Identification of QTLs for Morpho-Physiological Traits under Saline Stress in Indica MAGIC Rice Population †
Abstract
:1. Introduction
2. Material and Methods
3. Results and Discussion
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- FAO Director-General. Global map of salt-affected soils. In Proceedings of the World Map of Salt-Affected Soils, Rome, Italy, 20–22 October 2021. [Google Scholar]
- Singh, R.K.; Kota, S.; Flowers, T.J. Salt tolerance in rice: Seedling and reproductive stage QTL mapping come of age. Theor. Appl. Genet. 2021, 134, 3495–3533. [Google Scholar] [CrossRef] [PubMed]
- Warraich, A.S.; Krishnamurthy, S.L.; Sooch, B.S.; Vinaykumar, N.M.; Dushyanthkumar, B.M.; Bose, J.; Sharma, P.C. Rice GWAS reveals key genomic regions essential for salinity tolerance at reproductive stage. Acta Physiol. Plant. 2020, 42, 134. [Google Scholar] [CrossRef]
- Reddy, N.B.L.; Kim, B.K.; Yoon, I.S.; Kim, K.H.; Kwon, T.R. Salt Tolerance in Rice: Focus on Mechanisms and Approaches. Rice Sci. 2017, 24, 123–144. [Google Scholar] [CrossRef]
- Babu, N.N.; Krishnan, S.G.; Vinod, K.K.; Krishnamurthy, S.L.; Singh, V.K.; Singh, M.P.; Singh, R.; Ellur, R.K.; Rai, V.; Bollinedi, H.; et al. Marker Aided Incorporation of Saltol, a Major QTL Associated with Seedling Stage Salt Tolerance, into Oryza sativa ‘Pusa Basmati 1121’. Front. Plant Sci. 2017, 8, 41. [Google Scholar] [CrossRef] [PubMed]
- Prakash, N.R.; Lokeshkumar, B.M.; Rathore, S.; Warraich, A.S.; Yadav, S.; Vinaykumar, N.M.; Dushyanthkumar, B.M.; Krishnamurthy, S.L.; Sharma, P.C. Meta-analysis and validation of genomic loci governing seedling and reproductive stage salinity tolerance in rice. Physiol. Plant. 2022, 174, e13629. [Google Scholar] [CrossRef] [PubMed]
- Mazumder, A.; Rohilla, M.; Bisht, D.; Krishnamurthy, S.L.; Barman, M.; Sarma, R.; Sharma, T.; Mondal, T. Identification and mapping of quantitative trait loci (QTL) and epistatic QTL for salinity tolerance at seedling stage in traditional aromatic short grain rice landrace Kolajoha (Oryza sativa L.) of Assam. India. Euphytica 2020, 216, 75. [Google Scholar] [CrossRef]
- Gregorio, G.B. Tagging Salinity Tolerance Genes in Rice Using Amplified Fragment Length Polymorphism (AFLP). Ph.D. Thesis, University of the Philippines Los Banõs, Laguna, Philippines, 1997. [Google Scholar]
- Krishnamurthy, S.L.; Pundir, P.; Warraich, A.S.; Rathor, S.; Lokeshkumar, B.M.; Singh, N.K.; Sharma, P.C. Introgressed Saltol QTL Lines Improves the Salinity Tolerance in Rice at Seedling Stage. Front. Plant Sci. 2020, 11, 833. [Google Scholar] [CrossRef] [PubMed]
- Yadav, A.K.; Kumar, A.; Grover, N.; Ellur, R.K.; Krishnan, S.G.; Bollinedi, H.; Bhowmick, P.K.; Vinod, K.K.; Nagarajan, M.; Krishnamurthy, S.L.; et al. Marker aided introgression of ‘Saltol’, a major QTL for seedling stage salinity tolerance into an elite Basmati rice variety ‘Pusa Basmati 1509’. Sci. Rep. 2020, 10, 13877. [Google Scholar] [CrossRef] [PubMed]
