Skip to main content

Accelerating the development of new submergence tolerant rice varieties: the case of Ciherang-Sub1 and PSB Rc18-Sub1


Submergence is an escalating problem in many rice producing areas. A submergence tolerance gene, SUB1, derived from FR13A was previously introduced into six mega varieties through marker assisted backcrossing (MABC) with the final product selected at the BC2 or BC3 generation. Their phenotype was similar to the original varieties, but they could withstand complete inundation for up to 2 or 3 weeks. Several of these varieties have been released in South and Southeast Asia; nonetheless the development of additional submergence tolerant varieties is indispensable to provide farmers with diverse choices of varieties that are preferable for the local needs and to avoid ecological vulnerability due to planting only one variety across vast areas. To accelerate this effort, the SUB1 gene has now been introgressed into two new popular varieties from Indonesia and the Philippines, i.e. Ciherang and PSB Rc18, respectively, through MABC using only one backcross (BC1) with the previously developed IR64-Sub1 as the donor. Since this new donor is closely related to both recurrent parents, a more rapid MABC approach can be pursued due to the similarity of genetic backgrounds. Using this strategy, new submergence tolerant varieties Ciherang-Sub1 and PSB Rc18-Sub1 were developed in less than 2 years, presenting a promising approach to convert additional popular varieties in the future.

This is a preview of subscription content, access via your institution.

Fig. 1


  1. Frisch M, Bohn M, Melchinger AE (1999) Comparison of selection strategies for marker-assisted backcrossing of a gene. Crop Sci 39:1295–1301

    Article  Google Scholar 

  2. Fukao T, Bailey-Serres J (2008) Ethylene—a key regulator of submergence responses in rice. Plant Sci 175:43–51

    Article  CAS  Google Scholar 

  3. Iftekharuddaula KM, Newaz MA, Salam MA, Ahmed HU, Mahbub MAA, Septiningsih EM, Collard BCY, Sanchez DL, Pamplona AM, Mackill DJ (2011) Rapid and high-precision marker assisted backcrossing to introgress the SUB1 QTL into BR11, the rainfed lowland rice mega variety of Bangladesh. Euphytica 178:83–97

    Article  Google Scholar 

  4. Ismail AM, Singh US, Singh S, Dar MH, Mackill DJ (2013) The contribution of submergence-tolerant (Sub1) rice varieties to food security in flood-prone rainfed lowland areas in Asia. Field Crops Res 152:83–93

    Article  Google Scholar 

  5. Juliano BO, Villareal CP (1993) Grain quality evaluation of world rices. International Rice Research Institute (IRRI), Manila, p 99

    Google Scholar 

  6. Mackill DJ, Ismail AM, Singh US, Labios RV, Paris TR (2012) Development and rapid adoption of submergence-tolerant (Sub1) rice varieties. Adv Agron 115:303–356

    Google Scholar 

  7. Neeraja CN, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BCY, Septiningsih EM, Vergara G, Sanchez D, Xu K, Ismail AM, Mackill DJ (2007) A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 115:767–776

    Article  CAS  PubMed  Google Scholar 

  8. Septiningsih EM, Pamplona AM, Sanchez DL, Neeraja CN, Vergara GV, Heuer S, Ismail AM, Mackill DJ (2009) Development of submergence tolerant rice cultivars: the Sub1 locus and beyond. Ann Bot 103:151–160

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Septiningsih EM, Sanchez DL, Singh N, Sendon PMD, Pamplona AM, Heuer S, Mackill DJ (2012) Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru. Theor Appl Genet 124:867–874

    Article  PubMed  Google Scholar 

  10. Septiningsih EM, Collard BCY, Heuer S, Bailey-Serres J, Ismail AM, Mackill DJ (2013) Applying genomics tools for breeding submergence tolerance in rice. In: Varshney RK, Tuberosa R (eds) Translational genomics for crop breeding: improvement for abiotic stress, quality and yield improvement, vol 2. Wiley-Blackwell, USA, pp 9–30

    Chapter  Google Scholar 

  11. Singh S, Mackill DJ, Ismail AM (2009) Response of SUB1 rice introgression lines to submergence in the field: yield and grain quality. Field Crop Res 113:12–23

    Article  Google Scholar 

  12. Singh S, Mackill DJ, Ismail AM (2014) Physiological bases of tolerance to complete submergence in rice involves other genetic factors in addition to SUB1. Ann Bot (in press)

  13. Thomson MJ (2014) High-throughput SNP genotyping to accelerate crop improvement. Plant Breed Biotech 2:195–212

    Article  Google Scholar 

  14. Winkel A, Colmer TD, Ismail AM, Pedersen O (2013) Internal aeration of paddy field rice (Oryza sativa) during complete submergence-importance of light and floodwater O2. New Phyt 197:1193–1203

    Article  CAS  Google Scholar 

  15. Winkel A, Pedersen O, Ella E, Ismail AM, Colmer TD (2014) Gas film retention and underwater photosynthesis during field submergence of four rice genotypes. J Exp Bot. doi:10.1093/jxb/eru166

    PubMed Central  PubMed  Google Scholar 

  16. Xu K, Mackill DJ (1996) A major locus for submergence tolerance mapped on rice chromosome 9. Mol Breed 2:219–224

    Article  CAS  Google Scholar 

  17. Xu K, Xu X, Ronald PC, Mackill DJ (2000) A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1. Mol Gen Genet 263:681–689

    Article  CAS  PubMed  Google Scholar 

  18. Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708

    Article  CAS  PubMed  Google Scholar 

  19. Yun SH, Matheson NK (1990) Estimation of amylase content of starches after precipitation of amylopectin by concanavalin-A. Starch/Starke 42:302–305

    Article  CAS  Google Scholar 

  20. Zheng K, Subudhi PK, Domingo J, Magpantay G, Huang N (1995) Rapid DNA isolation for marker assisted selection in rice breeding. Rice Genet News 12:255–258

    Google Scholar 

Download references


We thank J. Mendoza, E. Suiton, J. Borgonia, R. Formaran, G. Perez, R. Garcia, and N. Ramos from IRRI and S. D. Indrasari from Grain Quality Laboratory at ICRR for technical assistance. The work reported here was supported in part by a grant from the Japan Ministry of Foreign Affairs (MoFA) and the Global Rice Science Partnership (GRiSP). The work conducted in ICRR was supported by the ICRR budget implementation list (DIPA).

Conflict of interest

We declare that there is no conflict of interest.

Author information



Corresponding author

Correspondence to Endang M. Septiningsih.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 14 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Septiningsih, E.M., Hidayatun, N., Sanchez, D.L. et al. Accelerating the development of new submergence tolerant rice varieties: the case of Ciherang-Sub1 and PSB Rc18-Sub1. Euphytica 202, 259–268 (2015).

Download citation


  • Rice (Oryza sativa)
  • Submergence tolerance
  • SUB1
  • One backcross strategy
  • Ciherang-Sub1
  • PSB Rc18-Sub1