Gene Mapping, Cloning and Association Analysis for Salt Tolerance in Rice

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2021 Nov 13

PMID 34769104

Citations 20

Authors

Xiaoru Fan

Hongzhen Jiang

Lijun Meng

Jingguang Chen

Affiliations

Soon will be listed here.

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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References

Mohammadi R, Mendioro M, Diaz G, Gregorio G, Singh R . Mapping quantitative trait loci associated with yield and yield components under reproductive stage salinity stress in rice (Oryza sativa L.). J Genet. 2013; 92(3):433-43. DOI: 10.1007/s12041-013-0285-4. View

Lee S, Ahn J, Cha Y, Yun D, Lee M, Ko J . Mapping of quantitative trait loci for salt tolerance at the seedling stage in rice. Mol Cells. 2006; 21(2):192-6. View

Ponce K, Meng L, Guo L, Leng Y, Ye G . Advances in Sensing, Response and Regulation Mechanism of Salt Tolerance in Rice. Int J Mol Sci. 2021; 22(5). PMC: 7956267. DOI: 10.3390/ijms22052254. View

Li B . Identification of Genes Conferring Plant Salt Tolerance using GWAS: Current Success and Perspectives. Plant Cell Physiol. 2020; 61(8):1419-1426. DOI: 10.1093/pcp/pcaa073. View

Al-Tamimi N, Brien C, Oakey H, Berger B, Saade S, Ho Y . Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping. Nat Commun. 2016; 7:13342. PMC: 5118543. DOI: 10.1038/ncomms13342. View

Al-Tamimi N, Oakey H, Tester M, Negrao S . Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping. Methods Mol Biol. 2021; 2238:339-375. DOI: 10.1007/978-1-0716-1068-8_23. View

Cui Y, Zhang F, Zhou Y . The Application of Multi-Locus GWAS for the Detection of Salt-Tolerance Loci in Rice. Front Plant Sci. 2018; 9:1464. PMC: 6180169. DOI: 10.3389/fpls.2018.01464. View

Wang Z, Cheng J, Chen Z, Huang J, Bao Y, Wang J . Identification of QTLs with main, epistatic and QTL × environment interaction effects for salt tolerance in rice seedlings under different salinity conditions. Theor Appl Genet. 2012; 125(4):807-15. DOI: 10.1007/s00122-012-1873-z. View

Soda N, Kushwaha H, Soni P, Singla-Pareek S, Pareek A . A suite of new genes defining salinity stress tolerance in seedlings of contrasting rice genotypes. Funct Integr Genomics. 2013; 13(3):351-65. DOI: 10.1007/s10142-013-0328-1. View

10.

Kumari S, Sabharwal V, Kushwaha H, Sopory S, Singla-Pareek S, Pareek A . Transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in Oryza sativa L. Funct Integr Genomics. 2008; 9(1):109-23. DOI: 10.1007/s10142-008-0088-5. View

11.

Gong J, Zheng X, DU B, Qian Q, Chen S, Zhu L . Comparative study of QTLs for agronomic traits of riceOriza sativa L.) between salt stress and nonstress environment. Sci China C Life Sci. 2008; 44(1):73-82. DOI: 10.1007/BF02882075. View

12.

Naveed S, Zhang F, Zhang J, Zheng T, Meng L, Pang Y . Identification of QTN and candidate genes for Salinity Tolerance at the Germination and Seedling Stages in Rice by Genome-Wide Association Analyses. Sci Rep. 2018; 8(1):6505. PMC: 5916932. DOI: 10.1038/s41598-018-24946-3. View

13.

Yadav A, Kumar A, Grover N, Ellur R, Bollinedi H, Krishnan S . Genome-Wide Association Study Reveals Marker-Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice. Plants (Basel). 2021; 10(3). PMC: 8000697. DOI: 10.3390/plants10030559. View

14.

Ismail A, Horie T . Genomics, Physiology, and Molecular Breeding Approaches for Improving Salt Tolerance. Annu Rev Plant Biol. 2017; 68:405-434. DOI: 10.1146/annurev-arplant-042916-040936. View

15.

Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A . High-throughput genotyping by whole-genome resequencing. Genome Res. 2009; 19(6):1068-76. PMC: 2694477. DOI: 10.1101/gr.089516.108. View

16.

Zhang M, Liang X, Wang L, Cao Y, Song W, Shi J . A HAK family Na transporter confers natural variation of salt tolerance in maize. Nat Plants. 2019; 5(12):1297-1308. DOI: 10.1038/s41477-019-0565-y. View

17.

Lin H, Zhu M, Yano M, Gao J, Liang Z, Su W . QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet. 2003; 108(2):253-60. DOI: 10.1007/s00122-003-1421-y. View

18.

van Zelm E, Zhang Y, Testerink C . Salt Tolerance Mechanisms of Plants. Annu Rev Plant Biol. 2020; 71:403-433. DOI: 10.1146/annurev-arplant-050718-100005. View

19.

Liu C, Chen K, Zhao X, Wang X, Shen C, Zhu Y . Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study. Rice (N Y). 2019; 12(1):88. PMC: 6889114. DOI: 10.1186/s12284-019-0349-z. View

20.

Toda Y, Tanaka M, Ogawa D, Kurata K, Kurotani K, Habu Y . RICE SALT SENSITIVE3 forms a ternary complex with JAZ and class-C bHLH factors and regulates jasmonate-induced gene expression and root cell elongation. Plant Cell. 2013; 25(5):1709-25. PMC: 3694701. DOI: 10.1105/tpc.113.112052. View