- Bandillo, N.; Raghavan, C.; Muyco, P.A.; Sevilla, M.A.; Lobina, I.T.; Dilla-Ermita, C.J.; Tung, C.W.; McCouch, S.; Thomson, M.; Mauleon, R.; et al. Multi-parent advanced generation inter-cross (MAGIC) populations in rice: Progress and potential for genetics research and breeding. Rice 2013, 6, 11. [Google Scholar] [CrossRef] [PubMed]
- Chai, C.; Shankar, R.; Jain, M. Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice. Sci. Rep. 2018, 8, 14218. [Google Scholar] [CrossRef] [PubMed]
- Kumar, R.; Subba, A.; Kaur, C.; Ariyadasa, T.U.; Sharan, A.; Pareek, A.; Soproy, S.K.; Singla-Pareek, S.L. OsCBSCBSPB4 is a two cystathionine-β-synthase domain-containing protein from rice that functions in abiotic stress tolerance. Curr. Genom. 2017, 19, 50–59. [Google Scholar] [CrossRef] [PubMed]
- Li, Y.; Xu, M. CCT family genes in cereal crops: A current overview. Crop J. 2017, 5, 449–458. [Google Scholar] [CrossRef]
- Lei, G.; Shen, M.; Li, Z.G.; Zhang, B.; Duan, K.X.; Wang, N.; Cao, Y.R.; Zhang, W.K.; Ma, B.; Ling, H.Q.; et al. EIN2 regulates salt stress response and interacts with a MA3 domain-containing protein ECIP1 in Arabidopsis. Plant Cell Environ. 2011, 34, 1678–1692. [Google Scholar] [CrossRef] [PubMed]
- Fekih, R.; Tamiru, M.; Kanzaki, H.; Abe, A.; Yoshida, K.; Kanzaki, E.; Saitoh, H.; Takagi, H.; Natsume, S.; Undan, J.R.; et al. The rice (Oryza sativa L.) lesion mimic resembling, which encodes an AAA-type ATPase, is implicated in defence response. Mol. Genet. Genom. 2015, 290, 611–622. [Google Scholar] [CrossRef] [PubMed]
- Hartl, F.; Bracher, A.; Hayer-Hartl, M. Molecular chaperones in protein folding and proteostasis. Nature 2011, 475, 324–332. [Google Scholar] [CrossRef] [PubMed]
- Wang, Y.; Huang, M.; Gao, P.; Chen, H.; Zheng, Y.; Yang, C.; Yang, Z.; Sun, Q. Expression of heat shock protein (HSP) genes and antioxidant enzyme genes in hybrid rice II YOU 838 during heat stress. Aust. J. Crop Sci. 2021, 4, 38–43. [Google Scholar] [CrossRef]
- Ganie, S.A.; Pani, D.R.; Mondal, T.K. Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice. PLoS ONE 2017, 12, e0182469. [Google Scholar] [CrossRef] [PubMed]
- Zhai, Y.; Wen, Z.; Han, Y.; Wang, F.; Xi, C.; Liu, J.; Gao, P.; Zhao, H.; Wang, Y.; Wang, Y.; et al. Heterogeneous expression of plasma-membrane-localised OsOSCA1.4 complements osmotic sensing based on hyperosmolality and salt stress in Arabidopsis osca1 mutant. Cell Calcium 2020, 91, 102261. [Google Scholar] [CrossRef] [PubMed]
Sr. No | Trait | QTL | Chromosome | Position | p Value | LOD | Locus ID | Gene Annotation |
---|---|---|---|---|---|---|---|---|
1 | Shoot length | Sal_SL 7.1 | 7 | 28443952 | 2.096 × 10−6 | 5.68 | LOC_Os07g47560 | Expressed protein |
2 | Root length | Sal_RL 1.1 | 1 | 32773208 | 2.647 × 10−6 | 5.58 | LOC_Os01g56790 | Expressed protein |
3 | Sal_RL 3.1 | 3 | 6323650 | 1.206 × 10−5 | 4.92 | LOC_Os03g12050 | Expressed protein | |
4 | Sal_RL 6.1 | 6 | 29408939 | 8.851 × 10−8 | 7.05 | LOC_Os06g48610 | CCT motif protein | |
