat, India
| | - Ankit Chaudhary
- Kishorbhai Institute of Agriculture Sciences and Research Centre, Uka Tarsadia University, Bardoli, Gujarat, India.
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
| | - Maulik Prajapati
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, India
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Chapagain S, Pruthi R, Singh L, Subudhi PK. Comparison of the genetic basis of salt tolerance at germination, seedling, and reproductive stages in an introgression line population of rice. Mol Biol Rep 2024; 51:252. [PMID: 38302786 DOI: 10.1007/s11033-023-09049-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 11/02/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND Salinity is a major limitation for rice farming due to climate change. Since salt stress adversely impact rice plants at germination, seedling, and reproductive stages resulting in poor crop establishment and reduced grain yield, enhancing salt tolerance at these vulnerable growth stages will enhance rice productivity in salinity prone areas. METHODS AND RESULTS An introgression line (ILs) population from a cross between a high yielding cultivar 'Cheniere' and a salt tolerant donor 'TCCP' was evaluated to map quantitative trait loci (QTLs) for traits associated with salt tolerance at germination, seedling, and reproductive stages. Using a genotyping-by-sequencing based high density SNP linkage map, a total of 7, 16, and 30 QTLs were identified for five germination traits, seven seedling traits, and ten reproductive traits, respectively. There was overlapping of QTLs for some traits at different stages indicating the pleiotropic effects of these QTLs or clustering of linked genes. Candidate genes identified for salt tolerance were OsSDIR1 and SERF for the seedling stage, WRKY55 and OsUBC for the reproductive stage, and MYB family transcription factors for all three stages. Gene ontology analysis revealed significant GO terms related to nucleotide binding, protein binding, protein kinase activity, antiporter activity, active transmembrane transporter activity, calcium-binding protein, and F- box protein interaction domain containing protein. CONCLUSIONS The colocalized QTLs for traits at different growth stages would be helpful to improve multiple traits simultaneously using marker-assisted selection. The salt tolerant ILs have the potential to be released as varieties or as pre-breeding lines for developing salt tolerant rice varieties.
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Affiliation(s)
- Sandeep Chapagain
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Rajat Pruthi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Lovepreet Singh
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Prasant K Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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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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Debsharma SK, Rahman MA, Khatun M, Disha RF, Jahan N, Quddus MR, Khatun H, Dipti SS, Ibrahim M, Iftekharuddaula KM, Kabir MS. Developing climate-resilient rice varieties (BRRI dhan97 and BRRI dhan99) suitable for salt-stress environments in Bangladesh. PLoS One 2024; 19:e0294573. [PMID: 38241319 PMCID: PMC10810675 DOI: 10.1371/journal.pone.0294573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/04/2023] [Indexed: 01/21/2024] Open
Abstract
Salinity variations are the main reason for rice yield fluctuations in salt-prone regions throughout the dry season (Boro season). Plant breeders must produce new rice varieties that are more productive, salt tolerant, and stable across a variety of settings to ensure Bangladesh's food sustainability. To assess the yield and stability, we used fifteen rice genotypes containing two tolerant checks BRRI dhan67, Binadhan-10 and the popular Boro rice variety BRRI dhan28 in different salinity "hotspot" in three successive years followed by additive main effects and multiplicative interaction (AMMI) model utilizing a randomized complete block (RCB) design with two replications. Parents selection was done based on estimated breeding values (EBVs). Eight parents with high EBVs (IR83484-3-B-7-1-1-1, IR87870-6-1-1-1-1-B, BR8992-B-18-2-26, HHZ5-DT20-DT2-DT1, HHZ12-SAL2-Y3-Y2, BR8980-B-1-3-5, BRRI dhan67, and Binadhan-10) might be used to develop new segregating breeding materials. Based on farmer preferences and grain acceptability, three genotypes (IR83484-3-B-7-1-1-1, HHZ5-DT20-DT2-DT1, and HHZ12-SAL2-Y3-Y2) were the winning and best ones. The above three genotypes in the proposed variety trial showed significantly higher yields than the respective check varieties, high salinity tolerance ability, and good grain quality parameters. Among them, HHZ5-DT20-DT2-DT1 and IR83484-3-B-7-1-1-1 harbored eight and four QTL/genes that regulate the valuable traits revealed through 20 SNP genotyping. Finally, two genotypes IR83484-3-B-7-1-1-1 and HHZ5-DT20-DT2-DT1 were released as high salinity-tolerant rice varieties BRRI dhan97 and BRRI dhan99, respectively in Bangladesh for commercial cultivation for sustaining food security and sustainability.
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Affiliation(s)
- Sanjoy K. Debsharma
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur,
Bangladesh
| | - M. Akhlasur Rahman
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur,
Bangladesh
| | - Mahmuda Khatun
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur,
Bangladesh
| | - Ribed F. Disha
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur,
Bangladesh
| | - Nusrat Jahan
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur,
Bangladesh
| | - Md. Ruhul Quddus
- Hybrid Rice Division, Bangladesh Rice Research Institute, Gazipur,
Bangladesh
| | - Hasina Khatun
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur,
Bangladesh
| | - Sharifa S. Dipti
- Grain Quality and Nutrition Division, Bangladesh Rice Research Institute,
Gazipur, Bangladesh
| | - Md. Ibrahim
- Rice Farming System Division, Bangladesh Rice Research Institute,
Gazipur, Bangladesh
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Raza A, Tabassum J, Fakhar AZ, Sharif R, Chen H, Zhang C, Ju L, Fotopoulos V, Siddique KHM, Singh RK, Zhuang W, Varshney RK. Smart reprograming of plants against salinity stress using modern biotechnological tools. Crit Rev Biotechnol 2023; 43:1035-1062. [PMID: 35968922 DOI: 10.1080/07388551.2022.2093695] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/08/2022] [Indexed: 01/19/2023]
Abstract
Climate change gives rise to numerous environmental stresses, including soil salinity. Salinity/salt stress is the second biggest abiotic factor affecting agricultural productivity worldwide by damaging numerous physiological, biochemical, and molecular processes. In particular, salinity affects plant growth, development, and productivity. Salinity responses include modulation of ion homeostasis, antioxidant defense system induction, and biosynthesis of numerous phytohormones and osmoprotectants to protect plants from osmotic stress by decreasing ion toxicity and augmented reactive oxygen species scavenging. As most crop plants are sensitive to salinity, improving salt tolerance is crucial in sustaining global agricultural productivity. In response to salinity, plants trigger stress-related genes, proteins, and the accumulation of metabolites to cope with the adverse consequence of salinity. Therefore, this review presents an overview of salinity stress in crop plants. We highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of "zero hunger," a worldwide sustainable development goal proposed by the FAO.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Javaria Tabassum
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Science (CAAS), Zhejiang, China
| | - Ali Zeeshan Fakhar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Luo Ju
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Science (CAAS), Zhejiang, China
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology & Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Rakesh K Singh
- Crop Diversification and Genetics, International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Rajeev K Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Murdoch's Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Australia
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7
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Saputro TB, Jakada BH, Chutimanukul P, Comai L, Buaboocha T, Chadchawan S. OsBTBZ1 Confers Salt Stress Tolerance in Arabidopsis thaliana. Int J Mol Sci 2023; 24:14483. [PMID: 37833931 PMCID: PMC10572369 DOI: 10.3390/ijms241914483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
Rice (Oryza sativa L.), one of the most important commodities and a primary food source worldwide, can be affected by adverse environmental factors. The chromosome segment substitution line 16 (CSSL16) of rice is considered salt-tolerant. A comparison of the transcriptomic data of the CSSL16 line under normal and salt stress conditions revealed 511 differentially expressed sequence (DEseq) genes at the seedling stage, 520 DEseq genes in the secondary leaves, and 584 DEseq genes in the flag leaves at the booting stage. Four BTB genes, OsBTBZ1, OsBTBZ2, OsBTBN3, and OsBTBN7, were differentially expressed under salt stress. Interestingly, only OsBTBZ1 was differentially expressed at the seedling stage, whereas the other genes were differentially expressed at the booting stage. Based on the STRING database, OsBTBZ1 was more closely associated with other abiotic stress-related proteins than other BTB genes. The highest expression of OsBTBZ1 was observed in the sheaths of young leaves. The OsBTBZ1-GFP fusion protein was localized to the nucleus, supporting the hypothesis of a transcriptionally regulatory role for this protein. The bt3 Arabidopsis mutant line exhibited susceptibility to NaCl and abscisic acid (ABA) but not to mannitol. NaCl and ABA decreased the germination rate and growth of the mutant lines. Moreover, the ectopic expression of OsBTBZ1 rescued the phenotypes of the bt3 mutant line and enhanced the growth of wild-type Arabidopsis under stress conditions. These results suggest that OsBTBZ1 is a salt-tolerant gene functioning in ABA-dependent pathways.
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Affiliation(s)
- Triono B. Saputro
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (T.B.S.); (B.H.J.)
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Bello H. Jakada
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (T.B.S.); (B.H.J.)
| | - Panita Chutimanukul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathumthani, Bangkok 12120, Thailand;
| | - Luca Comai
- Genome Center and Department of Plant Biology, UC Davis, Davis, CA 95616, USA;
| | - Teerapong Buaboocha
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (T.B.S.); (B.H.J.)
