In plants with C 4 photosynthesis, physiological mechanisms underlying variation in stable carbon isotope discrimination (D 13 C) are largely unknown, and genetic components influencing D 13 C have not been described. We analyzed a maize (Zea mays) introgression library derived from two elite parents to investigate whether D
13C is under genetic control in this C 4 species. High-density genotyping with the Illumina MaizeSNP50 Bead Chip was used for a detailed structural characterization of 89 introgression lines. Phenotypic analyses were conducted in the field and in the greenhouse for kernel D
13C as well as plant developmental and photosynthesis-related traits. Highly heritable significant genetic variation for D
13C was detected under field and greenhouse conditions. For several introgression library lines, D
13C values consistently differed from the recurrent parent within and across the two phenotyping platforms. D
13C was significantly associated with 22 out of 164 analyzed genomic regions, indicating a complex genetic architecture of D
13C. The five genomic regions with the largest effects were located on chromosomes 1, 2, 6, 7, and 9 and explained 55% of the phenotypic variation for D In C 3 plants, the important steps of CO 2 uptake include the diffusion of atmospheric CO 2 through the boundary layer and the stomata. Subsequently, CO 2 is taken up by the cell and enters the chloroplast, where carboxylation by Rubisco takes place. During photosynthetic carbon fixation, the strongest fractionation of carbon isotopes occurs during the carboxylation reaction of Rubisco (Roeske and O'Leary, 1984). A theoretical model of D 13 C in C 3 photosynthesis has been described by Farquhar et al. (1982), in which D 13 C depends linearly on the ratio of intercellular to ambient partial pressure of CO 2 (p i p a 21 ), and thus provides an indication of stomatal conductance and photosynthetic capacity. Additionally, the model includes the dependency of D
13C on the fractionation of carbon isotopes during CO 2 diffusion in the air and on the enzymatic properties of the Rubisco enzyme.For rice (Oryza sativa), tomato (Solanum lycopersicum), and wheat (Triticum aestivum), it has been shown that genetic variation for D
13C is quantitative, genotype-byenvironment interaction is small, and the trait heritability is high (Condon and Richards, 1992;Rebetzke et al., 2002;Comstock et al., 2005;Impa et al., 2005). Quantitative trait