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Chen T, Niu Y, Yang C, Liang Y, Xu J. Screening of Rice ( Oryza sativa L.) Genotypes for Salinity Tolerance and Dissecting Determinants of Tolerance Mechanism. PLANTS (BASEL, SWITZERLAND) 2024; 13:1036. [PMID: 38611565 PMCID: PMC11013488 DOI: 10.3390/plants13071036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
Soil salinity imposes osmotic, ionic, and oxidative stresses on plants, resulting in growth inhibition, developmental changes, metabolic adaptations, and ion sequestration or exclusion. Identifying salinity-tolerant resources and understanding physiological and molecular mechanisms of salinity tolerance could lay a foundation for the improvement of salinity tolerance in rice. In this study, a series of salinity-tolerance-related morphological and physiological traits were investigated in 46 rice genotypes, including Sea Rice 86, to reveal the main strategies of rice in responding to salinity stress at the seedling stage. No genotypes showed the same tolerance level as the two landraces Pokkali and Nona Bokra, which remain the donors for improving the salinity tolerance of rice. However, due to undesirable agronomic traits of these donors, alternative cultivars such as JC118S and R1 are recommended as novel source of salinity tolerance. Correlation and principal component analyses revealed that the salinity tolerance of rice seedlings is not only controlled by growth vigor but also regulated by ion transport pathways such as long-distance Na+ transport, root Na+ sequestration, and root K+ retention. Therefore, such key traits should be targeted in future breeding programs as the strategy of obtaining better Na+ exclusion is still the bottleneck for improving salinity tolerance in rice.
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Affiliation(s)
- Tianxiao Chen
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China; (T.C.); (C.Y.)
| | - Yanan Niu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Changdeng Yang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China; (T.C.); (C.Y.)
| | - Yan Liang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China; (T.C.); (C.Y.)
| | - Jianlong Xu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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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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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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Patel A, Miles A, Strackhouse T, Cook L, Leng S, Patel S, Klinger K, Rudrabhatla S, Potlakayala SD. Methods of crop improvement and applications towards fortifying food security. Front Genome Ed 2023; 5:1171969. [PMID: 37484652 PMCID: PMC10361821 DOI: 10.3389/fgeed.2023.1171969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023] Open
Abstract
Agriculture has supported human life from the beginning of civilization, despite a plethora of biotic (pests, pathogens) and abiotic (drought, cold) stressors being exerted on the global food demand. In the past 50 years, the enhanced understanding of cellular and molecular mechanisms in plants has led to novel innovations in biotechnology, resulting in the introduction of desired genes/traits through plant genetic engineering. Targeted genome editing technologies such as Zinc-Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) have emerged as powerful tools for crop improvement. This new CRISPR technology is proving to be an efficient and straightforward process with low cost. It possesses applicability across most plant species, targets multiple genes, and is being used to engineer plant metabolic pathways to create resistance to pathogens and abiotic stressors. These novel genome editing (GE) technologies are poised to meet the UN's sustainable development goals of "zero hunger" and "good human health and wellbeing." These technologies could be more efficient in developing transgenic crops and aid in speeding up the regulatory approvals and risk assessments conducted by the US Departments of Agriculture (USDA), Food and Drug Administration (FDA), and Environmental Protection Agency (EPA).
