Michael Thomson

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Michael Thomson

Mike is a former molecular geneticist and marker applications specialist at IRRI. He was responsible for the optimization of molecular marker technologies for breeding applications.

Mike led IRRI's Molecular Marker Applications Laboratory where he developed a high-throughput marker system aimed at integrating SNP markers into IRRI’s research programs. Mike coordinated genotyping efforts and generated breeding-ready marker sets for the rapid development of future molecular breeding products.

Mike also led IRRI's capacity building efforts to train the next generation of molecular breeders.


  • Molecular breeding
  • QTL mapping
  • SNP marker analysis


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


  • Scientist, Molecular Genetics, Plant Breeding, Genetics and Biotechnology Division, IRRI (2009-2015)
  • Post-doctoral Research with Dr. Abdelbagi Ismail, IRRI (2005-2008)
  • NSF International Research Fellow, ICABIOGRAD, Bogor, Indonesia (2003-2005)
  • Post-doctoral Research with Dr. Susan McCouch, Cornell University (2002-2003)


  • NSF International Research Fellowship (2003-2005)
  • Mentor Recognition; Siemens Foundation (2002-2003)
  • Gerald O. Mott Meritorious Graduate Student Award in Crop Science (2001)
  • Cornell Plant Cell and Molecular Biology Graduate Research Assistantship (1997-2001)
  • Phi Beta Kappa (1997)
  • National Merit Scholar (1992)


  • Ismail AM and Thomson, MJ (2011) Molecular Breeding of Rice for Problem Soils. In: de Oliveira AC and Varshney RK (eds.), Root Genomics, Springer, Berlin, pp. 289-311.
  • Mackill DJ, Singh US, Thomson MJ, Septiningsih E, Kumar A (2010) Technological opportunities for developing and deploying improved germplasm for key target traits. In: Pandey S, Byerlee D, Dawe D, Dobermann A, Mohanty S, Rozelle S, Hardy B (eds.), Rice in the global economy: strategic research and policy issues for food security, International Rice Research Institute, Los Baños, Philippines, pp. 433-448.
  • Thomson MJ, Ismail AM, McCouch SR, and Mackill DJ (2010) Marker assisted breeding. In: Pareek A, Sopory SK, Bohnert HJ and Govindjee (eds.), Abiotic stress adaptation in plants: physiological, molecular and genomic foundation, Springer, Netherlands, pp. 451–469.


  1. Alam R., Rahman MS, Seraj ZI, Thomson MJ, Ismail AM, Tumimbang-Raiz E, and Gregorio G (2011) Investigation of seedling-stage salinity tolerance QTLs using backcross lines derived from Oryza sativa L. Pokkali. Plant Breeding 130: 430-437.
  2. McCouch SR, Zhao K, Wright M, Tung CW, Ebana K, Thomson M, Reynolds A, Wang D, DeClerck G, Ali ML, McClung A, Eizenga G, Bustamante C (2010) Development of genome-wide SNP assays for rice. Breed Science 60:524-535.
  3. Tung CW, Zhao K, Wright K, Ali L, Jung J, Kimball J, Tyagi W, Thomson M, McNally KL, Leung H, Kim H, Ahn SN, Reynolds A, Scheffler B, Eizenga G, McClung A, Bustamante C, McCouch S (2010) Development of a research platform for dissecting phenotye-genotype associations in rice (Oryza spp.). Rice 3:205-217.
  4. Thomson MJ, de Ocampo M, Egdane J, Rahman MA, Sajise AG, Adorada DL, Tumimbang-Raiz E, Blumwald E, Seraj ZI, Singh RK, Gregorio GB, Ismail AM (2010) Characterizing the Saltol quantitative trait locus for salinity tolerance in rice. Rice 3:148-160.
  5. Widodo B, Broadley MR, Rose T, Frei M, Pariasca-Tanaka J, Yoshihashi T, Thomson M, Hammond JP, Aprile A, Close TJ, Ismail AM, Wissuwa M (2010) Response to zinc deficiency of two rice lines with contrasting tolerance is determined by root growth maintenance and organic acid exudation rates, and not by zinc-transporter activity. New Phytologist 186:400–414.
  6. Thomson MJ, Polato NR, Prasetiyono J, Trijatmiko KR, Silitonga TS, McCouch SR (2009) Genetic diversity of isolated populations of Indonesian landraces of rice (Oryza sativa L.) collected in East Kalimantan on the island of Borneo. Rice 2:80-92.
  7. Ismail AM, Heuer S, Thomson MJ, Wissuwa M (2007) Genetic and genomic approaches to develop rice germplasm for problem soils. Plant Mol. Biol. 65: 547-570.
  8. Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, Bustamante CD, McCouch SR (2007) Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet. 3: 1418-1424.
  9. Thomson MJ, Septiningsih EM, Suwardjo F, Santoso TJ, Silitonga TS, McCouch SR (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, Sweeney M, Li J, Jiang H, Thomson M, Septiningsih E, Edwards J, Moncada P, Xiao J, Garris A, Tai T, Martinez C, Tohme J, Sugiono M, McClung A, Yuan LP, Ahn SN (2007) Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica 154: 317-339.
  11. Thomson MJ, Edwards JD, Septiningsih EM, Harrington SE, McCouch SR (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. Sweeney MT, Thomson MJ, Pfeil BE, McCouch SR (2006) Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18: 283-294.
  13. Li J, Thomson M, McCouch SR (2004) Fine mapping of a grain-weight quantitative trait locus in the pericentromeric region of rice chromosome 3. Genetics 168: 2187-2195.
  14. Thomson MJ, Tai TH, McClung AM, Lai X-H, Hinga ME, Lobos KB, Xu Y, Martinez CP, McCouch SR (2003) Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor. Appl. Genet. 107: 479-493.
  15. Hessler TG, Thomson MJ, Benscher D, Nachit MM, Sorrels ME (2002) Association of a lipoxygenase locus, Lpx-B1, with variation in lipoxygenase activity in durum wheat seeds. Crop Sci. 42: 1695-1700.