Natural Variation in Chromium Accumulation and the Development of Related EST-SSR Molecular Markers in Miscanthus sinensis

Soil pollution by heavy metals is a serious environmental concern globally. Hexavalent (VI) chromium (Cr) is one of the main pollutants causing groundwater and soil heavy metal pollution. Miscanthus sinensis is a C4 perennial grass species with a high level of heavy metal tolerance. This species can effectively remove Cr from soils and maintain desirable biomass production under Cr stress. This research aimed to characterize and compare Cr accumulation in 58 genotypes of M. sinensis and to develop Expressed Sequence Tag–Simple Sequence Repeat (EST-SSR) markers associated with Cr tolerance. The results show that the pattern of translocation of Cr in plants differed among the 58 M. sinensis genotypes following treatment of 200 mg/L of Cr6+; however, in most genotypes, the Cr was primarily accumulated in roots. A total of 43,367 EST-SSRs were identified, and 88 EST-SSR primer pairs corresponding to candidate genes involved in Cr accumulation in M. sinensis were selected for validation. Subsequently, 170 polymorphic loci generated from 24 validated EST-SSRs were used for the population structure and marker–trait association analysis. Based on a general linear model (GLM), a total of 46 associations were identified (p < 0.05), with 14 EST-SSRs markers associated with target traits. Among them, four genes related to ABC transporters, wall-associated receptor kinases, as well as two high-affinity sulfate transporters (ST), were identified under Cr stress (p < 0.05). The results of this study help to accelerate the screening across M. sinensis genotypes for desirable traits under Cr stress and provide a platform for M. sinensis genetic improvement and molecular-marker-assisted breeding.