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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8
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Rawal HC, Ali S, Mondal TK. Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs. Int J Biol Macromol 2023; 242:125172. [PMID: 37268077 DOI: 10.1016/j.ijbiomac.2023.125172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Salinity is an imbalanced concentration of mineral salts in the soil or water that causes yield loss in salt-sensitive crops. Rice plant is vulnerable to soil salinity stress at seedling and reproductive stages. Different non-coding RNAs (ncRNAs) post-transcriptionally regulate different sets of genes during different developmental stages under varying salinity tolerance levels. While microRNAs (miRNAs) are well known small endogenous ncRNAs, tRNA-derived RNA fragments (tRFs) are an emerging class of small ncRNAs derived from tRNA genes with a demonstrated regulatory role, like miRNAs, in humans but unexplored in plants. Circular RNA (circRNA), another ncRNA produced by back-splicing events, acts as target mimics by preventing miRNAs from binding with their target mRNAs, thereby reducing the miRNA's action upon its target. Same may hold true between circRNAs and tRFs. Hence, the work done on these ncRNAs was reviewed and no reports were found for circRNAs and tRFs under salinity stress in rice, either at seedling or reproductive stages. Even the reports on miRNAs are restricted to seedling stage only, in spite of severe effects on rice crop production due to salt stress during reproductive stage. Moreover, this review sheds light on strategies to predict and analyze these ncRNAs in an effective manner.
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Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India; School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India; Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.
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Li S, Feng T, Zhang C, Zhang F, Li H, Chen Y, Liang L, Zhang C, Zeng W, Liu E, Shi Y, Li M, Meng L. Genetic Dissection of Salt Tolerance and Yield Traits of Geng ( japonica) Rice by Selective Subspecific Introgression. Curr Issues Mol Biol 2023; 45:4796-4813. [PMID: 37367054 DOI: 10.3390/cimb45060305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/13/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Salinity is a major factor limiting rice productivity, and developing salt-tolerant (ST) varieties is the most efficient approach. Seventy-eight ST introgression lines (ILs), including nine promising lines with improved ST and yield potential (YP), were developed from four BC2F4 populations from inter-subspecific crosses between an elite Geng (japonica) recipient and four Xian (indica) donors at the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences. Genome-wide characterization of donor introgression identified 35 ST QTLs, 25 of which harbor 38 cloned ST genes as the most likely QTL candidates. Thirty-four are Xian-Geng differentiated ones with the donor (Xian) alleles associated with ST, suggesting differentiated responses to salt stress were one of the major phenotypic differences between the two subspecies. At least eight ST QTLs and many others affecting yield traits were identified under salt/non-stress conditions. Our results indicated that the Xian gene pool contains rich 'hidden' genetic variation for developing superior Geng varieties with improved ST and YP, which could be efficiently exploited by selective introgression. The developed ST ILs and their genetic information on the donor alleles for ST and yield traits would provide a useful platform for developing superior ST and high-yield Geng varieties through breeding by design in the future.
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Affiliation(s)
- Simin Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Ting Feng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chenyang Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Fanlin Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Hua Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yanjun Chen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Lunping Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chaopu Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Wei Zeng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Lijun Meng
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528200, China
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Wang R, Zhou Z, Xiong M, Du M, Lin X, Liu C, Lu M, Liu Z, Chang Y, Liu E. Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112163. [PMID: 37299141 DOI: 10.3390/plants12112163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/18/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023]
Abstract
Mining salt tolerance genes is significant for breeding high-quality salt-tolerant rice varieties in order to improve the utilization of saline-alkaline land. In this study, 173 rice accessions were measured for their germination potential (GP), germination rate (GR), seedling length (SL), root length (RL), germination potential relative to salt damage rate (GPR), germination rate relative to salt damage rate (GRR), seedling length relative to salt damage rate (SLR), relative salt damage rate at the germination stage (RSD) and comprehensive relative salt damage rate in the early seedling stage (CRS) under normal and salt stress conditions. Genome-wide association analysis was performed with 1,322,884 high-quality SNPs obtained by resequencing. Eight quantitative trait loci (QTLs) related to salt tolerance traits at the germination stage were detected in 2020 and 2021. They were related to the GPR (qGPR2) and SLR (qSLR9), which were newly discovered in this study. Three genes were predicted as salt tolerance candidate genes: LOC_Os02g40664, LOC_Os02g40810, and LOC_Os09g28310. At present, marker-assisted selection (MAS) and gene-edited breeding are becoming more widespread. Our discovery of candidate genes provides a reference for research in this field. The elite alleles identified in this study may provide a molecular basis for cultivating salt-tolerant rice varieties.
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Affiliation(s)
- Rui Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Zhenzhen Zhou
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Mengyuan Xiong
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Mingyu Du
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Xingxing Lin
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Cuiping Liu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Mingwei Lu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Zhengbo Liu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yinping Chang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
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Xu S, Cui J, Cao H, Liang S, Ma T, Liu H, Wang J, Yang L, Xin W, Jia Y, Zou D, Zheng H. Identification of candidate genes for salinity tolerance in Japonica rice at the seedling stage based on genome-wide association study and linkage mapping. FRONTIERS IN PLANT SCIENCE 2023; 14:1184416. [PMID: 37235029 PMCID: PMC10206223 DOI: 10.3389/fpls.2023.1184416] [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: 03/11/2023] [Accepted: 04/11/2023] [Indexed: 05/28/2023]
Abstract
Background Salinity tolerance plays a vital role in rice cultivation because the strength of salinity tolerance at the seedling stage directly affects seedling survival and final crop yield in saline soils. Here, we combined a genome-wide association study (GWAS) and linkage mapping to analyze the candidate intervals for salinity tolerance in Japonica rice at the seedling stage. Results We used the Na+ concentration in shoots (SNC), K+ concentration in shoots (SKC), Na+/K+ ratio in shoots (SNK), and seedling survival rate (SSR) as indices to assess the salinity tolerance at the seedling stage in rice. The GWAS identified the lead SNP (Chr12_20864157), associated with an SNK, which the linkage mapping detected as being in qSK12. A 195-kb region on chromosome 12 was selected based on the overlapping regions in the GWAS and the linkage mapping. Based on haplotype analysis, qRT-PCR, and sequence analysis, we obtained LOC_Os12g34450 as a candidate gene. Conclusion Based on these results, LOC_Os12g34450 was identified as a candidate gene contributing to salinity tolerance in Japonica rice. This study provides valuable guidance for plant breeders to improve the response of Japonica rice to salt stress.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Detang Zou
- *Correspondence: Detang Zou, ; Hongliang Zheng,
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12
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Combining ability of extra-early maturing pro-vitamin A maize (Zea mays L.) inbred lines and performance of derived hybrids under Striga hermonthica infestation and low soil nitrogen. PLoS One 2023; 18:e0280814. [PMID: 36827415 PMCID: PMC9956606 DOI: 10.1371/journal.pone.0280814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 01/09/2023] [Indexed: 02/26/2023] Open
Abstract
Low soil nitrogen (low-N), Striga hermonthica infestation and vitamin A deficiency in normal endosperm maize are major challenges confronting maize production and nutrition of the people of sub-Saharan Africa (SSA). Development of pro-vitamin A (PVA) maize hybrids with combined resistance/tolerance to the two stress factors is crucial in mitigating the food insecurity and nutrition challenges resulting from low-N deficiency and Striga infestation. One hundred and fifty hybrids plus six hybrid checks were evaluated under low-N, Striga-infested and optimal conditions in Nigeria for two years. The study examined the combining ability of the PVA inbreds in contrasting environments, classified them into heterotic groups, examined the inter-relationships of grain yield and other agronomic traits of the inbreds in hybrid combinations and assessed the performance and stability of the PVA hybrids across environments. Additive gene action conditioned the inheritance of grain yield under Striga infestation and optimal conditions while non-additive gene action played the major role in the inheritance of grain yield under low-N. Hybrids TZEEIOR 217 × TZEEIOR 197 and TZEEIOR 245 × TZEEIOR 195 were the top-yielding under Striga and low-N conditions, respectively. Inbred lines were classified into three heterotic groups. Inbreds TZEEIOR 195 and TZEEIOR 221 were identified as testers while TZEEIOR 197 × TZEEIOR 82, TZEEIOR 132 × TZEEIOR 195 and TZEEIOR 205 × TZEEIOR 221 were identified as single-cross testers. Ear aspect had direct contribution to grain yield, justifying its inclusion in the multiple trait base index used for selection of Striga resistant and low-N tolerant maize genotypes in SSA. Hybrids TZEEIOR 195 × TZEEIOR 149, TZEEIOR 195 × TZEEIOR 150, TZEEIOR 245 × TZEEIOR 195, TZEEIOR 30 × TZEEIOR 150 and TZEEIOR 245 × TZEEIOR 30 were high-yielding and stable across test environments. These hybrids should be tested extensively in on-farm trials and commercialized to contribute to food security in SSA.
