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A major gene controlling grain cadmium (Cd) concentration, designated as Cdu-B1, has been mapped to the long arm of chromosome 5B, but the genetic factor(s) conferring the low Cd phenotype are currently unknown. Genetic mapping of markers linked to Cdu-B1 in a population of recombinant inbred substitution lines (RSLs) revealed that the gene(s) associated with variation in Cd concentration reside(s) in wheat deletion bin 5BL9 between fraction breakpoints 0.76 and 0.79, and linked to two candidate genes; PCS2 (phytochelatin synthetase) and Xwg644, which codes for a known ABC (ATP-binding cassette) protein. Genetic mapping and quantitative trait locus (QTL) analysis of grain Cd concentration was performed in a doubled haploid (DH) population and revealed that these genes were not associated with Cdu-B1. Two expressed sequence markers (ESMs), and five sequence tagged site (STS) markers were identified that co-segregated with Cdu-B1, and explained >80% of the phenotypic variation in grain Cd concentration. A gene coding for a P1B-ATPase, designated as OsHMA3 (heavy metal associated), has recently been associated with phenotypic variation in grain Cd concentration in rice. Mapping of the orthologous gene to OsHMA3 in the DH population revealed complete linkage with Cdu-B1 and was designated as HMA3-B1. Fine mapping of Cdu-B1 in >4000 F2 plants localized Cdu-B1 to a 0.14 cM interval containing HMA3-B1. Two bacterial artificial chromosomes (BACs) containing full-length coding sequence for HMA3-B1 and HMA3-A1 (homoeologous copy from the A genome) were identified and sequenced …