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Affiliation(s)
- Aayushi Patel
- Penn State Harrisburg, Middletown, PA, United States
| | - Andrew Miles
- Penn State University Park, State College, University Park, PA, United States
| | | | - Logan Cook
- Penn State Harrisburg, Middletown, PA, United States
| | - Sining Leng
- Shanghai United Cell Biotechnology Co Ltd, Shanghai, China
| | - Shrina Patel
- Penn State Harrisburg, Middletown, PA, United States
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Maniruzzaman S, Rahman MA, Hasan M, Rasul MG, Molla AH, Khatun H, Iftekharuddaula KM, Kabir MS, Akter S. Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice. Int J Mol Sci 2023; 24:11141. [PMID: 37446320 DOI: 10.3390/ijms241311141] [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: 05/26/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Achieving high-yield potential is always the ultimate objective of any breeding program. However, various abiotic stresses such as salinity, drought, cold, flood, and heat hampered rice productivity tremendously. Salinity is one of the most important abiotic stresses that adversely affect rice grain yield. The present investigation was undertaken to dissect new genetic loci, which are responsible for salt tolerance at the early seedling stage in rice. A bi-parental mapping population (F2:3) was developed from the cross between BRRI dhan28/Akundi, where BRRI dhan28 (BR28) is a salt-sensitive irrigated (boro) rice mega variety and Akundi is a highly salinity-tolerant Bangladeshi origin indica rice landrace that is utilized as a donor parent. We report reliable and stable QTLs for salt tolerance from a common donor (Akundi) irrespective of two different genetic backgrounds (BRRI dhan49/Akundi and BRRI dhan28/Akundi). A robust 1k-Rice Custom Amplicon (1k-RiCA) SNP marker genotyping platform was used for genome-wide analysis of this bi-parental population. After eliminating markers with high segregation distortion, 886 polymorphic SNPs built a genetic linkage map covering 1526.5 cM of whole rice genome with an average SNP density of 1.72 cM for the 12 genetic linkage groups. A total of 12 QTLs for nine different salt tolerance-related traits were identified using QGene and inclusive composite interval mapping of additive and dominant QTL (ICIM-ADD) under salt stress on seven different chromosomes. All of these 12 new QTLs were found to be unique, as no other map from the previous study has reported these QTLs in the similar chromosomal location and found them different from extensively studied Saltol, SKC1, OsSalT, and salT locus. Twenty-eight significant digenic/epistatic interactions were identified between chromosomal regions linked to or unlinked to QTLs. Akundi acts like a new alternate donor source of salt tolerance except for other usually known donors such as Nona Bokra, Pokkali, Capsule, and Hasawi used in salt tolerance genetic analysis and breeding programs worldwide, including Bangladesh. Integration of the seven novel, reliable, stable, and background independent salinity-resilient QTLs (qSES1, qSL1, qRL1, qSUR1, qSL8, qK8, qK1) reported in this investigation will expedite the cultivar development that is highly tolerant to salt stress.
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Affiliation(s)
- Sheikh Maniruzzaman
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - M Akhlasur Rahman
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - Mehfuz Hasan
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Mohammad Golam Rasul
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Abul Hossain Molla
- Department of Environmental Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Hasina Khatun
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - K M Iftekharuddaula
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - Md Shahjahan Kabir
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
| | - Salma Akter
- Plant Physiology Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh
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Haque US, Elias SM, Jahan I, Seraj ZI. Functional genomic analysis of K + related salt-responsive transporters in tolerant and sensitive genotypes of rice. FRONTIERS IN PLANT SCIENCE 2023; 13:1089109. [PMID: 36743539 PMCID: PMC9893783 DOI: 10.3389/fpls.2022.1089109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Salinity is a complex environmental stress that affects the growth and production of rice worldwide. But there are some rice landraces in coastal regions that can survive in presence of highly saline conditions. An understanding of the molecular attributes contributing to the salinity tolerance of these genotypes is important for developing salt-tolerant high yielding modern genotypes to ensure food security. Therefore, we investigated the role and functional differences of two K+ salt-responsive transporters. These are OsTPKa or Vacuolar two-pore potassium channel and OsHAK_like or a hypothetical protein of the HAK family. These transporters were selected from previously identified QTLs from the tolerant rice landrace genotype (Horkuch) and sensitive genotype (IR29). METHODS In silico comparative sequence analysis of the promoter sequences of two these genes between Horkuch and IR29 was done. Real-Time expression of the selected genes in leaves and roots of IR29 (salt-sensitive), I-14 and I-71 (Recombinant Inbred Lines of IR29(♀)× Horkuch), Horkuch and Pokkali (salt-tolerant) under salt-stress at different time points was analyzed. For further insight, OsTPKa and OsHAK_like were chosen for loss-of-function genomic analysis in Horkuch using the CRISPR/Cas9 tool. Furthermore, OsTPKa was chosen for cloning into a sensitive variety by Gateway technology to observe the effect of gain-of-function. RESULTS The promoter sequences of the OsTPKa and OsHAK_like genes showed some significant differences in promoter sequences which may give a survival advantage to Horkuch under salt-stress. These two genes were also found to be overexpressed in tolerant varieties (Horkuch and Pokkali). Moreover, a coordinated expression pattern between these two genes was observed in tolerant Horkuch under salt-stress. Independently transformed plants where the expression of these genes was significantly lowered, performed poorly in physiological tests for salinity tolerance. On the other hand, positively transformed T0 plants with the OsTPKa gene from Horkuch consistently showed growth advantage under both control and salt stress. DISCUSSION The poor performance of the transgenic plants with the down-regulated genes OsTPKa and OsHAK_like under salt stress supports the assumption that OsTPKa and OsHAK_like play important roles in defending the rice landrace Horkuch against salt stress, minimizing salt injury, and maintaining plant growth. Moreover, the growth advantage provided by overexpression of the vacuolar OsTPKa K+ transporter, particularly under salt stress reconfirms its important role in providing salt tolerance. The QTL locus from Horkuch containing these two transporters maybe bred into commercial rice to produce high-yielding salt tolerant rice.