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Mapping QTLs for Reproductive Stage Salinity Tolerance in Rice Using a Cross between Hasawi and BRRI dhan28. Int J Mol Sci 2022; 23:ijms231911376. [PMID: 36232678 PMCID: PMC9569796 DOI: 10.3390/ijms231911376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Salinity stress is a major constraint to rice production in many coastal regions due to saline groundwater and river sources, especially during the dry season in coastal areas when seawater intrudes further inland due to reduced river flows. Since salinity tolerance is a complex trait, breeding efforts can be assisted by mapping quantitative trait loci (QTLs) for complementary salt tolerance mechanisms, which can then be combined to provide higher levels of tolerance. While an abundance of seedling stage salinity tolerance QTLs have been mapped, few studies have investigated reproductive stage tolerance in rice due to the difficulty of achieving reliable stage-specific phenotyping techniques. In the current study, a BC1F2 mapping population consisting of 435 individuals derived from a cross between a salt-tolerant Saudi Arabian variety, Hasawi, and a salt-sensitive Bangladeshi variety, BRRI dhan28, was evaluated for yield components after exposure to EC 10 dS/m salinity stress during the reproductive stage. After selecting tolerant and sensitive progeny, 190 individuals were genotyped by skim sequencing, resulting in 6209 high quality single nucleotide polymorphic (SNP) markers. Subsequently, a total of 40 QTLs were identified, of which 24 were for key traits, including productive tillers, number and percent filled spikelets, and grain yield under stress. Importantly, three yield-related QTLs, one each for productive tillers (qPT3.1), number of filled spikelets (qNFS3.1) and grain yield (qGY3.1) under salinity stress, were mapped at the same position (6.7 Mb or 26.1 cM) on chromosome 3, which had not previously been associated with grain yield under salinity stress. These QTLs can be investigated further to dissect the molecular mechanisms underlying reproductive stage salinity tolerance in rice.
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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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Yadavalli VR, Balakrishnan D, Surapaneni M, Addanki K, Mesapogu S, Beerelli K, Desiraju S, Voleti SR, Neelamraju S. Mapping QTLs for yield and photosynthesis-related traits in three consecutive backcross populations of Oryza sativa cultivar Cottondora Sannalu (MTU1010) and Oryza rufipogon. PLANTA 2022; 256:71. [PMID: 36070104 DOI: 10.1007/s00425-022-03983-3] [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: 02/11/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Identification of trait enhancing QTLs for yield and photosynthesis-related traits in rice using interspecific mapping population and chromosome segment substitution lines derived from a cross between Oryza sativa and Oryza rufipogon. Wild rice contains novel genes which can help in improving rice yield. Common wild rice Oryza rufipogon is a known source for enhanced photosynthesis and yield-related traits. We developed BC2F2:3:4 mapping populations using O. rufipogon IC309814 with high photosynthetic rate as donor, and elite cultivar MTU1010 as recurrent parent. Evaluation of 238 BC2F2 families for 13 yield-related traits and 208 BC2F2 families for seven photosynthesis-related physiological traits resulted in identification of significantly different lines which performed better than MTU1010 for various yield contributing traits. 49 QTLs were identified for 13 yield traits and 7 QTLs for photosynthesis-related traits in BC2F2. In addition, 34 QTLs in BC2F3 and 26 QTLs in BC2F4 were also detected for yield traits.11 common QTLs were identified in three consecutive generations and their trait-increasing alleles were derived from O. rufipogon. Significantly, one major effect common QTL qTGW3.1 for thousand grain weight with average phenotypic variance 8.1% and one novel QTL qBM7.1 for biomass were identified. Photosynthesis-related QTLs qPN9.1, qPN12.1, qPN12.2 qSPAD1.1 and qSPAD6.1 showed additive effect from O. rufipogon. A set of 145 CSSLs were identified in BC2F2 which together represented 87% of O. rufipogon genome. In addition, 87 of the 145 CSSLs were significantly different than MTU1010 for at least one trait. The major effect QTLs can be fine mapped for gene discovery. CSSLs developed in this study are a good source of novel alleles from O. rufipogon in the background of Cottondora Sannalu for rapid improvement of any trait in rice.
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Affiliation(s)
- Venkateswara Rao Yadavalli
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Divya Balakrishnan
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
- Department of Plant Breeding and Genetics, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Malathi Surapaneni
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Krishnamraju Addanki
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Sukumar Mesapogu
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Kavitha Beerelli
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Subrahmanyam Desiraju
- Department of Plant Physiology, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Sitapati Rao Voleti
- Department of Plant Physiology, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Sarla Neelamraju
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India.
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16
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Genetic Mapping to Detect Stringent QTLs Using 1k-RiCA SNP Genotyping Platform from the New Landrace Associated with Salt Tolerance at the Seedling Stage in Rice. PLANTS 2022; 11:plants11111409. [PMID: 35684182 PMCID: PMC9183132 DOI: 10.3390/plants11111409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/02/2022]
Abstract
Rice is the world’s most important food crop, providing the daily calorie intake for more than half of the world’s population. Rice breeding has always been preoccupied with maximizing yield potential. However, numerous abiotic factors, such as salt, cold, drought, and heat, significantly reduce rice productivity. Salinity, one of the major abiotic stresses, reduces rice yield worldwide. This study was conducted to determine new quantitative trait loci (QTLs) that regulate salt tolerance in rice seedlings. One F2:3 mapping population was derived from a cross between BRRI dhan49 (a popular but sensitive rainfed rice variety) and Akundi (a salt-tolerant rice landrace in Bangladesh used as a donor parent). The 1k-Rice Custom Amplicon (1k-RiCA) single-nucleotide polymorphism (SNP) markers were used to genotype this mapping population. After removing segregation distortion and monomorphic markers, 884 SNPs generated a 1526.8 cM-long genetic linkage map with a mean marker density of 1.7 cM for the 12 linkage groups. By exploiting QGene and ICIM-ADD, a sum of 15 QTLs for nine traits was identified in salt stress on seven chromosomes. Four important genomic loci were identified (qSES1, qSL1, qSUR1 and qRL1) on chromosome 1. Out of these 15 QTLs, 14 QTLs are unique, as no other study has mapped in the same chromosomal location. We also detected 15 putative candidate genes and their functions. The ICIM-EPI approach identified 43 significant pairwise epistasis interactions between regions associated with and unassociated with QTLs. Apart from more well-known donors, Akundi serves as an important new donor source for global salt tolerance breeding initiatives, including Bangladesh. The introgression of the novel QTLs identified in this study will accelerate the development of new salt-tolerant varieties that are highly resistant to salt stress using marker-enabled breeding.
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de Ocampo MP, Ho VT, Thomson MJ, Mitsuya S, Yamauchi A, Ismail AM. QTL mapping under salt stress in rice using a Kalarata-Azucena population. EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2022; 218:74. [PMID: 36060537 PMCID: PMC9427886 DOI: 10.1007/s10681-022-03026-8] [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: 06/23/2020] [Accepted: 04/19/2022] [Indexed: 05/24/2023]
Abstract
UNLABELLED Salt stress is a major constraint across large rice production areas in Asia, because of the high sensitivity of modern rice varieties. To identify quantitative trait loci (QTL) associated with salt tolerance in rice, we developed an F2 population from a cross between the salt-tolerant landrace, Kalarata, and the salt-sensitive parent, Azucena. F3 families from this population were screened and scored for salt tolerance using IRRI's Standard evaluation system (SES). Growth, biomass, Na+ and K+ concentrations in leaf tissues, and chlorophyll concentration were determined. A genetic linkage map was constructed with 151 SSRs and InDel markers, which cover 1463 cM with an average distance of 9.69 cM between loci. A total of 13 QTL were identified using Composite Interval Mapping for 16 traits. Several novel QTL were identified in this study, the largest is for root sodium concentration (LOD = 11.0, R2 = 25.0) on chromosome 3, which also co-localize with a QTL for SES. Several QTL on the short arm of chromosome 1 coincide with the Saltol locus identified before. The novel QTL identified in this study constitute future targets for molecular breeding, to combine them with other QTL identified before, for higher tolerance and stable performance of rice varieties in salt affected soils. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10681-022-03026-8.
