| Summary: | Zinc (Zn) is an essential micronutrient for rice, but it is toxic at a high concentration, especially in acid soils. It is yet unknown which genes regulate Zn tolerance in rice. In the present study, a genome-wide association study (GWAS) was performed for Zn tolerance in rice at the seedling stage within a rice core collection, named Ting’s core collection, which showed extensive phenotypic variations in Zn toxicity with high-density single-nucleotide polymorphisms (SNPs). A total of 7 and 19 quantitative trait loci (QTL) were detected using root elongation (RE) and relative root elongation (RRE) under high Zn toxicity, respectively. Among them, 24 QTL were novel, and <i>qRRE15</i> was located in the same region where 3 QTL were reported previously. In addition, <i>qRE4</i> and <i>qRRE9</i> were identical. Furthermore, we found eight candidate genes that are involved in abiotic and biotic stress, immunity, cell expansion, and phosphate transport in the loci of <i>qRRE8</i>, <i>qRRE9</i>, and <i>qRRE15</i>. Moreover, four candidate genes, i.e., <i>Os01g0200700</i>, <i>Os06g0621900</i>, <i>Os06g0493600</i>, and <i>Os06g0622700</i>, were verified correlating to Zn tolerance in rice by quantitative real time-PCR (qRT-PCR). Taken together, these results provide significant insight into the genetic basis for Zn toxicity tolerance and tolerant germplasm for developing rice tolerance to Zn toxicity and improving rice production in Zn-contaminated soils.
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