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Affiliation(s)
- Umme Sabrina Haque
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Sabrina M. Elias
- Department of Life Sciences, Independent University Bangladesh, Dhaka, Bangladesh
| | - Israt Jahan
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Zeba I. Seraj
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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Nguyen TT, Dwiyanti MS, Sakaguchi S, Koide Y, Le DV, Watanabe T, Kishima Y. Identification of a Saltol-Independent Salinity Tolerance Polymorphism in Rice Mekong Delta Landraces and Characterization of a Promising Line, Doc Phung. RICE (NEW YORK, N.Y.) 2022; 15:65. [PMID: 36529786 PMCID: PMC9760585 DOI: 10.1186/s12284-022-00613-0] [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: 12/01/2021] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The Mekong Delta River in Vietnam is facing salinity intrusion caused by climate change and sea-level rise that is severely affecting rice cultivation. Here, we evaluated salinity responses of 97 rice accessions (79 landraces and 18 improved accessions) from the Mekong Delta population by adding 100 mM NaCl to the nutrient solution for up to 20 days. We observed a wide distribution in salinity tolerance/sensitivity, with two major peaks across the 97 accessions when using the standard evaluation system (SES) developed by the International Rice Research Institute. SES scores revealed strong negative correlations (ranging from - 0.68 to - 0.83) with other phenotypic indices, such as shoot elongation length, root elongation length, shoot dry weight, and root dry weight. Mineral concentrations of Na+ in roots, stems, and leaves and Ca2+ in roots and stems were positively correlated with SES scores, suggesting that tolerant accessions lower their cation exchange capacity in the root cell wall. The salinity tolerance of Mekong Delta accessions was independent from the previously described salinity tolerance-related locus Saltol, which encodes an HKT1-type transporter in the salinity-tolerant cultivars Nona Bokra and Pokkali. Indeed, genome-wide association studies using SES scores and shoot dry weight ratios of the 79 accessions as traits identified a single common peak located on chromosome 1. This SNP did not form a linkage group with other nearby SNPs and mapped to the 3' untranslated region of gene LOC_Os01g32830, over 6.5 Mb away from the Saltol locus. LOC_Os01g32830 encodes chloroplast glycolate/glycerate translocator 1 (OsPLGG1), which is responsible for photorespiration and growth. SES and shoot dry weight ratios differed significantly between the two possible haplotypes at the causal SNP. Through these analyses, we characterize Doc Phung, one of the most salinity-tolerant varieties in the Mekong Delta population and a promising new genetic resource.
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Affiliation(s)
- Tam Thanh Nguyen
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
- Mekong Delta Development Research Institute, Can Tho University, Campus 2 3-2 Street, Can Tho, Vietnam.
| | | | - Shuntaro Sakaguchi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Dung Viet Le
- College of Agriculture, Can Tho University, Campus 2 3-2 Street, Can Tho, Vietnam
| | - Toshihiro Watanabe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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Razi SMM, Shirzadian-Khorramabad R, Sabouri H, Rabiei B, Moghadam HH. Identification of Quantitative Trait Loci Related to Salt Tolerance of Indica Rice RIL Population in Different Growth Stages. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422090149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms. PLANTS 2022; 11:plants11111430. [PMID: 35684203 PMCID: PMC9182744 DOI: 10.3390/plants11111430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 01/04/2023]
Abstract
Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.