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Affiliation(s)
- Marjorie P. de Ocampo
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
| | - Viet The Ho
- Faculty of Biology and Environment, Ho Chi Minh City University of Food Industry, Ho Chi Minh City, Vietnam
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, 343C Heep Center, Texas A&M University, College Station, TX USA
| | - Shiro Mitsuya
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
| | - Abdelbagi M. Ismail
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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18
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Beerelli K, Balakrishnan D, Addanki KR, Surapaneni M, Rao Yadavalli V, Neelamraju S. Mapping of QTLs for Yield Traits Using F 2:3:4 Populations Derived From Two Alien Introgression Lines Reveals qTGW8.1 as a Consistent QTL for Grain Weight From Oryza nivara. FRONTIERS IN PLANT SCIENCE 2022; 13:790221. [PMID: 35356124 PMCID: PMC8959756 DOI: 10.3389/fpls.2022.790221] [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: 10/06/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Wild introgressions play a crucial role in crop improvement by transferring important novel alleles and broadening allelic diversity of cultivated germplasm. In this study, two stable backcross alien introgression lines 166s and 14s derived from Swarn/Oryza nivara IRGC81848 were used as parents to generate populations to map quantitative trait loci (QTLs) for yield-related traits. Field evaluation of yield-related traits in F2, F3, and F4 population was carried out in normal irrigated conditions during the wet season of 2015 and dry seasons of 2016 and 2018, respectively. Plant height, tiller number, productive tiller number, total dry matter, and harvest index showed a highly significant association to single plant yield in F2, F3, and F4. In all, 21, 30, and 17 QTLs were identified in F2, F2:3, and F2:4, respectively, for yield-related traits. QTLs qPH6.1 with 12.54% phenotypic variance (PV) in F2, qPH1.1 with 13.01% PV, qTN6.1 with 10.08% PV in F2:3, and qTGW6.1 with 15.19% PV in F2:4 were identified as major effect QTLs. QTLs qSPY4.1 and qSPY6.1 were detected for grain yield in F2 and F2:3 with PV 8.5 and 6.7%, respectively. The trait enhancing alleles of QTLs qSPY4.1, qSPY6.1, qPH1.1, qTGW6.1, qTGW8.1, qGN4.1, and qTDM5.1 were from O. nivara. QTLs of the yield contributing traits were found clustered in the same chromosomal region. qTGW8.1 was identified in a 2.6 Mb region between RM3480 and RM3452 in all three generations with PV 6.1 to 9.8%. This stable and consistent qTGW8.1 allele from O. nivara can be fine mapped for identification of causal genes. From this population, lines C212, C2124, C2128, and C2143 were identified with significantly higher SPY and C2103, C2116, and C2117 had consistently higher thousand-grain weight values than both the parents and Swarna across the generations and are useful in gene discovery for target traits and further crop improvement.
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Affiliation(s)
- Kavitha Beerelli
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Divya Balakrishnan
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Krishnam Raju Addanki
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Malathi Surapaneni
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | - Sarla Neelamraju
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
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Kumar P, Choudhary M, Halder T, Prakash NR, Singh V, V. VT, Sheoran S, T. RK, Longmei N, Rakshit S, Siddique KHM. Salinity stress tolerance and omics approaches: revisiting the progress and achievements in major cereal crops. Heredity (Edinb) 2022; 128:497-518. [DOI: 10.1038/s41437-022-00516-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023] Open
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20
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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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21
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Chen G, Hu K, Zhao J, Guo F, Shan W, Jiang Q, Zhang J, Guo Z, Feng Z, Chen Z, Wu X, Zhang S, Zuo S. Genome-Wide Association Analysis for Salt-Induced Phenotypic and Physiologic Responses in Rice at Seedling and Reproductive Stages. FRONTIERS IN PLANT SCIENCE 2022; 13:822618. [PMID: 35222481 PMCID: PMC8863738 DOI: 10.3389/fpls.2022.822618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Salinity is one of the main adverse environmental factors severely inhibiting rice growth and decreasing grain productivity. Developing rice varieties with salt tolerance (ST) is one of the most economical approaches to cope with salinity stress. In this study, the salt tolerance of 220 rice accessions from rice diversity panel l (RDP1), representing five subpopulations, were evaluated based on 16 ST indices at both seedling and reproductive stages under salt stress. An apparent inconsistency was found for ST between the two stages. Through a gene-based/tightly linked genome-wide association study with 201,332 single nucleotide polymorphisms (SNPs) located within genes and their flanking regions were used, a total of 214 SNPs related to 251 genes, significantly associated with 16 ST-related indices, were detected at both stages. Eighty-two SNPs with low frequency favorable (LFF) alleles in the population were proposed to hold high breeding potential in improving rice ST. Fifty-four rice accessions collectively containing all these LFF alleles were identified as donors of these alleles. Through the integration of meta-quantitative trait locus (QTL) for ST and the response patterns of differential expression genes to salt stress, thirty-eight candidate genes were suggested to be involved in the regulation of rice ST. In total, the present study provides valuable information for further characterizing ST-related genes and for breeding ST varieties across whole developmental stages through marker-assisted selection (MAS).
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Affiliation(s)
- Gang Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Keming Hu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Jianhua Zhao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Feifei Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Wenfeng Shan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Qiuqing Jiang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Jinqiao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Zilong Guo
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiming Feng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Zongxiang Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Xiaoxia Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Shengwei Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shimin Zuo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Co-innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Institutes of Agricultural Science and Technology Development, Yangzhou University, The Ministry of Education of China, Yangzhou, China
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22
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Singh RK, Kota S, Flowers TJ. Salt tolerance in rice: seedling and reproductive stage QTL mapping come of age. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3495-3533. [PMID: 34287681 PMCID: PMC8519845 DOI: 10.1007/s00122-021-03890-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 06/09/2021] [Indexed: 05/15/2023]
Abstract
Reproductive stage salinity tolerance is most critical for rice as it determines the yield under stress. Few studies have been undertaken for this trait as phenotyping was cumbersome, but new methodology outlined in this review seeks to redress this deficiency. Sixty-three meta-QTLs, the most important genomic regions to target for enhancing salinity tolerance, are reported. Although rice has been categorized as a salt-sensitive crop, it is not equally affected throughout its growth, being most sensitive at the seedling and reproductive stages. However, a very poor correlation exists between sensitivity at these two stages, which suggests that the effects of salt are determined by different mechanisms and sets of genes (QTLs) in seedlings and during flowering. Although tolerance at the reproductive stage is arguably the more important, as it translates directly into grain yield, more than 90% of publications on the effects of salinity on rice are limited to the seedling stage. Only a few studies have been conducted on tolerance at the reproductive stage, as phenotyping is cumbersome. In this review, we list the varieties of rice released for salinity tolerance traits, those being commercially cultivated in salt-affected soils and summarize phenotyping methodologies. Since further increases in tolerance are needed to maintain future productivity, we highlight work on phenotyping for salinity tolerance at the reproductive stage. We have constructed an exhaustive list of the 935 reported QTLs for salinity tolerance in rice at the seedling and reproductive stages. We illustrate the chromosome locations of 63 meta-QTLs (with 95% confidence interval) that indicate the most important genomic regions for salt tolerance in rice. Further study of these QTLs should enhance our understanding of salt tolerance in rice and, if targeted, will have the highest probability of success for marker-assisted selections.
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Affiliation(s)
- Rakesh Kumar Singh
- Crop Diversification and Genetics, International Center for Biosaline Agriculture (ICBA), Dubai, UAE
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Banos, Philippines
| | - Suneetha Kota
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Banos, Philippines
- Genetics and Plant Breeding Department, Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Timothy J Flowers
- School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK.
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23
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Fan X, Jiang H, Meng L, Chen J. Gene Mapping, Cloning and Association Analysis for Salt Tolerance in Rice. Int J Mol Sci 2021; 22:11674. [PMID: 34769104 PMCID: PMC8583862 DOI: 10.3390/ijms222111674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Soil salinization caused by the accumulation of sodium can decrease rice yield and quality. Identification of rice salt tolerance genes and their molecular mechanisms could help breeders genetically improve salt tolerance. We studied QTL mapping of populations for rice salt tolerance, period and method of salt tolerance identification, salt tolerance evaluation parameters, identification of salt tolerance QTLs, and fine-mapping and map cloning of salt tolerance QTLs. We discuss our findings as they relate to other genetic studies of salt tolerance association.
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Affiliation(s)
- Xiaoru Fan
- School of Chemistry and Life Science, Anshan Normal University, Anshan 114007, China;
| | - Hongzhen Jiang
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China;
| | - Lijun Meng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528200, China
| | - Jingguang Chen
- School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China;
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24
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Mohanavel V, Yesudhas AS, Sharma A, Ramasamy A, Muthu Arjuna Samy P, Subramanian M, Muthusamy R. Haplotype and diversity analysis of indigenous rice for salinity tolerance in early-stage seedling using simple sequence repeat markers. ACTA ACUST UNITED AC 2021; 31:e00666. [PMID: 34557392 PMCID: PMC8446578 DOI: 10.1016/j.btre.2021.e00666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/11/2021] [Accepted: 08/08/2021] [Indexed: 11/04/2022]
Abstract
Rice is a staple food for more than three billion people, and rice cultivars have evolved over thousands of years of adaptation to different environmental stresses in different regions. Domestication of rice cultivation led to the diversity of cultivars though phenotypic selection for desirable characters. India is blessed with great diversity of rice germplasm, and these are still conserved for many reasons. The aim of the study was to show the seedling-stage salt tolerance of a total of 50 indigenous rice genotypes from coastal Tamil Nadu, India. Using a hydroponic system, we studied the different agronomic characters from seedling to plant growth hight 14 days after exposure to six different concentrations of saline solution. Rice genotypes showed significant interaction and differential response towards salinity were assessed at the molecular level using simple sequence repeat (SSR) markers linked with salt-tolerance QTL. We found wide genetic distance among the genotypes studied. The combination of morphological findings and molecular assessment revealed better salt-tolerance in a few genotypes. This is, to the best of our knowledge, the first study on the indigenous rice landraces of coastal Tamil Nadu, India.
