Endang Septiningsih

  • About

Endang SeptiningsihSepti is a former molecular geneticist and breeder on abiotic stress tolerance at IRRI. She was mainly responsible for developing varieties that are suitable for anaerobic direct seeded rice (ADSR) conditions in both rainfed and irrigated rice ecosystems.

Septi led the ADSR breeding program at IRRI with the main focus on developing varieties that combine tolerance to flooding during germination (referred to as anaerobic germination) and good early seedling vigor among other traits.

Her team also focused on identifying QTLs and genes enabling germination in anaerobic conditions from several highly tolerant donors. This provides essential tools for understanding the different molecular mechanisms underlying tolerance and breeding for direct-seeded varieties that can survive flooding during germination.

Septi also served as an Adjunct Associate Professor in Crop Science Cluster, College of Agriculture, at the University of the Philippines Los BaƱos (UPLB).


  • QTL mapping, fine mapping and gene cloning
  • Marker-assisted selection and QTL pyramiding
  • Breeding improved varieties for direct-seeded systems


  • PhD minor in Plant Molecular Biology and Plant Pathology, Cornell University, Plant Breeding (2002)


  • Molecular Geneticist and Breeder, IRRI (2010-2015)
  • Molecular Geneticist, IRRI (2009-2010)
  • Postdoctoral Fellow, IRRI (2005-2008)
  • Scientist, ICABIOGRAD, IAARD, Bogor, Indonesia (2003-2005)
  • Postdoctoral Fellow, Cornell University, USA (2002-2003)


  • PhD Scholarship award, Rockefeller Foundation
  • Advanced Course in Plant Breeding (IAARD award), Mediterranean Agronomic Institute of Zaragoza (IAMZ), Spain
  • Best Student Award, Department of Agriculture, Gadjah Mada University


  • Member of the Society for the Advancement of Breeding Researches in Asia and Oceania (SABRAO) (2009-present)
  • Member of the International Society of Plant Anaerobiosis (ISPA) (2010-present)


  1. Septiningsih EM, DL Sanchez, N Singh, PMD Sendon, AM Pamplona, S Heuer, DJ Mackill. 2011. Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru. Theor Appl Genet. DOI: 10.1007/s00122-011-17510
  2. Li Z-X, EM Septiningsih, SM Quilloy-Mercado, KL McNally, DJ Mackill. 2011. Identification of SUB1A alleles from wild rice Oryza rufipogon Griff. Genet Resour Crop Evol. 58: 1237-1242
  3. Iftekharuddaula KM, MA Newaz, MA Salam, HU Ahmed, MAA Mahbub, EM Septiningsih, BCY Collard, DL Sanchez, AM Pamplona, and DJ Mackill. 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
  4. Singh N, TTM Dang, GV Vergara, DM Pandey, D Sanchez, CN Neeraja, EM Septiningsih, M Mendioro , EM Tecson-Mendoza, AM Ismail, DJ Mackill, S Heuer. 2010. Molecular marker survey and expression analyses of the rice submergence-tolerance genes SUB1A and SUB1C. Theor Appl Genet. 121: 1441-1453
  5. Angaji SA, EM Septiningsih, DJ Mackill, AM Ismail. 2010. QTLs associated with tolerance to anaerobic conditions during germination in rice (Oryza sativa L.). Euphytica 172: 159-168
  6. Mackill DJ, Ismail AM, Pamplona AM, Sanchez DL, Carandang JJ, Septiningsih E. 2010. Stress-tolerant rice varieties for adaptation to a changing climate. Crop, Environment and Bioinformatics 7: 250-259
  7. Septiningsih, EM, AM Pamplona, DL Sanchez, CN Neeraja, GV Vergara, S Heuer, AM Ismail, DJ Mackill. 2009. Development of Submergence Tolerant Rice Cultivars: TheSub1 Locus and Beyond. Ann Bot.103: 151-160
  8. Neeraja C, R Maghirang-Rodriguez, A Pamplona, S Heuer, B Collard, E Septiningsih, G Vergara, D Sanchez, K Xu, A Ismail, D Mackill. 2007. A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet.115: 767-776
  9. Thomson MJ, EM Septiningsih, F Suwardjo, TJ Santoso, TS Silitonga, SR McCouch. 2007. Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor Appl Genet 114: 559-568.
  10. McCouch SR, M Sweeney, J Li, H Jiang, M Thomson, E Septiningsih, J Edwards, P Moncada, J Xiao, A Garris, T Tai, C Martinez, J Tohme, M Sugiono, A McClung, LP Yuan, SN Ahn. 2007. Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica 154: 317-339.
  11. Thomson MJ, JD Edwards, EM Septiningsih, SE Harrington, SR McCouch. 2006. Substitution mapping of dth1.1, a flowering time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL. Genetics 172: 2501-2514.
  12. Septiningsih EM, J Prasetiyono, E Lubis, TH Tai, T Tjubaryat, S Moeljopawiro, SR McCouch. 2003. Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107: 1419-1432.
  13. Septiningsih EM, KR Trijatmiko, S Moeljopawiro, SR McCouch. 2003. Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107: 1433-1432.