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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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12
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Debsharma SK, Rahman MA, Quddus MR, Khatun H, Disha RF, Roy PR, Ahmed S, El-Sharnouby M, Iftekharuddaula KM, Aloufi S, Alzuaibr FM, Alqurashi M, Sakran MI, Kabir MS. SNP Based Trait Characterization Detects Genetically Important and Stable Multiple Stress Tolerance Rice Genotypes in Salt-Stress Environments. PLANTS 2022; 11:plants11091150. [PMID: 35567151 PMCID: PMC9100962 DOI: 10.3390/plants11091150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/14/2022] [Accepted: 04/20/2022] [Indexed: 11/16/2022]
Abstract
Soil salinity is a major constraint to rice production in coastal areas around the globe, and modern high-yielding rice cultivars are more sensitive to high salt stress, which limits rice productivity. Traditional breeding programs find it challenging to develop stable salt-tolerant rice cultivars with other stress-tolerant for the saline environment in Bangladesh due to large yield variations caused by excessive salinity fluctuations during the dry (boro) season. We examined trait characterization of 18 advanced breeding lines using SNP genotyping and among them, we found line G6 (BR9621-B-1-2-11) (single breeding line with multiple-stress-tolerant QTL/genes) possessed 9 useful QTLs/genes, and two lines (G4:BR9620-2-7-1-1 and G14: IR 103854-8-3-AJY1) carried 7 QTLs/genes that control the desirable traits. To evaluate yield efficiency and stability of 18 rice breeding lines, two years of field experiment data were analyzed using AMMI (additive main effect and multiplicative interaction) and GGE (Genotype, Genotype Environment) biplot analysis. The AMMI analysis of variance demonstrated significant genotype, environment, and their interaction, accounting for 14.48%, 62.38%, and 19.70% of the total variation, respectively, and revealed that among the genotypes G1, G13, G14, G17, and G18 were shown to some extent promising. Genotype G13 (IR 104002-CMU 28-CMU 1-CMU 3) was the most stable yield based on the AMMI stability value. The GGE biplot analysis indicates 76% of the total variation (PC1 48.5% and PC2 27.5%) which is performed for revealing genotype × environment interactions. In the GGE biplot analysis, genotypes were checked thoroughly in two mega-environments (ME). Genotype G14 (IR103854-8-3-AJY1) was the winning genotype in ME I, whereas G1 (BR9627-1-3-1-10) in ME II. Because of the salinity and stability factors, as well as the highest averages of grain yield, the GGE and AMMI biplot model can explain that G1 and G13 are the best genotypes. These (G1, G6, G13, G14, G17, and G18) improved multiple-stress-tolerant breeding lines with stable grain yield could be included in the variety release system in Bangladesh and be used as elite donor parents for the future breeding program as well as for commercial purposes with sustainable production.
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Affiliation(s)
- Sanjoy K. Debsharma
- Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh; (S.K.D.); (M.R.Q.); (H.K.); (R.F.D.); (K.M.I.); (M.S.K.)
| | - Mohammad Akhlasur Rahman
- Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh; (S.K.D.); (M.R.Q.); (H.K.); (R.F.D.); (K.M.I.); (M.S.K.)
- Correspondence:
| | - Mohammad Ruhul Quddus
- Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh; (S.K.D.); (M.R.Q.); (H.K.); (R.F.D.); (K.M.I.); (M.S.K.)
| | - Hasina Khatun
- Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh; (S.K.D.); (M.R.Q.); (H.K.); (R.F.D.); (K.M.I.); (M.S.K.)
| | - Ribed F. Disha
- Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh; (S.K.D.); (M.R.Q.); (H.K.); (R.F.D.); (K.M.I.); (M.S.K.)
| | - Popy R. Roy
- Seed Certification Agency, Ministry of Agriculture, The Peoples Republic of Bangladesh Government, Gazipur 1701, Bangladesh;
| | - Sharif Ahmed
- International Rice Research Institute, Bangladesh Office, Dhaka 1213, Bangladesh;
| | - Mohamed El-Sharnouby
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Khandakar Md. Iftekharuddaula
- Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh; (S.K.D.); (M.R.Q.); (H.K.); (R.F.D.); (K.M.I.); (M.S.K.)
