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Mapping of QTLs associated with yield and related traits under reproductive stage drought stress in rice using SNP linkage map

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Abstract

Background

Drought stress is a major constraint for rice production worldwide. Reproductive stage drought stress (RSDS) leads to heavy yield losses in rice. The prospecting of new donor cultivars for identification and introgression of QTLs of major effect (Quantitative trait locus) for drought tolerance is crucial for the development of drought-resilient rice varieties.

Methods and results

Our study aimed to map QTLs associated with yield and its related traits under RSDS conditions. A saturated linkage map was constructed using 3417 GBS (Genotyping by sequencing) derived SNP (Single nucleotide polymorphism) markers spanning 1924.136 cM map length with an average marker density of 0.56 cM, in the F3 mapping population raised via cross made between the traditional ahu rice cultivar, Koniahu (drought tolerant) and a high-yielding variety, Disang (drought susceptible). Using the Inclusive composite interval mapping approach, 35 genomic regions governing yield and related traits were identified in pooled data from 198 F3 and F4 segregating lines evaluated for two consecutive seasons under both RSDS and irrigated control conditions. Of the 35 QTLs, 23 QTLs were identified under RSDS with LOD (Logarithm of odds) values ranging between 2.50 and 7.83 and PVE (phenotypic variance explained) values of 2.95–12.42%. Two major QTLs were found to be linked to plant height (qPH1.29) and number of filled grains per panicle (qNOG5.12) under RSDS. Five putative QTLs for grain yield namely, qGY2.00, qGY5.05, qGY6.16, qGY9.19, and qGY10.20 were identified within drought conditions. Fourteen QTL regions having ≤ 10 Mb QTL interval size were further analysed for candidate gene identification and a total of 4146 genes were detected out of these 2263 (54.63%) genes were annotated to at least one gene ontology (GO) term.

Conclusion

Several QTLs associated with grain yield and yield components and putative candidate genes were identified. The putative QTLs and candidate genes identified could be employed to augment drought resilience in rice after further validation through MAS strategies.

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Acknowledgements

The authors gratefully acknowledge the Department of Biotechnology, and DBT-NECAB, Assam Agricultural University, Jorhat, Assam for providing the financial support for conducting this work. Rahul Kaldate gratefully acknowledges Indian Council of Agricultural Research, New Delhi for providing Senior Research Fellowship.

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Authors and Affiliations

  1. Department of Agricultural Biotechnology, Assam Agricultural University (AAU), Jorhat, Assam, 785013, India

    Rahul Kaldate, Mayuri D. Mahalle, Akhil Ranjan Baruah & Mahendra Kumar Modi

  2. Department of Biotechnology-North East Centre for Agricultural Biotechnology (DBT-NECAB), AAU, Jorhat, Assam, 785013, India

    Rahul Kumar Verma & Sushil Kumar Singh

  3. Assam Rice Research Institute, Titabar, Assam, 785630, India

    Sanjay Kumar Chetia & Pradip Chandra Dey

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  1. Rahul Kaldate
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Kaldate, R., Verma, R.K., Chetia, S.K. et al. Mapping of QTLs associated with yield and related traits under reproductive stage drought stress in rice using SNP linkage map. Mol Biol Rep 50, 6349–6359 (2023). https://doi.org/10.1007/s11033-023-08550-x

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