We evaluated the seedling-stage salt tolerance of a total of 50 indigenous rice genotypes from coastal Tamil Nadu. Using a hydroponic system, we studied the different agronomic characters 14 days after exposure to six different concentrations of saline solution. Shoot and root length as well as plant biomass at seedling stage decreased with increasing salinity. Genotypes showing significant interaction and differential response towards salinity were assessed at the molecular level using 20 simple sequence repeat (SSR) markers linked with salt-tolerance QTL. These genotypes were grouped into eleven clusters based on molecular diversity analysis and eight clusters based on D2 statistical analysis. We found wide genetic distance among the genotypes studied. Simple correlation analysis revealed highly significant associations among the traits studied. The combination of morphological findings and molecular assessment revealed better salt-tolerance in a few genotypes viz. Kuzhi adichan, Poonkar, Kallundai, and Sornamugi.
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Affiliation(s)
- Vignesh Mohanavel
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, Tamil Nadu 608002, India.,Center for Plant Molecular Biology, Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu 641003, India
| | - Anbu Selvam Yesudhas
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, Tamil Nadu 608002, India
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300,, Zhejiang, China
| | - Anandan Ramasamy
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, Tamil Nadu 608002, India
| | - Prakash Muthu Arjuna Samy
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, Tamil Nadu 608002, India
| | - Murugan Subramanian
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, Tamil Nadu 608002, India
| | - Ramakrishnan Muthusamy
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300,, Zhejiang, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China.,Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
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25
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Ahmadizadeh M, Babaeian-Jelodar N, Mohammadi-Nejad G, Bagheri N, Singh RK. High-density linkage mapping for agronomic and physiological traits of rice (Oryza sativa L.) under reproductive-stage salt stress. J Genet 2021. [DOI: 10.1007/s12041-021-01301-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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26
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Sun J, Wang J, Guo W, Yin T, Zhang S, Wang L, Xie D, Zou D. Identification of alkali-tolerant candidate genes using the NGS-assisted BSA strategy in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:44. [PMID: 37309384 PMCID: PMC10236117 DOI: 10.1007/s11032-021-01228-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/03/2021] [Indexed: 06/14/2023]
Abstract
Rice (Oryza sativa L.) is a saline-alkali-sensitive crop. Saline-alkali environments can seriously affect the growth, development, and yield of rice. The mechanisms of salt tolerance and alkali tolerance in rice are different; thus, it is very important to study and explore the alkali-tolerant gene loci to improve the saline-alkali tolerance of rice varieties. In this study, the japonica rice varieties Dongnong 425 (DN425) and Changbai 10 (CB10) and a hybridized recombinant inbred line (RIL) population were used as materials to be irrigated with Na2CO3 solution under field test conditions. A resistant pool (R-pool) and a sensitive pool (S-pool) were constructed by selecting the lines with extremely high and extremely low 1000-grain weight (TGW), respectively, from the RIL population under alkali treatment. Four candidate TGW regions on chromosomes (Chr.) 2 and 3 were associated using the bulked segregant analysis (BSA) strategy assisted by next-generation sequencing (NGS) technology (NGS-assisted BSA). Using the linkage analysis, QTL-qATGW2-2 in the candidate region was mapped within a range of 116 Kb between the SSR marker RM13592 and the Indel marker Indel3 of Chr. 2, which contained 18 predictive genes. The BSA sequencing results showed that Os02g39884 contained a nonsynonymous substitution mutation SNP (nsSNP), leading to the transformation of a residue from arginine (cGg) to glutamine (cAg); thus, Os02g39884 was inferred to be the candidate gene of qATGW2-2. The results of the qRT-PCR analysis also confirmed this. This paper provides important information for the rapid and accurate identification of the alkali-tolerant gene loci in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01228-x.
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Affiliation(s)
- Jian Sun
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Chinese Ministry of Education (Northeast Agricultural University), Harbin, 150030 China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Chinese Ministry of Education (Northeast Agricultural University), Harbin, 150030 China
| | - Wei Guo
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Chinese Ministry of Education (Northeast Agricultural University), Harbin, 150030 China
| | - Tianjiao Yin
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Chinese Ministry of Education (Northeast Agricultural University), Harbin, 150030 China
| | - Shuli Zhang
- Biotechnology Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 China
| | - Liang Wang
- Kunming Tobacco Company of Yunnan Province, Kunming, 650051 China
| | - Dongwei Xie
- School of Life Sciences, Nantong University, Nantong, 226019 China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Chinese Ministry of Education (Northeast Agricultural University), Harbin, 150030 China
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27
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Le TD, Gathignol F, Vu HT, Nguyen KL, Tran LH, Vu HTT, Dinh TX, Lazennec F, Pham XH, Véry AA, Gantet P, Hoang GT. Genome-Wide Association Mapping of Salinity Tolerance at the Seedling Stage in a Panel of Vietnamese Landraces Reveals New Valuable QTLs for Salinity Stress Tolerance Breeding in Rice. PLANTS 2021; 10:plants10061088. [PMID: 34071570 PMCID: PMC8228224 DOI: 10.3390/plants10061088] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/18/2021] [Accepted: 05/25/2021] [Indexed: 01/18/2023]
Abstract
Rice tolerance to salinity stress involves diverse and complementary mechanisms, such as the regulation of genome expression, activation of specific ion-transport systems to manage excess sodium at the cell or plant level, and anatomical changes that avoid sodium penetration into the inner tissues of the plant. These complementary mechanisms can act synergistically to improve salinity tolerance in the plant, which is then interesting in breeding programs to pyramidize complementary QTLs (quantitative trait loci), to improve salinity stress tolerance of the plant at different developmental stages and in different environments. This approach presupposes the identification of salinity tolerance QTLs associated with different mechanisms involved in salinity tolerance, which requires the greatest possible genetic diversity to be explored. To contribute to this goal, we screened an original panel of 179 Vietnamese rice landraces genotyped with 21,623 SNP markers for salinity stress tolerance under 100 mM NaCl treatment, at the seedling stage, with the aim of identifying new QTLs involved in the salinity stress tolerance via a genome-wide association study (GWAS). Nine salinity tolerance-related traits, including the salt injury score, chlorophyll and water content, and K+ and Na+ contents were measured in leaves. GWAS analysis allowed the identification of 26 QTLs. Interestingly, ten of them were associated with several different traits, which indicates that these QTLs act pleiotropically to control the different levels of plant responses to salinity stress. Twenty-one identified QTLs colocalized with known QTLs. Several genes within these QTLs have functions related to salinity stress tolerance and are mainly involved in gene regulation, signal transduction or hormone signaling. Our study provides promising QTLs for breeding programs to enhance salinity tolerance and identifies candidate genes that should be further functionally studied to better understand salinity tolerance mechanisms in rice.
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Affiliation(s)
- Thao Duc Le
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Floran Gathignol
- UMR DIADE, Université de Montpellier, IRD, 34095 Montpellier, France; (F.G.); (F.L.)
| | - Huong Thi Vu
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Khanh Le Nguyen
- Faculty of Agricultural Technology, University of Engineering and Technology, Hanoi 00000, Vietnam;
| | - Linh Hien Tran
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Hien Thi Thu Vu
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Vietnam National University of Agriculture, Hanoi 00000, Vietnam;
| | - Tu Xuan Dinh
- Incubation and Support Center for Technology and Science Enterprises, Hanoi 00000, Vietnam;
| | - Françoise Lazennec
- UMR DIADE, Université de Montpellier, IRD, 34095 Montpellier, France; (F.G.); (F.L.)
| | - Xuan Hoi Pham
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Anne-Aliénor Véry
- UMR BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France;
| | - Pascal Gantet
- UMR DIADE, Université de Montpellier, IRD, 34095 Montpellier, France; (F.G.); (F.L.)
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
- Correspondence: (P.G.); (G.T.H.); Tel.: +33-467-416-414 (P.G.); +84-397-600-496 (G.T.H.)
| | - Giang Thi Hoang
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
- Correspondence: (P.G.); (G.T.H.); Tel.: +33-467-416-414 (P.G.); +84-397-600-496 (G.T.H.)
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28
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Neang S, de Ocampo M, Egdane JA, Platten JD, Ismail AM, Seki M, Suzuki Y, Skoulding NS, Kano-Nakata M, Yamauchi A, Mitsuya S. A GWAS approach to find SNPs associated with salt removal in rice leaf sheath. ANNALS OF BOTANY 2020; 126:1193-1202. [PMID: 33009812 PMCID: PMC7684702 DOI: 10.1093/aob/mcaa139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/02/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND AND AIMS The ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice. METHODS In this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl- concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress. KEY RESULTS For the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress. CONCLUSIONS These GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress.