| | - Salman Aloufi
- Department of Biotechnology, Faculty of Science, Taif University, Taif 21974, Saudi Arabia; (S.A.); (M.A.)
| | - Fahad M. Alzuaibr
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Mohammed Alqurashi
- Department of Biotechnology, Faculty of Science, Taif University, Taif 21974, Saudi Arabia; (S.A.); (M.A.)
| | - Mohamed I. Sakran
- Biochemistry Section, Chemistry Department, Faculty of Science, Tanta University, Tanta 31527, Egypt;
- Biochemistry Department, Faculty of Science, University of Tabuk, Tabuk 47512, Saudi Arabia
| | - Mohammad Shahjahan Kabir
- Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh; (S.K.D.); (M.R.Q.); (H.K.); (R.F.D.); (K.M.I.); (M.S.K.)
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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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14
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Radha B, Sunitha NC, Sah RP, T P MA, Krishna GK, Umesh DK, Thomas S, Anilkumar C, Upadhyay S, Kumar A, Ch L N M, S B, Marndi BC, Siddique KHM. Physiological and molecular implications of multiple abiotic stresses on yield and quality of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:996514. [PMID: 36714754 PMCID: PMC9874338 DOI: 10.3389/fpls.2022.996514] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 12/05/2022] [Indexed: 05/12/2023]
Abstract
Abiotic stresses adversely affect rice yield and productivity, especially under the changing climatic scenario. Exposure to multiple abiotic stresses acting together aggravates these effects. The projected increase in global temperatures, rainfall variability, and salinity will increase the frequency and intensity of multiple abiotic stresses. These abiotic stresses affect paddy physiology and deteriorate grain quality, especially milling quality and cooking characteristics. Understanding the molecular and physiological mechanisms behind grain quality reduction under multiple abiotic stresses is needed to breed cultivars that can tolerate multiple abiotic stresses. This review summarizes the combined effect of various stresses on rice physiology, focusing on grain quality parameters and yield traits, and discusses strategies for improving grain quality parameters using high-throughput phenotyping with omics approaches.
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Affiliation(s)
- Beena Radha
- Department of Plant Physiology, Kerala Agricultural University-College of Agriculture, Vellayani, Thiruvananthapuram, Kerala, India
| | | | - Rameswar P Sah
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Md Azharudheen T P
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - G K Krishna
- Department of Plant Physiology, Kerala Agricultural University-College of Agriculture, Thrissur, Kerala, India
| | - Deepika Kumar Umesh
- Mulberry Breeding & Genetics Section, Central Sericultural Research and Training Institute-Berhampore, Central Silk Board, Murshidabad, West Bengal, India
| | - Sini Thomas
- Department of Plant Physiology, Kerala Agricultural University-Regional Agricultural Research Station, Kumarakom, Kerala, India
| | - Chandrappa Anilkumar
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Sameer Upadhyay
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Awadhesh Kumar
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Manikanta Ch L N
- Department of Plant Physiology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Behera S
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Bishnu Charan Marndi
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Kadambot H M Siddique
- The University of Western Australia Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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15
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Jahan N, Javed MA, Khan A, Manan FA, Tabassum B. Genetic architecture of Al 3+ toxicity tolerance in rice F 2:3 populations determined through QTL mapping. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:794-805. [PMID: 33871748 DOI: 10.1007/s10646-021-02413-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Aluminum (Al3+) toxicity is one of the factors limiting crop production in acidic soils. Identifying quantitative trait loci (QTLs)/genes for tolerance to Al3+ toxicity at seed germination can aid the development of new tolerant cultivars. The segregating population derived from Pak Basmati (Indica) × Pokkali (Indica) was used for mapping QTLs linked with tolerance to Al3+ toxicity ranging from 0 to 20 mM at pH 4 ± 0.2 at germination. The favorable alleles for all new QTLs were analyzed based on germination traits, i.e., final germination percentage (FG%), germination energy (GE), germination speed (GS), germination index (GI), mean germination time (MGT), germination value (GV), germination velocity (GVe), peak value of germination (GPV), and germination capacity (GC), and growth traits, such as root length (RL), shoot length (SL), total dry biomass (TDB) and germination vigor index (GVI). The phenotypic evolution showed transgressive variations. For genome-wide mapping, 90 polymorphic SSRs with 4 gene-specific markers and Win QTL Cart were used for QTL analysis. In all, 35 QTLs for germination and 11 QTLs for seedling growth were detected in distinct chromosomal regions by composite interval mapping (CIM), and multiple interval mapping (MIM) confirmed the pleiotropy at region RM128 on chromosome 1. Based on our genetic mapping studies, the genes/QTLs underlying tolerance to Al3+ toxicity could differ for both the germination and seedling stages in segregated populations. The QTLs identified in this study could be a source of new alleles for improving tolerance to Al3+ toxicity in rice.
