Euphytica (2010) 172:149–158 DOI 10.1007/s10681-009-0011-8 123 Quantitative trait loci for stomatal density and size in lowland rice Ma. Rebecca C. Laza · Motohiko Kondo · Osamu Ideta · Edward Barlaan · Tokio Imbe Received: 8 August 2008 / Accepted: 4 August 2009 / Published online: 25 August 2009  Springer Science+Business Media B.V. 2009 Abstract Genotypic variation in stomatal density and size has been reported but little is known of the genetic mechanisms behind these leaf traits. Using 101 recombinant inbred lines derived from a cross between a tropical japonica, IR69093-41-3-2-2 and an indica variety, IR72, we conducted a Weld study to determine stomatal density and size and identify quantitative trait loci (QTL) controlling these traits under lowland con- ditions. Ten QTLs for stomatal density and four QTLs for size were identiWed across growth stages and leaf surfaces (adaxial and abaxial). The contribution of each QTL to total phenotypic variation ranged from 9.3 to 15.2% for stomatal density and 9.7 to 14.3% for size. The allele from IR72 increased stomatal density and that from IR69093-41-3-2-2 increased size. The expression of the QTLs for stomatal density and size diVered by growth stage indicating that these traits might be genetically controlled depending on growth stage or that each QTL had a diVerent function by growth stage. SigniWcant negative genetic correlations between stomatal density and size at both vegetative (r = ¡0.308**) and heading (r = ¡0.484**) stages were observed but no common QTL for these traits was detected across growth stages and leaf surfaces. These results indicate that the QTLs for density and size may neither be genetically linked nor pleiotropically con- trolled and Wndings can be used as basis for selection at the leaf level on the balance of carbon and water uptake. Further study is needed to fully understand the mechanism underlying the observed genetic associa- tion and to elucidate the function of the QTLs involved. Keywords QTL · Recombinant inbred line · Rice · Stomatal density · Stomatal size Abbreviations LOD Logarithm of the odds NPT New plant type QTL Quantitative trait loci RIL Recombinant inbred line Ma. R. C. Laza (&) Crop and Environmental Sciences Division, The International Rice Research Institute, DAPO BOX 7777, Metro Manila, Philippines e-mail: m.r.laza@cgiar.org M. Kondo · T. Imbe Department of Rice Research, National Institute of Crop Science (NICS), 2-1-18, Kannondai, Tsukuba, Ibaraki 305-8518, Japan O. Ideta National Agricultural Research Center for Western Region (WeNARC), 6-12-1 Nishi-fukatsucho, Fukuyama, Hiroshima 721-8514, Japan E. Barlaan Kikkokai Social Welfare Corporation, Ichikawa-minami 1-3-2-305, Ichikawa City, Chiba 272-0033, Japan Present Address: T. Imbe National Agricultural Research Center for Kyushu Okinawa Region, 2421 Suya, Koshi, Kumamoto 861-1192, Japan