5 | Sal_RL 8.1 | 8 | 1122340 | 6.223 × 10−5 | 4.21 | LOC_Os08g02690 | MA3 domain | |
6 | Sal_RL 12.1 | 12 | 7176380 | 2.351 × 10−6 | 5.63 | LOC_Os12g12950 | Expressed protein | |
7 | Na+ | Sal_Na 1.1 | 1 | 954124 | 1.509 × 10−5 | 4.82 | LOC_Os01g02750 | LRk-type protein |
8 | K+ | Sal_K 6.1 | 6 | 1590002 | 1.548 × 10−5 | 4.81 | LOC_Os06g03940 | Spastin, putative |
9 | Ca2+ | Sal_Ca 5.1 | 5 | 4870881 | 9.084 × 10−5 | 4.04 | ||
10 | 5 | 4877897 | 9.084 × 10−5 | 4.04 | LOC_Os05g08840 | DnaK family protein | ||
11 | 5 | 4878113 | 9.084 × 10−5 | 4.04 | ||||
12 | 5 | 4878119 | 9.084 × 10−5 | 4.04 | ||||
13 | 5 | 4878122 | 9.084 × 10−5 | 4.04 | ||||
14 | Mg2+ | Sal_Mg 2.1 | 2 | 3204128 | 1.407 × 10−6 | 5.85 | LOC_Os02g06410 | CBS domain |
15 | K+/Na+ | Sal_K/Na 1.1 | 1 | 11703845 | 2.617 × 10−6 | 5.58 | LOC_Os01g20950 | Sulfotransferase domain |
16 | Sal_K/Na 4.1 | 4 | 24365577 | 9.658 × 10−5 | 4.02 | |||
17 | 4 | 24387802 | 9.658 × 10−5 | 4.02 | ||||
18 | 4 | 24408803 | 9.658 × 10−5 | 4.02 | ||||
19 | 4 | 24415765 | 4.248 × 10−5 | 4.37 | ||||
20 | 4 | 24454895 | 8.873 × 10−5 | 4.05 | ||||
21 | 4 | 24466526 | 8.873 × 10−5 | 4.05 | LOC_Os04g41229 | bHLH domain | ||
22 | 4 | 24471326 | 8.873 × 10−5 | 4.05 | ||||
23 | 4 | 24471339 | 8.873 × 10−5 | 4.05 | ||||
24 | 4 | 24497553 | 8.873 × 10−5 | 4.05 | ||||
25 | Sal_K/Na5.1 | 5 | 1480306 | 4.36 × 10−6 | 5.36 | LOC_Os05g03500 | Expressed protein | |
26 | Sal_K/Na 7.1 | 7 | 21655201 | 5.235 × 10−6 | 5.28 | LOC_Os07g36230 | BTB domain | |
27 | Sal_K/Na 10.1 | 10 | 23089194 | 3.406 × 10−6 | 5.47 | LOC_Os10g42820 | Early-responsive dehydration protein |
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Lokeshkumar, B.M.; Krishnamurthy, S.L.; Rathor, S.; Warraich, A.S.; Yadav, S.; Sharma, P.C.; Singh, R.K. Identification of QTLs for Morpho-Physiological Traits under Saline Stress in Indica MAGIC Rice Population. Environ. Sci. Proc. 2022, 16, 29. https://doi.org/10.3390/environsciproc2022016029
Lokeshkumar BM, Krishnamurthy SL, Rathor S, Warraich AS, Yadav S, Sharma PC, Singh RK. Identification of QTLs for Morpho-Physiological Traits under Saline Stress in Indica MAGIC Rice Population. Environmental Sciences Proceedings. 2022; 16(1):29. https://doi.org/10.3390/environsciproc2022016029
Chicago/Turabian StyleLokeshkumar, Bayragondlu M., Saraswathipura L. Krishnamurthy, Suman Rathor, Arvinder S. Warraich, Satyendra Yadav, Parbodh C. Sharma, and Rakesh Kumar Singh. 2022. "Identification of QTLs for Morpho-Physiological Traits under Saline Stress in Indica MAGIC Rice Population" Environmental Sciences Proceedings 16, no. 1: 29. https://doi.org/10.3390/environsciproc2022016029
APA StyleLokeshkumar, B. M., Krishnamurthy, S. L., Rathor, S., Warraich, A. S., Yadav, S., Sharma, P. C., & Singh, R. K. (2022). Identification of QTLs for Morpho-Physiological Traits under Saline Stress in Indica MAGIC Rice Population. Environmental Sciences Proceedings, 16(1), 29. https://doi.org/10.3390/environsciproc2022016029