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Affiliation(s)
- Sarin Neang
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | | | - James A Egdane
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | | | | | - Masahide Seki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Japan
| | | | - Mana Kano-Nakata
- International Center for Research and Education in Agriculture, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Shiro Mitsuya
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
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29
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Mirdar Mansuri R, Shobbar ZS, Babaeian Jelodar N, Ghaffari M, Mohammadi SM, Daryani P. Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach. BMC PLANT BIOLOGY 2020; 20:452. [PMID: 33004003 PMCID: PMC7528482 DOI: 10.1186/s12870-020-02679-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 09/24/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Salinity, as one of the main abiotic stresses, critically threatens growth and fertility of main food crops including rice in the world. To get insight into the molecular mechanisms by which tolerant genotypes responds to the salinity stress, we propose an integrative meta-analysis approach to find the key genes involved in salinity tolerance. Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. DEGs were then confirmed by meta-QTL analysis and literature review. RESULTS A total of 3449 DEGs were detected in 46 meta-QTL positions, among which 1286, 86, 1729 and 348 DEGs were observed in root, shoot, seedling, and leaves tissues, respectively. Moreover, functional annotation of DEGs located in the meta-QTLs suggested some involved biological processes (e.g., ion transport, regulation of transcription, cell wall organization and modification as well as response to stress) and molecular function terms (e.g., transporter activity, transcription factor activity and oxidoreductase activity). Remarkably, 23 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes. Some promising candidate genes were detected such as pectinesterase, peroxidase, transcription regulator, high-affinity potassium transporter, cell wall organization, protein serine/threonine phosphatase, and CBS domain cotaining protein. CONCLUSIONS The obtained results indicated that, the salt tolerant genotypes use qualified mechanisms particularly in sensing and signalling of the salt stress, regulation of transcription, ionic homeostasis, and Reactive Oxygen Species (ROS) scavenging in response to the salt stress.
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Affiliation(s)
- Raheleh Mirdar Mansuri
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran
- Faculty of Crop Science, Department of Plant breeding and Biotechnology, Sari Agricultural Science and Natural Resources University, Sari, Iran
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran
| | - Nadali Babaeian Jelodar
- Faculty of Crop Science, Department of Plant breeding and Biotechnology, Sari Agricultural Science and Natural Resources University, Sari, Iran
| | - Mohammadreza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran
| | - Seyed Mahdi Mohammadi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran
| | - Parisa Daryani
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran
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Lei L, Zheng H, Bi Y, Yang L, Liu H, Wang J, Sun J, Zhao H, Li X, Li J, Lai Y, Zou D. Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.) Using QTL-Seq and RNA-Seq. RICE (NEW YORK, N.Y.) 2020; 13:55. [PMID: 32778977 PMCID: PMC7417472 DOI: 10.1186/s12284-020-00416-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 08/04/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Salt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final yield in the direct seeding cultivation model. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for salt tolerance at the bud burst stage are limited. RESULTS Here, an F2:3 population derived from a cross between IR36 (salt-sensitive) and Weiguo (salt-tolerant) was used to identify salt-tolerant QTL interval at the bud burst stage using a whole-genome sequencing-based QTL-seq containing 40 extreme salt-tolerant and 40 extreme salt-sensitive individuals. A major QTL, qRSL7, related to relative shoot length (RSL) was detected on chromosome 7 using ΔSNP index algorithms and Euclidean Distance (ED) algorithms. According to single nucleotide polymorphisms (SNPs) between the parents, 25 Kompetitive allele-specific PCR (KASP) markers were developed near qRSL7, and regional QTL mapping was performed using 199 individuals from the F2:3 population. We then confirmed and narrowed down qRSL7 to a 222 kb genome interval. Additionally, RNA sequencing (RNA-seq) was performed for IR36 and Weiguo at 36 h after salt stress and control condition at the bud burst stage, and 5 differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Furthermore, sequence analysis revealed a 1 bp Indel difference in Os07g0569700 (OsSAP16) between IR36 and Weiguo. OsSAP16 encodes a stress-associated protein whose expression is increased under drought stress. CONCLUSION These results indicate that OsSAP16 was the candidate gene of qRSL7. The results is useful for gene cloning of qRSL7 and for improving the salt tolerance of rice varieties by marker assisted selection (MAS).
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Affiliation(s)
- Lei Lei
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150030, China
| | - Yanli Bi
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Luomiao Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jian Sun
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Xianwei Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jiaming Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Yongcai Lai
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
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Chen C, Norton GJ, Price AH. Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel. FRONTIERS IN PLANT SCIENCE 2020; 11:576479. [PMID: 33193518 PMCID: PMC7644878 DOI: 10.3389/fpls.2020.576479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/02/2020] [Indexed: 05/04/2023]
Abstract
Salinity is a major abiotic stress which inhibits rice production in coastal, arid and semi-aid areas in many countries, such as India and Bangladesh. Identification of salt tolerant cultivars, quantitative trait loci (QTLs) and genes is essential for breeding salt tolerant rice. The aus subpopulation of rice is considered to have originated predominantly from Bangladesh and India and have rich genetic diversity with wide variation in abiotic stress resistance. The objective of this study was to identify QTLs, and subsequently candidate genes using cultivars from the aus subpopulation and compare the results of two different seedling stage screening methods. Salt tolerance at the rice seedling stage was evaluated on 204 rice accessions from the Bengal and Assam Aus Panel (BAAP) grown in both hydroponics and soil under control and salt stress conditions. Ten salt related traits of stress symptoms, plant growth and the content of sodium and potassium were measured. Three cultivars, BRRI dhan 47, Goria, and T 1 showed more salt tolerance than the tolerant check Pokkali in both systems. Genome-wide association mapping was conducted on salt indices traits with 2 million SNPs using an efficient mixed model (EMMA) controlling population structure and kinship, and a significance threshold of P < 0.0001 was used to determine significant SNPs. A total of 97 and 74 QTLs associated with traits in hydroponic and soil systems were identified, respectively, including 11 QTLs identified in both systems. A total of 65 candidate genes were found including a well-known major gene OsHKT1;5. The most significant QTL was detected at around 40 Mb on chromosome 1 coinciding with two post-translational modifications SUMOylation genes (OsSUMO1 and OsSUMO2), this QTL was investigated. The salt tolerance rice cultivars and QTLs/genes identified here will provide useful information for future studies on genetics and breeding salt tolerant rice.
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Jaiswal S, Gautam RK, Singh RK, Krishnamurthy SL, Ali S, Sakthivel K, Iquebal MA, Rai A, Kumar D. Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective. RICE (NEW YORK, N.Y.) 2019; 12:89. [PMID: 31802312 PMCID: PMC6892996 DOI: 10.1186/s12284-019-0347-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/06/2019] [Indexed: 05/12/2023]
Abstract
Half of the global human population is dependent on rice as a staple food crop and more than 25% increase in rice productivity is required to feed the global population by 2030. With increase in irrigation, global warming and rising sea level, rising salinity has become one of the major challenges to enhance the rice productivity. Since the loss on this account is to the tune of US$12 billion per annum, it necessitates the global attention. In the era of technological advancement, substantial progress has been made on phenomics and genomics data generation but reaping benefit of this in rice salinity variety development in terms of cost, time and precision requires their harmonization. There is hardly any comprehensive holistic review for such combined approach. Present review describes classical salinity phenotyping approaches having morphological, physiological and biochemical components. It also gives a detailed account of invasive and non-invasive approaches of phenomic data generation and utilization. Classical work of rice salinity QLTs mapping in the form of chromosomal atlas has been updated. This review describes how QTLs can be further dissected into QTN by GWAS and transcriptomic approaches. Opportunities and progress made by transgenic, genome editing, metagenomics approaches in combating rice salinity problems are discussed. Major aim of this review is to provide a comprehensive over-view of hitherto progress made in rice salinity tolerance research which is required to understand bridging of phenotype based breeding with molecular breeding. This review is expected to assist rice breeders in their endeavours by fetching greater harmonization of technological advances in phenomics and genomics for better pragmatic approach having practical perspective.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - R K Gautam
- Division of Field Crop Improvement & Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744105, India.
| | - R K Singh
- Division of Plant Breeding Genetics and Biotechnology, International Rice Research Institute, DAPO Box 7777, Los Banos, Metro Manila, Philippines
| | - S L Krishnamurthy
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - S Ali
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - K Sakthivel
- Division of Field Crop Improvement & Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744105, India
| | - M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India.
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Chakraborty K, Chattaopadhyay K, Nayak L, Ray S, Yeasmin L, Jena P, Gupta S, Mohanty SK, Swain P, Sarkar RK. Ionic selectivity and coordinated transport of Na + and K + in flag leaves render differential salt tolerance in rice at the reproductive stage. PLANTA 2019; 250:1637-1653. [PMID: 31399792 DOI: 10.1007/s00425-019-03253-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/01/2019] [Indexed: 05/27/2023]
Abstract
The present study shows that salt tolerance in the reproductive stage of rice is primarily governed by the selective Na+ and K+ transport from the root to upper plant parts. Ionic discrimination at the flag leaf, governed by differential expression of Na+- and K+-specific transporters/ion pumps, is associated with reduced spikelet sterility and reproductive stage salt tolerance. Reproductive stage salt tolerance is crucial in rice to guarantee yield under saline condition. In the present study, differential ionic selectivity and the coordinated transport (from root to flag leaf) of Na+ and K+ were investigated to assess their impact on reproductive stage salt tolerance. Four rice genotypes having differential salt sensitivity were subjected to reproductive stage salinity stress in pots. The selective Na+ and K+ transport from the root to upper plant parts was observed in tolerant genotypes. We noticed that prolonged salt exposure did not alter flag leaf greenness even up to 6 weeks; however, it had a detrimental effect on panicle development especially in the salt-susceptible genotype Sabita. But more precise chlorophyll fluorescence imaging analysis revealed salinity-induced damages in Sabita. The salt-tolerant genotype Pokkali (AC41585), a potential Na+ excluder, managed to sequester higher Na+ load in the roots with little upward transport as evident from greater expression of HKT1 and HKT2 transporters. In contrast, the moderately salt-tolerant Lunidhan was less selective in Na+ transport, but possessed a higher capacity to Na+ sequestration in leaves. Higher K+ uptake and tissue-specific redistribution mediated by HAK and AKT transporters showed robust control in selective K+ movement from the root to flag leaf and developing panicles. On the contrary, expressions of Na+-specific transporters in developing panicles were either down-regulated or unaffected in tolerant and moderately tolerant genotypes. Yet, in the panicles of the susceptible genotype Sabita, some of the Na+-specific transporter genes (SOS1, HKT1;5, HKT2;4) were upregulated. Apart from the ionic regulation strategy, cellular energy balance mediated by different plasma-membrane and tonoplastic H+-pumps were also associated with the reproductive stage salt tolerance in rice.