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Affiliation(s)
- Nusrat Jahan
- Department of Biotechnology, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Pakistan.
- Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia (UTM), Skudai, 81310, Johor Bahru, Johor, Malaysia.
| | - Muhammad Arshad Javed
- Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia (UTM), Skudai, 81310, Johor Bahru, Johor, Malaysia
| | - Anwar Khan
- Department of Microbiology, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Pakistan
| | - Fazilah Abd Manan
- Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia (UTM), Skudai, 81310, Johor Bahru, Johor, Malaysia
| | - Bushra Tabassum
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
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16
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Nakhla WR, Sun W, Fan K, Yang K, Zhang C, Yu S. Identification of QTLs for Salt Tolerance at the Germination and Seedling Stages in Rice. PLANTS (BASEL, SWITZERLAND) 2021; 10:428. [PMID: 33668277 PMCID: PMC7996262 DOI: 10.3390/plants10030428] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/08/2021] [Accepted: 02/19/2021] [Indexed: 11/30/2022]
Abstract
Rice is highly sensitive to salinity stress during the seedling establishment phase. Salt stress is widely occurring in cultivated areas and severely affects seed germination ability and seedling establishment, which may result in a complete crop failure. The objective of the present study is to identify quantitative trait loci (QTLs) related to salt tolerance of the germination and seedling stages in a rice backcross inbred line (BIL) population that was derived from a backcross of an Africa rice ACC9 as donor and indica cultivar Zhenshan97 (ZS97) as the recurrent parent. Under salt stress, ACC9 exhibited a higher germination percentage, but more repressed seedling growth than ZS97. Using the BIL population, 23 loci for germination parameters were detected at the germination stage and 46 loci were identified for several morphological and physiological parameters at the seedling stage. Among them, nine and 33 loci with the ACC9 alleles increased salt tolerance at the germination and seedling stages, respectively. Moreover, several major QTLs were found to be co-localized in the same or overlapping regions of previously reported genes for salt stress. These major loci will facilitate improving salt-tolerance rice in genome-breeding programs.
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Affiliation(s)
- Walid Raafat Nakhla
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.R.N.); (W.S.); (K.F.); (K.Y.); (C.Z.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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17
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Advances and Challenges in the Breeding of Salt-Tolerant Rice. Int J Mol Sci 2020; 21:ijms21218385. [PMID: 33182265 PMCID: PMC7664944 DOI: 10.3390/ijms21218385] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/06/2020] [Accepted: 11/07/2020] [Indexed: 12/16/2022] Open
Abstract
Soil salinization and a degraded ecological environment are challenging agricultural productivity and food security. Rice (Oryza sativa), the staple food of much of the world’s population, is categorized as a salt-susceptible crop. Improving the salt tolerance of rice would increase the potential of saline-alkali land and ensure food security. Salt tolerance is a complex quantitative trait. Biotechnological efforts to improve the salt tolerance of rice hinge on a detailed understanding of the molecular mechanisms underlying salt stress tolerance. In this review, we summarize progress in the breeding of salt-tolerant rice and in the mapping and cloning of genes and quantitative trait loci (QTLs) associated with salt tolerance in rice. Furthermore, we describe biotechnological tools that can be used to cultivate salt-tolerant rice, providing a reference for efforts aimed at rapidly and precisely cultivating salt-tolerance rice varieties.
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