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
Abstract
:1. Introduction
2. Results
2.1. Investigating the Salt Stress Responses
2.1.1. Characterizing Agronomic Traits under Salt Stress
2.1.2. Physiological Traits under Salt Stress
2.2. Correlation Analysis between Traits
2.3. Path Analysis to Assess the Contribution of Traits (Independent Variables) to Salt Tolerance (Dependent Variable) through Partitioning
2.4. Marker Segregation and Genetic Linkage Mapping
2.5. Salinity Tolerance QTL for Component Agronomic Traits
2.6. QTL for Physiological Traits
2.7. Identification of Functional Genes in the QTL Region
2.8. Epistasis Interaction
3. Discussion
3.1. Salt Stress Responses of the Parental Lines and Selected F2:3 Progenies and Path Coefficient Analysis
3.2. Genetic Map Construction and QTL Detection
3.3. Genomic Regions for Salinity Tolerance
3.4. Comparison between New QTL from the Current and Previously Mapped QTLs
4. Materials and Methods
4.1. Parent Selection
4.2. Details of the Cross, Confirmation and Management of the F1s and the Segregating Population
4.3. Growing Conditions
4.4. Characterization of Agronomic Traits
4.5. Physiological Characterization
4.6. SPAD Reading
4.7. Correlation Analysis for Trait Associations
4.8. Path Coefficient Analysis
4.9. Residual Effect
4.10. Genotyping and Construction of a Genetic Linkage Map
4.11. QTL Analysis
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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Variable | Correlation | Survival Rate | Shoot Length | Shoot Dry Weight | Root Length | SPAD Value | Na+ Conc. | K+ Conc. | Na+/K+ Ratio | Total Effect |
---|---|---|---|---|---|---|---|---|---|---|
Survival rate | −0.257 | −0.301 | 0.148 | 0.009 | −0.014 | −0.011 | −0.003 | −0.088 | 0.002 | −0.257 |
Shoot length | 0.226 | −0.074 | 0.605 | 0.024 | −0.134 | 0.010 | −0.004 | −0.190 | −0.011 | 0.226 |
Shoot dry weight | 0.141 | −0.059 | 0.304 | 0.047 | −0.096 | −0.008 | −0.010 | −0.083 | 0.046 | 0.141 |
Root length | −0.306 | −0.011 | 0.208 | 0.012 | −0.390 | −0.008 | −0.001 | −0.103 | −0.012 | −0.306 |
SPAD value | −0.310 | −0.046 | −0.089 | 0.006 | −0.046 | −0.068 | −0.002 | −0.058 | −0.005 | −0.310 |
Na+ conc. | 0.114 | −0.060 | 0.151 | 0.028 | −0.026 | −0.007 | −0.016 | −0.044 | 0.088 | 0.114 |
K+ conc. | −0.183 | −0.090 | 0.388 | 0.013 | −0.136 | −0.013 | −0.002 | −0.296 | −0.045 | −0.183 |
Na+/K+ ratio | 0.218 | −0.007 | −0.060 | 0.019 | 0.042 | 0.003 | −0.013 | 0.120 | 0.112 | 0.218 |
Trait | QTL | Chr. | Peak Marker | QTL Position (cM) | Add Effect | LOD | PVE (%) | Method of QTL Detection | Contributor of Favorable Allele | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|
QGene | ICIM | QGene | ICIM | QGene | ICIM | |||||||
SES | qSES1 | 1 | Chr01_38632196 | 151.8 | - | −0.61 | 3.4 | - | 15.6 | 3.80 | SMR | Akundi |
qSES3 | 3 | Chr03_2885423 | 11.3 | - | −0.70 | 4.8 | - | 21.6 | 4.50 | SMR, CIM | Akundi | |
Survival rate (%) | qSUR1 | 1 | chr01_12941687 | 50 | 54.8 | 31.91 | 4.3 | 5.0 | 19.9 | 0.98 | IM, CIM | BR49 |
qSUR5.1 | 5 | chr05_14412355 | 56 | - | 20.25 | 7.5 | - | 31.6 | - | IM, CIM | BR49 | |
qSUR5.2 | 5 | chr05_2291156 | 10 | 11.2 | −10.36 | 3.1 | 5.0 | 14.9 | 0.94 | IM, CIM | Akundi | |
Shoot length | qSL1 | 1 | QSES1-2_2 | 156 | 151.8 | 4.86 | 7.2 | 4.0 | 30.7 | 16.28 | IM, CIM | BR49 |
Shoot dry weight | qSDW 5 | 5 | chr05_20551103 | 82.2 | - | 0.35 | 3.5 | - | 16.3 | - | IM, CIM | BR49 |
qSDW11 | 11 | Chr11_10741559 | 41.0 | - | 0.27 | 3.0 | - | 14 | - | IM, CIM | BR49 | |
