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Anthocyanin pigmentation is an important morphological marker that is commonly used to identify rice varieties and for linkage analysis. The following study investigates the genetic factors involved in the purple stigma (Ps) and purple apiculus (Pa) traits of an important indica rice cross between Zhenshan 97 (purple stigma and purple apiculus) and Minghui 63 (grey stigma and colourless apiculus). A recombinant inbred line (RIL) population derived from this cross was used for quantitative trait loci (QTL) mapping of the purple stigma and purple apiculus traits. As a result, one major QTL for the purple stigma trait, temporarily designated qPS-1-1, and one major QTL for the purple apiculus trait, temporarily designated qPA-1-1, were mapped to the short arm of chromosome 6 in the interval between the two markers Y4073L and *P. The LOD peaks of qPS-1-1 and qPA-1-1 were 44.0127 and 173.3585, respectively. In addition, qPS-1-1 and qPA-1-1 explained 66.7416% and 98.6441% of the total phenotypic variance, respectively. The Zhenshan 97 allele increased the purple stigma trait by approximately 8.0355% (for qPS-1-1) and 9.8863% (for qPA-1-1). Moreover, since qPS-1-1 and qPA-1-1 were strongly correlated, they were also located in the same vicinity of the C gene on the short arm of chromosome 6, which suggested that the two QTL might be the same. By comparing these and previous results, it was deduced that qPS-1-1 or qPA-1-1 was the C gene and was pleiotropic for both the colouration of the apiculus and the colouration of the stigma in rice.

Mapping of quantitative trait loci for purple stigma and purple apiculus in rice by using a Zhenshan 97B/Minghui 63 RIL population