Identification of Quantitative Trait Loci for d 13 C and Productivity in Irrigated Lowland Rice Ma. R. Laza, M. Kondo,* O. Ideta, E. Barlaan, and T. Imbe ABSTRACT Stable carbon isotope ratio (d 13 C) in plants has been suggested as a useful indicator for cumulative Ci/Ca signature in a leaf, water use efficiency, and crop productivity, and is known to have genotypic vari- ation in rice (Oryza sativa L.). We conducted a field study to identify quantitative trait loci (QTLs) for d 13 C and other related leaf traits, such as leaf N, specific leaf area, and SPAD value, using recombinant inbred lines derived from an indica 3 japonica cross grown under flooded conditions. We also examined the genetic associations of d 13 C with yield, yield components, and biomass productivity. Putative QTLs for d 13 C were identified on chromosomes 2, 4, 8, 9, 11, and 12 across plant parts, stages, and years. Differential expression of QTL for d 13 C among stages suggests that each QTL had different functions by stages. The QTLs for d 13 C were associated with a few colocated QTLs for leaf traits indicating that their physiological and genetic associa- tions with leaf traits may be complex. Values of d 13 C at maturity were negatively correlated with harvest index and grain yield. However, genetic association of these traits could not be clarified due to the absence of co-located QTLs. Further examination would be useful to elucidate the physiological and morphological functions of QTLs for d 13 C found in this study. T HE STABLE carbon isotope ratio (d 13 C) in plants, which is largely based on carbon isotope discrimina- tion (CID) against 13 C/ 12 C by leaves during photosyn- thesis, has been used as a valuable index for cumulative Ci/Ca signature in a leaf, higher transpiration efficiency, and productivity under water limited conditions (Farqu- har and Richards, 1984; Rebetzke et al., 2002). It has been suggested that higher CID was associated with higher yield under well-watered conditions in crops such as wheat (Triticum aestivum L.) (Condon et al., 1987), durum wheat (Triticum turgidum L.) (Araus et al., 2003), and peanut (Arachis hypogaea L.) (Wright et al., 1993). Under nonlimiting water conditions with flooded soils, biological and grain yield of rice were both positively correlated with CID (Kondo et al., 2004). These findings suggest that it is important to examine the mechanisms responsible for the physiological and genetic associations between CID, yield, and biomass productivity under both water limited and well-watered conditions in crops including rice. Genotypic variation in CID was reported among rice groups; the japonica types showed lower CID or high d 13 C values compared with the indica types (Samejima, 1985; Dingkuhn et al., 1991; Peng et al., 1998; Kondo et al., 2004) suggesting that CID is strongly affected by genetic factors. Genotypic variation in CID was found in a number of studies that dealt with the CID and its cor- relation with other physiological traits (Condon et al., 1990; Johnson, 1993; Geber and Dawson, 1997; Saranga et al., 1999). Despite the number of studies dealing with genotypic variation in CID and its association with other physiological and yield-related traits, the physiological basis and genetic information to explain such associa- tions are still lacking. Genotypic variation in CID is possibly caused by two factors, that is, leaf conductance to CO 2 and CO 2 incorporation (Farquhar et al., 1982). Identifying morphological and physiological factors, par- ticularly leaf characters, related to the processes that determine genotypic variation in CID is essential in eval- uating the value of CID as a criterion either for tran- spiration efficiency, productivity, or both. Using molecular marker techniques, information on genetic bases for a large number of quantitatively in- herited traits related to yield and other agronomic and physiological traits of crops has accumulated. In rice, a number of reports focused on genetic factors related to yield and yield components (Lin et al., 1996; Xiao et al., 1996; Lu et al., 1997; Zhuang et al., 1997; Yan et al., 1998; Ishimaru et al., 2001b; Ishimaru, 2003; Cui et al., 2003), panicle number (Liao et al., 2001), plant height (Li et al., 1995; Yan et al., 1998; Yu et al., 2002; Ishimaru et al., 2004), and growth duration (Yano et al., 1997). Ex- cept for a limited number of reports on leaf N (Ishimaru et al., 2001a) and photosynthetic rate (Teng et al., 2004), little information is available on the genetic factors that govern physiological functions of leaf traits related to photosynthesis. Quantitative trait loci for d 13 C in crops such as soybean [Glycine max (L.) Merr.], cotton (Gossypium hirsutum L.), and barley (Hordeum vulgare L.) have been reported (Handley et al., 1994; Specht et al., 2001; Teulat et al., 2002; Saranga et al., 2004). In rice, while CID is highly affected by genotypic factor, very little effort has been directed toward understanding its genetic basis and its association with related plant traits and biomass production. Although QTLs for d 13 C have been reported (Price et al., 2002; Ishimaru et al., 2001b), their association with other traits related to photosynthesis and productivity under lowland irrigated condition is not known. In addition, the effects of growth Ma. R. Laza, M. Kondo, O. Ideta, and T. Imbe, Department of Rice Research, National Institute of Crop Science (NICS), 2-1-18, Kannon- dai, Tsukuba-city, Ibaraki, 305-8518, Japan; E. Barlaan, Nagasaki Industrial Promotion Foundation, 5-717-1 Fukahori, Nagasaki-city, Nagasaki, 851-0301, Japan. Received 6 June 2005. *Corresponding author (chokai@naro.affrc.go.jp). Published in Crop Sci. 46:763–773 (2006). Crop Physiology & Metabolism doi:10.2135/cropsci2005.05.0084 ª Crop Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA Abbreviations: Ci/Ca, ratio of intercellular and ambient partial pres- sures of CO 2 ; CID, carbon isotope discrimination; d 13 C, 13 C/ 12 C ratio expressed with a differential notation; DTH, days to heading; HI, harvest index; LOD, logarithm of the odds; NPT, new plant type; QTLs, quantitative trait loci; RILs, recombinant inbred lines; SLA, specific leaf area; SLN, specific leaf N; TDW, aboveground dry weight. Reproduced from Crop Science. Published by Crop Science Society of America. All copyrights reserved. 763 Published online February 24, 2006