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Genome-wide SNP discovery, linkage mapping, and analysis of QTL for morpho-physiological traits in rice during vegetative stage under drought stress

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Abstract

Drought tolerance in rice is controlled by several genes and is inherited quantitatively. Low genetic map density and the use of phenotypic traits that do not reflect the corresponding tolerance level have been obstacles in genetic analyses performed to identify genes that control drought-tolerant traits in rice. The current study aimed to construct a genetic map from high-density single-nucleotide polymorphism (SNP) markers generated from genome sequences of recombinant inbred lines (RILs), derived from IR64 × Hawara Bunar. Moreover, it sought to analyze the quantitative trait loci (QTL) and identify the drought tolerance candidate genes. A linkage map along 1980 cM on the 12 rice chromosomes was constructed employing 55,205 SNP markers resulting from the RIL genome sequences. A total of 175 morpho-physiological traits pertaining to drought stress were determined. A total of 41 QTLs were detected in 13 regions on rice chromosomes 1, 3, 6, 8, 9, and 12. Moreover, three hotspot QTL regions were found on chromosomes 6 and 8, along with two major QTL on chromosome 9. Differential gene expression for the loci within the QTL physical map intervals revealed many potential candidate genes. The markers tightly linked to the QTL and their candidate genes can potentially be used for pyramiding in marker-assisted breeding in order to achieve genetic improvement concerning the tolerance of rice to drought stress.

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Acknowledgements

This work was supported by funding from the Ministry of Research and Technology, Indonesia. We thank Prof. Taku Demura, Dr. Tadashi Kunieda, and Dr. Ryosuke Sano from Nara Institute of Science and Technology (NAIST), Japan, for assisting us in conducting genotyping-by-sequencing analysis.

Funding

This work was funded by the World Class Research (WCR) F.Y. 2019–2020, Grant No. 1536/IT3.L1/PN/2019, awarded to Dr. Miftahudin from the Ministry of Research and Technology, the Republic of Indonesia. The research was also partially supported by the ‘Program Magister Menuju Doktor untuk Sarjana Unggul’ (PMDSU) F.Y. 2016–2019 from the Ministry of Research, Technology, and Higher Education, the Republic of Indonesia. 

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Authors and Affiliations

  1. Plant Biology Graduate Program, Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Kampus IPB Dramaga, Bogor, 16680, Indonesia

    Rizky Dwi Satrio & Miftahul Huda Fendiyanto

  2. Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Kampus IPB Dramaga, Bogor, 16680, Indonesia

    Ence Darmo Jaya Supena, Sony Suharsono & Miftahudin Miftahudin

  3. Department of Biology, Faculty of Military Mathematics and Natural Sciences, The Republic of Indonesia Defense University (Unhan RI), Komplek Indonesia Peace and Security Center (IPSC) Sentul, Bogor, 16810, Indonesia

    Rizky Dwi Satrio & Miftahul Huda Fendiyanto

  4. Faculty of Military Mathematics and Natural Sciences, The Republic of Indonesia Defense University (Unhan RI), Komplek Indonesia Peace and Security Center (IPSC) Sentul, Bogor, 16810, Indonesia

    Ence Darmo Jaya Supena

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  1. Rizky Dwi Satrio
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  2. Miftahul Huda Fendiyanto
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Contributions

All authors contributed to the study conception and design. The population of recombinant inbred lines was developed by MM. RDS phenotyped and analyzed the RIL data, performed DNA isolation, constructed the high-resolution genetic map, ran the quantitative trait loci analysis of the RILs, and wrote the manuscript under the supervision of EDJS, SS, and MM. MHF performed DNA isolation and phenotyped the RILs. All authors read and approved the final manuscript.

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Correspondence to Miftahudin Miftahudin.

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Satrio, R.D., Fendiyanto, M.H., Supena, E.D.J. et al. Genome-wide SNP discovery, linkage mapping, and analysis of QTL for morpho-physiological traits in rice during vegetative stage under drought stress. Physiol Mol Biol Plants 27, 2635–2650 (2021). https://doi.org/10.1007/s12298-021-01095-y

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