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SNP-based discovery of salinity-tolerant QTLs in a bi-parental population of rice (Oryza sativa)

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Abstract

Breeding for salt tolerance is the most promising approach to enhance the productivity of saline prone areas. However, polygenic inheritance of salt tolerance in rice acts as a bottleneck in conventional breeding for salt tolerance. Hence, we set our goals to construct a single nucleotide polymorphism (SNP)-based molecular map employing high-throughput SNP marker technology and to investigate salinity tolerant QTLs with closest flanking markers using an elite rice background. Seedling stage salinity responses were assessed in a population of 281 recombinant inbred lines (RILs) derived from the cross between At354 (salt tolerant) and Bg352 (salt susceptible), by 11 morpho-physiological indices under a hydroponic system. Selected extreme 94 RILs were genotyped using Illumina Infinium rice 6K SNP array and densely saturated molecular map spanning 1460.81 cM of the rice genome with an average interval of 1.29 cM between marker loci was constructed using 1135 polymorphic SNP markers. The results revealed 83 significant QTLs for 11 salt responsive traits explaining 12.5–46.7 % of phenotypic variation in respective traits. Of them, 72 QTLs responsible for 10 traits were co-localized together forming 14 QTL hotspots at 14 different genomic regions. The all QTL hotspots were flanked less than 1 Mb intervals and therefore the SNP loci associated with these QTL hotspots would be important in candidate gene discovery for salt tolerance.

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Acknowledgments

Global Rice Science scholarship 2011, awarded by the International Rice Research Institute (IRRI) is greatly appreciated for providing financial support and research facilities. National Science Foundation (NSF) in Sri Lanka is also acknowledged for financial support during initial phase of this project.

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  1. Glenn B. Gregorio

    Present address: East–West Seed Company (EWS), Km. 54 Cagayan Valley Road, Sampaloc, San Rafael, 3008, Bulacan, Philippines

Authors and Affiliations

  1. Department of Biotechnology, Faculty of Agriculture and Plantation Management, Wayamba Univesity of Sri Lanka, Makandura, Gonawila (NWP), 60170, Sri Lanka

    D. R. Gimhani & N. S. Kottearachchi

  2. International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

    Glenn B. Gregorio

  3. Rice Research and Development Institute, Batalagoda, Ibbagamuwa, Sri Lanka

    W. L. G. Samarasinghe

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  1. D. R. Gimhani
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  2. Glenn B. Gregorio
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  3. N. S. Kottearachchi
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  4. W. L. G. Samarasinghe
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Correspondence to D. R. Gimhani.

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This study was funded by the Global Rice Science scholarship 2011, awarded by the International Rice Research Institute (IRRI) and the National Science Foundation (NSF) in Sri Lanka (NSF/RG/2011/BT/02).

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Communicated by S. Hohmann.

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Gimhani, D.R., Gregorio, G.B., Kottearachchi, N.S. et al. SNP-based discovery of salinity-tolerant QTLs in a bi-parental population of rice (Oryza sativa). Mol Genet Genomics 291, 2081–2099 (2016). https://doi.org/10.1007/s00438-016-1241-9

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