Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Evaluation
2.2. Correlation among Traits Related to Salt Stress
2.3. Population Structure
2.4. Genome-Wide Association Study for Traits Associated with Salinity Tolerance
3. Discussion
4. Material and Methods
4.1. Plant Materials
4.2. Evaluation for Seedling Stage Salinity Tolerance
4.3. Measurement of Morpho-Physiological Characters
4.4. Estimation of Na+ and K+ Ion Concentration
4.5. Data Analysis
4.6. DNA Isolation and SNP Genotyping
4.7. Population Structure Analysis
4.8. Genome-Wide Association Study
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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S.No | Traits | MTAs | SNP | Chr. | Position | p Value | R2 | Previous Report |
---|---|---|---|---|---|---|---|---|
1 | SL | qSL2 | AX-95920196 | 2 | 23947447 | 6.74 × 10−5 | 15.11 | qPH2 [24]; qGP-2 [41] |
2 | RL | qRL2 | AX-95920196 | 2 | 23947447 | 7.54 × 10−5 | 19.26 | qPH2 [24]; qGP-2 [41] |
3 | SFW | qSFW2 | AX-95921620 | 2 | 23533590 | 5.18 × 10−4 | 14.64 | qPH2, qRKC2, qCHL2 [24]; qGP-2 [41] |
qSFW7 | AX-95937657 | 7 | 20788892 | 6.79 × 10−4 | 13.98 | qRSW7 [42] | ||
qSFW9 | AX-95931839 | 9 | 16483542 | 4.61 × 10−4 | 14.92 | qSNK9, qRNK9, qSES9 [24]; qGP-9 [41] | ||
4 | RFW | qRFW2 | AX-95921620 | 2 | 23533590 | 5.18 × 10−4 | 14.64 | qPH2, qRKC2, qCHL2 [24]; qGP-2 [41] |
5 | SEW | qSEW2 | AX-95921620 | 2 | 23533590 | 3.87 × 10−4 | 15.43 | qPH2, qRKC2, qCHL2 [24]; qGP-2 [41] |
qSEW7 | AX-95937657 | 7 | 20788892 | 4.07 × 10−4 | 15.31 | qRSW7 [42] | ||
qSEW9 | AX-95931839 | 9 | 16483542 | 5.06 × 10−4 | 14.77 | qSNK9, qRNK9 [24]; qGP-9 [41] | ||
6 | SDW | qSDW2.1 | AX-95920663 | 2 | 5664763 | 1.42 × 10−5 | 25.51 | - |
qSDW2.2 | AX-95934798 | 2 | 10213902 | 4.05 × 10−5 | 22.52 | OsVTE1 [43]; OsGMST1 [44] | ||
qSDW12.1 | AX-95939149 | 12 | 17404747 | 9.22 × 10−5 | 20.24 | qSES12, qSUR12, qCHL12 [24] | ||
7 | RDW | qRDW6 | AX-95956901 | 6 | 29729562 | 5.79 × 10−5 | 22.05 | OsCMO [45] |
qRDW7 | AX-95929366 | 7 | 20782724 | 4.74 × 10−5 | 22.62 | qSES7.1, KR7.1 [46] | ||
8 | RNC | qRNC2.1 | AX-95921298 | 2 | 23260124 | 6.30 × 10−5 | 18.17 | qRKC2 [24]; qGP-2 [41] |
qRNC2.2 | AX-95920628 | 2 | 22172032 | 9.45 × 10−5 | 15.15 | qRKC2 [24]; qGP-2 [41] | ||
9 | SNC | qSNC1 | AX-95940587 | 1 | 13758487 | 8.16 × 10−5 | 16.26 | qSKC, qSNK, qRNK [24] |
qSNC2 | AX-95920537 | 2 | 22171212 | 8.35 × 10−5 | 16.64 | qRKC2 [24]; qGP-2 [41] | ||
qSNC5 | AX-95927105 | 5 | 19697164 | 9.39 × 10−5 | 18.08 | - | ||
10 | SKC | qSKC1 | AX-95940587 | 1 | 13758487 | 7.86 × 10−5 | 16.26 | qSKC, qSNK, qRNK [24] |
qSKC6 | AX-95937335 | 6 | 3429601 | 8.21 × 10−5 | 14.33 | qRFWn6.1, qRDWn6.1 [47] | ||
