Genome wide association mapping for cadmium tolerance and accumulation in an Aus population

Rice consumption is a major exposure route of humans to cadmium, and cadmium also causes toxicity to rice plants. In this study the Bengal and Assam Aus Panel (BAAP) of rice was screened in hydroponics for cadmium tolerance and cadmium accumulation. Across the population, there were significant cultivar, treatment, and cultivar by treatment interactions for root and shoot length, and root, shoot and total dry weights. For treatment effects, the mean reductions caused by the cadmium treatment compared to control were 15%, 21%, 32%, 23% and 24% for root length, shoot length, root dry weight, shoot dry weight, and total dry weight respectively. Cultivars in the BAAP population displayed shoot cadmium concentrations in the range of 22–187 mg kg⁻¹, with most of the rice cultivars having a cadmium concentration between 40 and 85 mg kg⁻¹. GWA mapping identified 49 quantitative trait loci (QTL) across all traits, with 13 detected for more than one trait. Thirty-nine QTLs detected in this study were found to co-localise with previously identified QTLs for cadmium traits. A number of candidate genes for cadmium tolerance and accumulation were identified in these QTL regions. The QTL on chromosome 7 between 8.59 and 9.04 Mb contained both the candidate genes OsNRAMP1 and OsNRAMP5. The QTL on chromosome 6 at 29.20–29.73 Mb contained the candidate gene OsHMA2, while the QTL on chromosome 4 at 19.03 – 19.53 Mb contained the candidate gene OsHIPP29. The haplotype variation of these candidate genes is further explored in this study.