Root length | qRL1 | 1 | Chr01_12335190 | 48.8 | - | −1.59 | 3.3 | - | 15.8 | - | IM | Akundi |
SPAD | qSPAD12 | 12 | Chr12_26259494 | 103.4 | - | 3.05 | 3.5 | - | 16.3 | - | IM, CIM | BR49 |
Na+ conc. | qNa6 | 6 | SSIIA-3B | 26 | 27 | −1.98 | 3.6 | 4.0 | 16.8 | 8.18 | CIM, IM | Akundi |
K+ conc. | qK8 | 8 | chr08_4853081 | 18.8 | - | −0.34 | 4.7 | - | 21.2 | - | IM, CIM | Akundi |
qK12 | 12 | Chr12_18881059 | 73.4 | - | 11.4 | 3.5 | - | 16.3 | - | IM, CIM, | BR49 | |
Na+/K+ ratio | qNaKR8 | 8 | DTH8-IR24 | 17 | - | 0.08 | 3.0 | - | 0.1 | - | SMR | BR49 |
qNaKR11 | 11 | IRGSP1_C11_27391141 | 107.6 | 108 | −0.04 | 3.0 | 3.0 | 12.9 | 16.80 | SMR` | Akundi |
Traits | QTL | Chr. | Position (bp) | Total no. of Locus | Candidate Genes | Putative Function | References |
---|---|---|---|---|---|---|---|
SES | qSES1 | 1 | 38,723,347–38,724,165 | 16 | LOC_Os01g66670 | Expressed protein (drought-induced proteins, anther and pollen wall remodeling/metabolism proteins contribute to the tolerance of rice to salt stress). | [25,26] |
qSES3 | 3 | 2,878,828–2,880,890 | 20 | LOC_Os03g05770 | Peroxidase precursor, putative, expressed (increases protection against oxidative stress and is highly tolerant to different stresses, allowing survival when water supply is a limiting factor). | [27,28] | |
Survival rate (%) | qSUR1 | 1 | 12,756,935–12,757,588 | 17 | LOC_Os01g22700 | Organic cation transporter-related, putative, expressed (affects root development, carnitine-related responses under stress, and numerous biological processes, including transcription, translation, cell signaling, and ion channel activity). | [29,30] |
qSUR5.1 | 5 | 14,280,156–14,292,389 | 10 | LOC_Os05g24680 | Retrotransposon protein, putative, Ty3-gypsy subclass, expressed (enable plants to cope with drought stress conditions; impact on biological process under stress response). | [31,32] | |
qSUR5.2 | 5 | 2,548,592–2,559,171 | 17 | LOC_Os05g05230 | Expressed protein (drought-induced proteins, anther and pollen wall remodeling/metabolism proteins contribute to the tolerance of rice to salt stress). | [25,26] | |
Shoot length | qSL1 | 1 | 39,794,226–39,799,341 | 18 | LOC_Os01g68490 | Tetratricopeptide-like helical, putative, expressed (abscisic acid responses and osmotic stress tolerance enable plants to cope with adverse environmental conditions). | [33,34] |
Shoot dry weight | qSDW 5 | 5 | 20,966,622–20,969,373 | 17 | LOC_Os05g35310 | Ankyrin repeat family protein, putative, expressed (implicated in plant growth, development and signal transduction; response to biotic and abiotic stresses). | [35,36] |
qSDW11 | 11 | 10,456,526–10,459,838 | 18 | LOC_Os11g18550 | Transposon protein, putative, CACTA, En/Spm sub-class, expressed (contributes significantly to genome size, produces a large number of cDNA sequences in plant tissues different conditions of stress). | [37,38] | |
Root length | qRL1 | 1 | 12,444,630–12,446,150 | 12 | LOC_Os01g22150 | Transposon protein, putative, CACTA, En/Spm sub-class (contributes significantly to genome size, produces a large number of cDNA sequences in plant tissues under different conditions of stress). | [37,38] |
SPAD | qSPAD12 | 12 | 26,377,868–26,379,849 | 17 | LOC_Os12g42440 | Chaperone protein dnaJ, putative, expressed (response to NaCl stress, involved in basal resistance to M. oryzae in rice). | [39,40] |
Na+ Conc. | qNa6 | 6 | 6,643,235–6,643,552 | 11 | LOC_Os06g12300 | Expressed protein (drought-induced proteins, anther and pollen wall remodeling/metabolism proteins contribute to the tolerance of rice to salt stress). | [25,26] |
