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Article

Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

by
Ashutosh Kumar Yadav
1,2,
Aruna Kumar
2,
Nitasha Grover
1,
Ranjith Kumar Ellur
1,
Haritha Bollinedi
1,
Subbaiyan Gopala Krishnan
1,
Prolay Kumar Bhowmick
1,
Kunnummal Kurungara Vinod
1,
Mariappan Nagarajan
3 and
Ashok Kumar Singh
1,*
1
Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India
2
Amity Institute of Biotechnology, Amity University, Noida 201303, India
3
Rice Breeding and Genetics Research Centre, ICAR—Indian Agricultural Research Institute, Aduthurai 612101, Tamil Nadu, India
*
Author to whom correspondence should be addressed.
Plants 2021, 10(3), 559; https://doi.org/10.3390/plants10030559
Submission received: 12 February 2021 / Revised: 4 March 2021 / Accepted: 10 March 2021 / Published: 16 March 2021
(This article belongs to the Special Issue Plants Subjected to Salinity Stress)
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Abstract

Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker–trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.
Keywords: rice; salt stress; salinity tolerance; SNP; GWAS; MTAs rice; salt stress; salinity tolerance; SNP; GWAS; MTAs

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MDPI and ACS Style

Yadav, A.K.; Kumar, A.; Grover, N.; Ellur, R.K.; Bollinedi, H.; Krishnan, S.G.; Bhowmick, P.K.; Vinod, K.K.; Nagarajan, M.; Singh, A.K. Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice. Plants 2021, 10, 559. https://doi.org/10.3390/plants10030559

AMA Style

Yadav AK, Kumar A, Grover N, Ellur RK, Bollinedi H, Krishnan SG, Bhowmick PK, Vinod KK, Nagarajan M, Singh AK. Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice. Plants. 2021; 10(3):559. https://doi.org/10.3390/plants10030559

Chicago/Turabian Style

Yadav, Ashutosh Kumar, Aruna Kumar, Nitasha Grover, Ranjith Kumar Ellur, Haritha Bollinedi, Subbaiyan Gopala Krishnan, Prolay Kumar Bhowmick, Kunnummal Kurungara Vinod, Mariappan Nagarajan, and Ashok Kumar Singh. 2021. "Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice" Plants 10, no. 3: 559. https://doi.org/10.3390/plants10030559

APA Style

Yadav, A. K., Kumar, A., Grover, N., Ellur, R. K., Bollinedi, H., Krishnan, S. G., Bhowmick, P. K., Vinod, K. K., Nagarajan, M., & Singh, A. K. (2021). Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice. Plants, 10(3), 559. https://doi.org/10.3390/plants10030559

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