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Affiliation(s)
| | | | - Lopamudra Nayak
- ICAR, National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Soham Ray
- ICAR, National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Lucina Yeasmin
- ICAR, National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Priyanka Jena
- ICAR, National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Sunanda Gupta
- ICAR, National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Sangram K Mohanty
- ICAR, National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Padmini Swain
- ICAR, National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Ramani K Sarkar
- ICAR, National Rice Research Institute, Cuttack, Odisha, 753006, India
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Mitsuya S, Murakami N, Sato T, Kazama T, Toriyama K, Skoulding NS, Kano-Nakata M, Yamauchi A. Evaluation of rice grain yield and yield components of Nona Bokra chromosome segment substitution lines with the genetic background of Koshihikari, in a saline paddy field. AOB PLANTS 2019; 11:plz040. [PMID: 31632626 PMCID: PMC6790112 DOI: 10.1093/aobpla/plz040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 07/11/2019] [Indexed: 05/27/2023]
Abstract
The ability to tolerate salt differs with the growth stages of rice and thus the yield components that are determined during various growth stages, are differentially affected by salt stress. In this study, we utilized chromosome segment substitution lines (CSSLs) from Nona Bokra, a salt-tolerant indica landrace, with the genetic background of Koshihikari, a salt-susceptible japonica variety. These were screened to find superior CSSLs under long-term saline conditions that showed higher grain yield and yield components in comparison to Koshihikari. One-month-old seedlings were transplanted into a paddy field without salinity. These were allowed to establish for 1 month further, then the field was flooded, with saline water maintained at 7.41 dS m-1 salinity until harvest. The experiments were performed twice, once in 2015 and a targeted study in 2016. Salt tolerance of growth and reproductive stage parameters was evaluated as the Salt Effect Index (SEI) which was computed as the difference in each parameter within each line between control and saline conditions. All CSSLs and Koshihikari showed a decrease in grain yield and yield components except panicle number under salinity. SL538 showed a higher SEI for grain yield compared with Koshihikari under salinity throughout the two experiments. This was attributed to the retained grain filling and harvest index, yet the mechanism was not due to maintaining Na+, Cl- and K+ homeostasis. Few other CSSLs showed greater SEI for grain weight under salinity compared with Koshihikari, which might be related to low concentration of Na+ in leaves and panicles. These data indicate that substitution of different Nona Bokra chromosome segments independently contributed to the maintenance of grain filling and grain weight of Koshihikari under saline conditions.
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Affiliation(s)
- Shiro Mitsuya
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Norifumi Murakami
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Tadashi Sato
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Tomohiko Kazama
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
| | | | - Mana Kano-Nakata
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
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35
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Detection of QTL for panicle architecture in $$\hbox {F}_{2}$$ population of rice. J Genet 2019. [DOI: 10.1007/s12041-019-1088-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Lekklar C, Pongpanich M, Suriya-arunroj D, Chinpongpanich A, Tsai H, Comai L, Chadchawan S, Buaboocha T. Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand. BMC Genomics 2019; 20:76. [PMID: 30669971 PMCID: PMC6343365 DOI: 10.1186/s12864-018-5317-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Salt stress, a major plant environmental stress, is a critical constraint for rice productivity. Dissecting the genetic loci controlling salt tolerance in rice for improving productivity, especially at the flowering stage, remains challenging. Here, we conducted a genome-wide association study (GWAS) of salt tolerance based on exome sequencing of the Thai rice accessions. RESULTS Photosynthetic parameters and cell membrane stability under salt stress at the flowering stage; and yield-related traits of 104 Thai rice (Oryza sativa L.) accessions belonging to the indica subspecies were evaluated. The rice accessions were subjected to exome sequencing, resulting in 112,565 single nucleotide polymorphisms (SNPs) called with a minor allele frequency of at least 5%. LD decay analysis of the panel indicates that the average LD for SNPs at 20 kb distance from each other was 0.34 (r2), which decayed to its half value (~ 0.17) at around 80 kb. By GWAS performed using mixed linear model, two hundred loci containing 448 SNPs on exons were identified based on the salt susceptibility index of the net photosynthetic rate at day 6 after salt stress; and the number of panicles, filled grains and unfilled grains per plant. One hundred and forty six genes, which accounted for 73% of the identified loci, co-localized with the previously reported salt quantitative trait loci (QTLs). The top four regions that contained a high number of significant SNPs were found on chromosome 8, 12, 1 and 2. While many are novel, their annotation is consistent with potential involvement in plant salt tolerance and in related agronomic traits. These significant SNPs greatly help narrow down the region within these QTLs where the likely underlying candidate genes can be identified. CONCLUSIONS Insight into the contribution of potential genes controlling salt tolerance from this GWAS provides further understanding of salt tolerance mechanisms of rice at the flowering stage, which can help improve yield productivity under salinity via gene cloning and genomic selection.
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Affiliation(s)
- Chakkree Lekklar
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Duangjai Suriya-arunroj
- Nakhon Ratchasima Rice Research Center, Rice Department, Ministry of Agriculture and Cooperatives, Nakhon Ratchasima, Thailand
| | - Aumnart Chinpongpanich
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Helen Tsai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA USA
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA USA
| | - Supachitra Chadchawan
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Teerapong Buaboocha
- Center of Excellent in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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37
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Patishtan J, Hartley TN, Fonseca de Carvalho R, Maathuis FJM. Genome-wide association studies to identify rice salt-tolerance markers. PLANT, CELL & ENVIRONMENT 2018; 41:970-982. [PMID: 28436093 DOI: 10.1111/pce.12975] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/03/2017] [Accepted: 04/03/2017] [Indexed: 05/17/2023]
Abstract
Salinity is an ever increasing menace that affects agriculture worldwide. Crops such as rice are salt sensitive, but its degree of susceptibility varies widely between cultivars pointing to extensive genetic diversity that can be exploited to identify genes and proteins that are relevant in the response of rice to salt stress. We used a diversity panel of 306 rice accessions and collected phenotypic data after short (6 h), medium (7 d) and long (30 d) salinity treatment (50 mm NaCl). A genome-wide association study (GWAS) was subsequently performed, which identified around 1200 candidate genes from many functional categories, but this was treatment period dependent. Further analysis showed the presence of cation transporters and transcription factors with a known role in salinity tolerance and those that hitherto were not known to be involved in salt stress. Localization analysis of single nucleotide polymorphisms (SNPs) showed the presence of several hundred non-synonymous SNPs (nsSNPs) in coding regions and earmarked specific genomic regions with increased numbers of nsSNPs. It points to components of the ubiquitination pathway as important sources of genetic diversity that could underpin phenotypic variation in stress tolerance.
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Affiliation(s)
- Juan Patishtan
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Tom N Hartley
- Department of Biology, University of York, York, YO10 5DD, UK
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Surapaneni M, Balakrishnan D, Mesapogu S, Addanki KR, Yadavalli VR, Tripura Venkata VGN, Neelamraju S. Identification of Major Effect QTLs for Agronomic Traits and CSSLs in Rice from Swarna/ Oryza nivara Derived Backcross Inbred Lines. FRONTIERS IN PLANT SCIENCE 2017; 8:1027. [PMID: 28690618 PMCID: PMC5480306 DOI: 10.3389/fpls.2017.01027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/29/2017] [Indexed: 05/04/2023]
Abstract
Backcross inbred lines (BILs) derived from elite x wild crosses are very useful for basic studies and breeding. The aim of this study was to map quantitative trait loci (QTLs) associated with yield and related traits and to identify chromosomal segment substitution lines (CSSLs) from unselected BC2F8 BILs of Swarna/Oryza nivara IRGC81848. In all, 94 BILs were field evaluated in 2 years (wet seasons, 2014 and 2015) for nine traits; days to 50% flowering, days to maturity (DM), plant height (PH), number of tillers, number of productive tillers, panicle weight, yield per plant, bulk yield, and biomass. BILs were genotyped using 111 polymorphic simple sequence repeats distributed across the genome. Fifteen QTLs including 10 novel QTLs were identified using composite interval mapping, Inclusive composite interval mapping and multiple interval mapping (MIM). O. nivara alleles were trait-enhancing in 26% of QTLs. Only 3 of 15 QTLs were also reported previously in BC2F2 of the same cross. These three included the two major effect QTLs for DM and PH detected in both years with 13 and 20% phenotypic variance. Further, a set of 74 CSSLs was identified using CSSL Finder and 22 of these showed significantly higher values than Swarna for five yield traits. CSSLs, 220S for panicle weight and 10-2S with consistent high yield in both years are worthy of large scale field evaluation. The major QTLs and 22 significantly different CSSLs are a useful resource for rice improvement and dissecting yield related traits.
