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QTL mapping for tolerance of anaerobic germination from IR64 and the aus landrace Nanhi using SNP genotyping

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Abstract

Direct seeding is becoming more popular mainly due to its labor-saving nature. However, flooding during germination caused by unleveled fields and unpredicted heavy rain can prevent crop establishment. On the other hand, flooding just after sowing protects the seeds from rats and birds and is also a viable means of weed control. Thus, the development of varieties able to tolerate flooding during germination, referred to as anaerobic germination (AG), is essential. A study was conducted to identify QTLs associated with tolerance of flooding during germination from an F2:3 mapping population derived from the cross of IR64 and the tolerant aus landrace Nanhi. Phenotyping was performed by counting the rate of seedling survival of 300 lines under the stress. Selective genotyping was employed by genotyping the 48 most tolerant and 48 most susceptible lines using a 384-plex SNP Indica/Indica set on the Illumina BeadXpress Reader, resulting in 234 polymorphic markers for the study. A major QTL for AG derived from Nanhi, named qAG7, was detected on chromosome 7 with an LOD of 13.93 and 22.3 % of the phenotypic variance explained. A second QTL of smaller effect, qAG11, was also derived from Nanhi, while one QTL with an increased effect from IR64 was detected on chromosome 2 (qAG2.1). The QTLs detected in this study can be used to further elucidate the mechanisms underlying AG tolerance in rice, and can also be used in marker-assisted selection and QTL pyramiding to provide higher AG tolerance to enable improved crop establishment in direct-seeded systems.

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Acknowledgments

We thank R. Garcia, J. Mendoza, J. A. Tarun, V. Bartolome and C. J. Dilla-Ermita for technical assistance, and B. Hardy for editing the manuscript. The work reported here was supported in part by a grant from the Bill & Melinda Gates Foundation (BMGF) through the project “Stress-Tolerant Rice for Africa and South Asia (STRASA)” and by the Global Rice Science Partnership (GRiSP).

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Authors and Affiliations

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

    Miriam D. Baltazar, John Carlos I. Ignacio, Michael J. Thomson, Abdelbagi M. Ismail & Endang M. Septiningsih

  2. University of the Philippines, 4031, Los Banos, Laguna, Philippines

    Miriam D. Baltazar & Merlyn S. Mendioro

Authors
  1. Miriam D. Baltazar
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  2. John Carlos I. Ignacio
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  3. Michael J. Thomson
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  4. Abdelbagi M. Ismail
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  5. Merlyn S. Mendioro
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  6. Endang M. Septiningsih
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Correspondence to Endang M. Septiningsih.

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Baltazar, M.D., Ignacio, J.C.I., Thomson, M.J. et al. QTL mapping for tolerance of anaerobic germination from IR64 and the aus landrace Nanhi using SNP genotyping. Euphytica 197, 251–260 (2014). https://doi.org/10.1007/s10681-014-1064-x

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