K+ Conc. | qK8 | 8 | 4,794,164–4,799,199 | 12 | LOC_Os08g08350 | Retrotransposon protein, putative, Ty1-copia subclass, expressed (tuning gene expression during plant development salinity; plays a major role in shaping genome structure and size during salinity). | [41,42] |
qK12 | 12 | 18,717,286–18,718,979 | 10 | LOC_Os12g31120 | Transposon protein, putative, CACTA, En/Spm sub-class, expressed (contributes significantly to genome size, produces a large number of cDNA sequences in plant tissues different conditions of stress). | [37,38] | |
NaK ratio | qNaK-R8 | 8 | 4,333,717–4,335,434 | 13 | LOC_Os08g07740 | Histone-like transcription factor and archaeal histone, putative, expressed (regulating vegetative growth, sexual reproduction, virulence and hyperosmotic stresses, response to salt stress). | [43,44] |
qNaK-R11 | 11 | 27,449,823–27,452,792 | 12 | LOC_Os11g45380 | Zinc finger family protein, putative, expressed (plant growth, development, and stress signal transduction, effective role in stress tolerance). | [45,46] |
Traits | Chr1 | Position1 (cM) | FM1 | Chr2 | Position2 (cM) | FM2 | LOD | PVE (%) | Add1 | Add2 | Add by Add | Type of interaction |
---|---|---|---|---|---|---|---|---|---|---|---|---|
SES | 4 | 10.7 | C308–C309 | 7 | 27 | C548–C549 | 42 | 2.628 | −0.003 | −0.953 | −0.951 | Between complementary loci |
2 | 120.4 | C190–C191 | 12 | 26.4 | C865–C866 | 48 | 2.637 | −0.706 | 1.198 | −0.206 | Between complementary loci | |
7 | 67 | C557–C558 | 12 | 26.4 | C865–C866 | 45 | 2.638 | −0.322 | 0.322 | −0.674 | Between complementary loci | |
Survival | 3 | 111.9 | C276–C277 | 8 | 30.8 | C608–C609 | 21 | 0.056 | 3.260 | −0.444 | −2.893 | Between complementary loci |
4 | 130.7 | C380–C381 | 10 | 70.6 | C763–C764 | 10 | 1.826 | 12.950 | 4.923 | −10.412 | Between complementary loci | |
5 | 10.2 | C394–C395 | 10 | 70.6 | C763–C764 | 10 | 1.947 | 4.950 | −6.390 | 1.673 | Between complementary loci | |
6 | 101 | C516–C517 | 10 | 70.6 | C763–C764 | 10 | 1.584 | 3.374 | 2.100 | −14.695 | Between complementary loci | |
1 | 65.8 | C47–C48 | 10 | 75.6 | C770–C771 | 10 | 2.222 | 1.557 | 7.981 | 6.373 | Between QTLs and background | |
Shoot Length | 2 | 15.4 | C132–C134 | 2 | 75.4 | C160–C161 | 6 | 9.206 | 4.177 | 0.113 | −4.192 | Between complementary loci |
2 | 75.4 | C160–C161 | 8 | 70.8 | C640–C641 | 6 | 6.744 | 1.225 | −5.466 | 3.291 | Between complementary loci | |
8 | 15.8 | C595–C596 | 8 | 70.8 | C640–C641 | 5 | 9.325 | −1.393 | −1.560 | 6.540 | Between complementary loci | |
6 | 71 | C507–C508 | 11 | 56 | C799–C800 | 5 | 7.587 | −2.065 | −1.355 | 5.903 | Between complementary loci | |
7 | 7 | C542–C543 | 11 | 96 | C836–C839 | 5 | 7.724 | 0.024 | 0.512 | 3.333 | Between complementary loci | |
Shoot dry weight | 9 | 30.6 | C694–C695 | 10 | 75.6 | C770–C771 | 6 | 9.656 | −0.001 | 0.000 | −0.017 | Between complementary loci |
2 | 75.4 | C160–C161 | 11 | 21 | C782–C783 | 6 | 9.723 | −0.004 | 0.000 | 0.003 | Between complementary loci | |
12 | 11.4 | C857–C858 | 12 | 56.4 | C884–C885 | 8 | 8.903 | −0.013 | 0.017 | 0.012 | Between complementary loci | |
6 | 86 | C512–C513 | 12 | 76.4 | C901–C902 | 19 | 1.480 | 0.003 | 0.004 | 0.007 | Between complementary loci | |
1 | 155.8 | C104–C105 | 12 | 86.4 | C906–C907 | 6 | 9.417 | −0.003 | 0.011 | −0.011 | Between complementary loci | |
Root length | 4 | 135.7 | C381–C382 | 9 | 0.6 | C671–C672 | 10 | 1.423 | 0.074 | 0.209 | 0.074 | Between complementary loci |