11 | RNK | qRNK1 | AX-95918556 | 1 | 11022718 | 6.26 × 10−6 | 25.11 | qRNK1, qSNC, qSKC, qRKC [24] |
12 | SNK | qSNK1 | AX-95940642 | 1 | 13322813 | 2.93 × 10−6 | 29.88 | qSKC, qSNK, qRNK [24] |
Chr. | MSU-RAP ID | Position (bp) | Description or Putative Function |
---|---|---|---|
2 | LOC_Os02g10580 | 5,565,956 | NB-ARC domain containing disease resistance protein |
LOC_Os02g10590 | 5,569,801 | Peptidyl-prolyl cis-trans isomerase, FKBP-type | |
LOC_Os02g10600 | 5,573,182 | OsFBA1—F-box and FBA domain containing protein | |
LOC_Os02g10630 | 5,593,645 | GRAM and C2 domains containing protein | |
LOC_Os02g10640 | 5,600,889 | 26S protease regulatory subunit, | |
LOC_Os02g10650 | 5,604,236 | CRAL/TRIO domain containing protein | |
LOC_Os02g10660 | 5,614,461 | Gycosyl hydrolases family 17 | |
LOC_Os02g10690 | 5,623,352 | Targeting protein for Xklp2 | |
LOC_Os02g10700 | 5,631,315 | OsFBL7—F-box domain and LRR containing protein | |
LOC_Os02g10710 | 5,640,360 | hsp20/alpha crystallin family protein | |
LOC_Os02g10750 | 5,672,334 | CBL-interacting protein kinase | |
LOC_Os02g10760 | 5,688,698 | AP2 domain containing protein | |
LOC_Os02g10770 | 5,697,834 | DEAD-box ATP-dependent RNA helicase 41 | |
LOC_Os02g10780 | 5,706,636 | SPX domain containing protein | |
LOC_Os02g10800 | 5,736,606 | Mitochondrial carrier protein | |
LOC_Os02g10810 | 5,742,520 | Protein of unknown function domain containing protein | |
LOC_Os02g10820 | 5,748,141 | Sel1 repeat domain containing protein | |
LOC_Os02g10830 | 5,749,500 | Serine acetyltransferase protein | |
5 | LOC_Os05g33500 | 19,678,142 | mTERF domain containing protein |
LOC_Os05g33510 | 19,681,732 | Peptide methionine sulfoxide reductase msrB | |
LOC_Os05g33550 | 19,704,966 | Methyl-binding domain protein MBD | |
LOC_Os05g33554 | 19,707,432 | Methyl-binding domain protein MBD | |
LOC_Os05g33570 | 19,737,857 | Pyruvate, phosphate dikinase, chloroplast precursor | |
LOC_Os05g33590 | 19,744,851 | Cytochrome P450, putative, expressed | |
LOC_Os05g33600 | 19,758,913 | Cytochrome P450 72A1, putative, expressed | |
LOC_Os05g33630 | 19,785,962 | Inosine-uridine preferring nucleoside hydrolase family protein | |
LOC_Os05g33644 | 19,805,637 | Inosine-uridine preferring nucleoside hydrolase family protein | |
LOC_Os05g33690 | 19,828,422 | Receptor-like protein kinase precursor | |
LOC_Os05g33700 | 19,834,008 | 4F5 protein family protein | |
LOC_Os05g33710 | 19,846,592 | WD domain, G-beta repeat domain containing protein | |
LOC_Os05g33730 | 19,868,419 | Gibberellin receptor GID1L2 |
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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
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 StyleYadav, 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