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Mishra S, Singh B, Panda K, Singh BP, Singh N, Misra P, Rai V, Singh NK. Association of SNP Haplotypes of HKT Family Genes with Salt Tolerance in Indian Wild Rice Germplasm. RICE (NEW YORK, N.Y.) 2016; 35:2295-2308. [PMID: 27025598 DOI: 10.1007/s00299-016-2035-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/26/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND Rice is one of the most important crops for global food security but its productivity is adversely affected by salt stress prevalent in about 30 % of the cultivated land. For developing salt-tolerant rice varieties through conventional breeding or biotechnological interventions, there is an urgent need to identify natural allelic variants that may confer salt tolerance. Here, 299 wild rice accessions collected from different agro-climatic regions of India were evaluated during growth under salt stress. Of these 95 representative accessions were sequenced for members of HKT ion transporter family genes by employing Ion Torrent PGM sequencing platform. RESULTS Haplotype analysis revealed haplotypes H5 and H1 of HKT1;5 and HKT2;3, respectively associated with high salinity tolerance. This is the first study of allele mining of eight members of HKT gene family from Indian wild rice reporting a salt tolerant allele of HKT2;3. HKT1;5 also showed a salt tolerant allele from wild rice. Phylogenetic analysis based on the nucleotide sequences showed different grouping of the HKT family genes as compared to the prevailing protein sequence based classification. CONCLUSIONS The salt tolerant alleles of the HKT genes from wild rice may be introgressed into modern high yielding cultivars to widen the existing gene pool and enhance rice production in the salt affected areas.
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Affiliation(s)
- Shefali Mishra
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- Jacob School of Biotechnology and Bioengineering, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad, 211007, India
| | - Balwant Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Kabita Panda
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Bikram Pratap Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Nisha Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Pragati Misra
- Jacob School of Biotechnology and Bioengineering, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad, 211007, India
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Nagendra Kumar Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
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40
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Mishra S, Singh B, Panda K, Singh BP, Singh N, Misra P, Rai V, Singh NK. Association of SNP Haplotypes of HKT Family Genes with Salt Tolerance in Indian Wild Rice Germplasm. RICE (NEW YORK, N.Y.) 2016; 9:15. [PMID: 27025598 PMCID: PMC4811800 DOI: 10.1186/s12284-016-0083-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/08/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND Rice is one of the most important crops for global food security but its productivity is adversely affected by salt stress prevalent in about 30 % of the cultivated land. For developing salt-tolerant rice varieties through conventional breeding or biotechnological interventions, there is an urgent need to identify natural allelic variants that may confer salt tolerance. Here, 299 wild rice accessions collected from different agro-climatic regions of India were evaluated during growth under salt stress. Of these 95 representative accessions were sequenced for members of HKT ion transporter family genes by employing Ion Torrent PGM sequencing platform. RESULTS Haplotype analysis revealed haplotypes H5 and H1 of HKT1;5 and HKT2;3, respectively associated with high salinity tolerance. This is the first study of allele mining of eight members of HKT gene family from Indian wild rice reporting a salt tolerant allele of HKT2;3. HKT1;5 also showed a salt tolerant allele from wild rice. Phylogenetic analysis based on the nucleotide sequences showed different grouping of the HKT family genes as compared to the prevailing protein sequence based classification. CONCLUSIONS The salt tolerant alleles of the HKT genes from wild rice may be introgressed into modern high yielding cultivars to widen the existing gene pool and enhance rice production in the salt affected areas.
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Affiliation(s)
- Shefali Mishra
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- Jacob School of Biotechnology and Bioengineering, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad, 211007, India
| | - Balwant Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Kabita Panda
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Bikram Pratap Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Nisha Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Pragati Misra
- Jacob School of Biotechnology and Bioengineering, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad, 211007, India
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Nagendra Kumar Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
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41
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Bacchetta L, Visioli F, Cappelli G, Caruso E, Martin G, Nemeth E, Bacchetta G, Bedini G, Wezel A, van Asseldonk T, van Raamsdonk L, Mariani F. A manifesto for the valorization of wild edible plants. JOURNAL OF ETHNOPHARMACOLOGY 2016; 191:180-187. [PMID: 27321281 DOI: 10.1016/j.jep.2016.05.061] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/30/2016] [Accepted: 05/30/2016] [Indexed: 05/28/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Wild foods constitute an essential component of people's diets around the world, but despite their widespread use and their cultural importance, wild edible plants (WEPs) lack recognition as significant contributors to the human diet in developed countries. MATERIALS AND METHODS We stimulate national and international bodies dealing with food and agriculture, to increase their attention and investments on WEPs, leveraging the results of scientific investigation, enhancing the link between in situ conservation strategies and sustainable use of plant genetic diversity. RESULTS AND CONCLUSIONS WEPs should be reconsidered throughout their value chain, capturing their important socio-cultural, health, and economic benefits to indigenous and local communities and family farmers who are engaged in their production and wild-harvesting.
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Affiliation(s)
| | - Francesco Visioli
- Department of Molecular Medicine, University of Padova, Italy; IMDEA-Food, CEI UAM+CSIC, Madrid, Spain.
| | - Giulia Cappelli
- Institute Cell Biology and Neurobiology, National Research Council, Monterotondo, RM, Italy
| | | | | | - Eva Nemeth
- Szent István University Budapest, Hungary
| | | | | | | | | | | | - Francesca Mariani
- Institute Cell Biology and Neurobiology, National Research Council, Monterotondo, RM, Italy
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42
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Tiwari S, SL K, Kumar V, Singh B, Rao AR, Mithra SV A, Rai V, Singh AK, Singh NK. Mapping QTLs for Salt Tolerance in Rice (Oryza sativa L.) by Bulked Segregant Analysis of Recombinant Inbred Lines Using 50K SNP Chip. PLoS One 2016; 11:e0153610. [PMID: 27077373 PMCID: PMC4831760 DOI: 10.1371/journal.pone.0153610] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 03/31/2016] [Indexed: 11/19/2022] Open
Abstract
Soil salinity is a major constraint to rice production in large inland and coastal areas around the world. Modern high yielding rice varieties are particularly sensitive to high salt stress. There are salt tolerant landraces and traditional varieties of rice but with limited information on genomic regions (QTLs) and genes responsible for their tolerance. Here we describe a method for rapid identification of QTLs for reproductive stage salt tolerance in rice using bulked segregant analysis (BSA) of bi-parental recombinant inbred lines (RIL). The number of RILs required for the creation of two bulks with extreme phenotypes was optimized to be thirty each. The parents and bulks were genotyped using a 50K SNP chip to identify genomic regions showing homogeneity for contrasting alleles of polymorphic SNPs in the two bulks. The method was applied to ‘CSR11/MI48’ RILs segregating for reproductive stage salt tolerance. Genotyping of the parents and RIL bulks, made on the basis of salt sensitivity index for grain yield, revealed 6,068 polymorphic SNPs and 21 QTL regions showing homogeneity of contrasting alleles in the two bulks. The method was validated further with ‘CSR27/MI48’ RILs used earlier for mapping salt tolerance QTLs using low-density SSR markers. BSA with 50K SNP chip revealed 5,021 polymorphic loci and 34 QTL regions. This not only confirmed the location of previously mapped QTLs but also identified several new QTLs, and provided a rapid way to scan the whole genome for mapping QTLs for complex agronomic traits in rice.
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Affiliation(s)
- Sushma Tiwari
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | | | - Vinod Kumar
- Central Soil Salinity Research Institute, Karnal, India
| | - Balwant Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - AR Rao
- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Amitha Mithra SV
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Ashok K. Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Nagendra K. Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
- * E-mail:
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43
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Kumar V, Singh A, Mithra SVA, Krishnamurthy SL, Parida SK, Jain S, Tiwari KK, Kumar P, Rao AR, Sharma SK, Khurana JP, Singh NK, Mohapatra T. Genome-wide association mapping of salinity tolerance in rice (Oryza sativa). DNA Res 2015; 22:133-45. [PMID: 25627243 PMCID: PMC4401324 DOI: 10.1093/dnares/dsu046] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/26/2014] [Indexed: 02/07/2023] Open
Abstract
Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na+/K+ ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5–18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na+/K+ ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.
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Affiliation(s)
- Vinod Kumar
- National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - Anshuman Singh
- National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - S V Amitha Mithra
- National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - S L Krishnamurthy
- Central Soil Salinity Research Institute, Karnal, Haryana 132001, India
| | - Swarup K Parida
- National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - Sourabh Jain
- National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - Kapil K Tiwari
- National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - Pankaj Kumar
- National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - Atmakuri R Rao
- Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - S K Sharma
- Central Soil Salinity Research Institute, Karnal, Haryana 132001, India
| | | | - Nagendra K Singh
- National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - Trilochan Mohapatra
- National Research Centre on Plant Biotechnology, New Delhi 110012, India Central Rice Research Institute, Cuttack, Odisha 753006, India
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