8 | 75.8 | C644–C645 | 12 | 76.4 | C901–C902 | 89 | 7.637 | −0.409 | −0.427 | −0.427 | Between complementary loci | |
SPAD | 1 | 115.8 | C73–C74 | 3 | 136.9 | C296–C297 | 6 | 8.485 | −0.478 | 2.305 | 3.562 | Between complementary loci |
1 | 115.8 | C73–C74 | 4 | 55.7 | C335–C336 | 5 | 5.614 | 2.343 | 4.534 | 1.190 | Between complementary loci | |
3 | 56.9 | C246–C247 | 4 | 55.7 | C335–C336 | 6 | 3.118 | −2.093 | 0.707 | 4.291 | Between complementary loci | |
3 | 11.9 | C217–C218 | 5 | 50.2 | C417–C418 | 5 | 7.909 | 2.494 | 0.180 | −1.053 | Between complementary loci | |
1 | 115.8 | C73–C74 | 6 | 101 | C516–C517 | 5 | 8.103 | 1.306 | 2.094 | 3.784 | Between complementary loci | |
4 | 25.7 | C314–C315 | 7 | 27 | C548–C549 | 6 | 6.784 | −2.153 | −0.795 | 1.959 | Between complementary loci | |
11 | 21 | C782–C783 | 11 | 96 | C836–C839 | 6 | 6.641 | 2.780 | 1.330 | 0.550 | Between complementary loci | |
9 | 45.6 | C702–C703 | 12 | 81.4 | C904–C905 | 6 | 1.772 | −0.103 | −0.503 | 0.583 | Between complementary loci | |
Na+ Conc. | 2 | 135.4 | C199–C200 | 4 | 55.7 | C335–C336 | 6 | 4.625 | 0.012 | −0.028 | −0.013 | Between complementary loci |
3 | 116.9 | C279–C280 | 5 | 45.2 | C416–C417 | 5 | 0.533 | 0.006 | 0.006 | −0.016 | Between complementary loci | |
1 | 55.8 | C38–C39 | 5 | 50.2 | C417–C418 | 6 | 10.06 | −0.020 | −0.022 | 0.019 | Between complementary loci | |
1 | 0.8 | C1–C2 | 6 | 101 | C516–C517 | 6 | 5.709 | −0.015 | 0.012 | −0.018 | Between complementary loci | |
1 | 65.8 | C47–C48 | 7 | 97 | C577–C578 | 6 | 8.641 | −0.013 | −0.046 | 0.037 | Between complementary loci | |
3 | 1.9 | C208–C209 | 10 | 5.6 | C728–C729 | 6 | 6.317 | 0.015 | 0.024 | 0.012 | Between complementary loci | |
1 | 65.8 | C47–C48 | 11 | 106 | C842–C843 | 5 | 9.005 | 0.019 | −0.018 | −0.049 | Between complementary loci | |
9 | 50.6 | C706–C707 | 12 | 21.4 | C865–C866 | 5 | 8.375 | 0.010 | −0.011 | −0.002 | Between complementary loci | |
K+ conc. | 1 | 90.8 | C62–C63 | 3 | 66.9 | C251–C252 | 9 | 12.65 | −0.025 | −0.014 | 0.014 | Between complementary loci |
3 | 66.9 | C251–C252 | 5 | 15.2 | C397–C398 | 9 | 12.69 | −0.014 | −0.025 | 0.014 | Between complementary loci | |
3 | 71.9 | C254–C255 | 8 | 75.8 | C644–C645 | 9 | 1.718 | 0.002 | −0.011 | 0.002 | Between complementary loci | |
4 | 90.7 | C354–C355 | 9 | 75.6 | C715–C716 | 6 | 8.798 | 0.026 | 0.000 | 0.000 | Between complementary loci | |
Na+/K+ ratio | 8 | 20.8 | C599–C600 | 8 | 60.8 | C637–C638 | 7 | 1.569 | −0.016 | −0.002 | 0.002 | Between QTLs and background |
3 | 71.9 | C254–C255 | 8 | 75.8 | C644–C645 | 9 | 5.615 | 0.004 | −0.017 | 0.004 | Between complementary loci | |
4 | 90.7 | C354–C355 | 9 | 75.6 | C715–C716 | 6 | 27.54 | 0.041 | 0.002 | 0.002 | Between complementary loci |
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Maniruzzaman, S.; Rahman, M.A.; Hasan, M.; Rasul, M.G.; Molla, A.H.; Khatun, H.; Akter, S. 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, 1409. https://doi.org/10.3390/plants11111409
Maniruzzaman S, Rahman MA, Hasan M, Rasul MG, Molla AH, Khatun H, Akter S. 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(11):1409. https://doi.org/10.3390/plants11111409
Chicago/Turabian StyleManiruzzaman, Sheikh, Mohammad Akhlasur Rahman, Mehfuz Hasan, Mohammad Golam Rasul, Abul Hossain Molla, Hasina Khatun, and Salma Akter. 2022. "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 11, no. 11: 1409. https://doi.org/10.3390/plants11111409