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Molecular mapping of drought-responsive QTLs during the reproductive stage of rice using a GBS (genotyping-by-sequencing) based SNP linkage map

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Abstract

Background

In rice, drought stress at reproductive stage drastically reduces yield, which in turn hampers farmer’s efforts towards crop production. The majority of the rice varieties have resistance genes against several abiotic and biotic stresses. Therefore, the traditional landraces were studied to identify QTLs/candidate genes associated with drought tolerance.

Methods and results

A high-density SNP-based genetic map was constructed using a Genotyping-by-sequencing (GBS) approach. The recombinant inbred lines (RILs) derived from crossing ‘Banglami × Ranjit’ were used for QTL analysis. A total map length of 1306.424 cM was constructed, which had an average inter-marker distance of 0.281 cM. The phenotypic evaluation of F6 and F7 RILs were performed under drought stress and control conditions. A total of 42 QTLs were identified under drought stress and control conditions for yield component traits explaining 1.95–13.36% of the total phenotypic variance (PVE). Among these, 19 QTLs were identified under drought stress conditions, whereas 23 QTLs were located under control conditions. A total of 4 QTLs explained a PVE ≥ 10% which are considered as the major QTLs. Moreover, bioinformatics analysis revealed the presence of 6 candidate genes, which showed differential expression under drought and control conditions.

Conclusion

These QTLs/genes may be deployed for marker-assisted pyramiding to improve drought tolerance in the existing rice varieties.

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Acknowledgements

The authors are highly thankful to DBT-NECAB, AAU Jorhat and Department of Agricultural Biotechnology (ABT), AAU, Jorhat for financial and technical help during the entire research programme. The authors are also grateful towards the contribution of NextGen BioSciences Diagnostics Private Limited, New Delhi for sequencing purposes. The authors also acknowledge Distributed Information Centre (DIC), Department of ABT, AAU, Jorhat for providing necessary help during GBS data analysis. The authors also appreciate the help of Dr. Anjan Gowda S. North Carolina State University, Raleigh, North Carolina, United States for his immense support during the data analysis and critical explanations on different parts of the research work.

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Author notes

  1. Nabarun Roy and Rahul Kumar Verma have contributed equally to this work.

Authors and Affiliations

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

    Nabarun Roy, Vinay Sharma, Priyabrata Sen & Mahendra Kumar Modi

  2. School of Smart Agriculture, Adamas University, Kolkata, West Bengal, 700126, India

    Nabarun Roy

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

    Rahul Kumar Verma

  4. Regional Agricultural Research Station, Titabar, Jorhat, Assam, 785630, India

    Sanjay Kumar Chetia

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  1. Nabarun Roy
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Contributions

Conceptualization: (MKM); Investigation: (NR, RKV, PS, MKM); Resources: (SKC, MKM, RKV); Methodology: (RKV, NR, VS, MKM); Data analysis (NR, RKV); Writing, review and editing (NR, RKV, VS, MKM).

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Correspondence to Mahendra Kumar Modi.

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Roy, N., Verma, R.K., Chetia, S.K. et al. Molecular mapping of drought-responsive QTLs during the reproductive stage of rice using a GBS (genotyping-by-sequencing) based SNP linkage map. Mol Biol Rep 50, 65–76 (2023). https://doi.org/10.1007/s11033-022-08002-y

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