Submergence stress can cause the death of grass plants. Identification of the association between molecular markers and submergence tolerance-related traits facilitates an efficient selection of the tolerant cultivars for commercial production. A global collection of 99 diverse perennial ryegrass (Lolium perenne L.) accessions was evaluated for submergence tolerance and analyzed with 109 simple sequence repeat (SSR) markers. Submergence significantly reduced leaf color, chlorophyll fluorescence (F(v)/F(m)), maximum plant height (HT), and relative growth rate (RGR). Significant variations in these trait values were observed among the accessions under submerged conditions. Rapid linkage-disequilibrium (LD) decay was identified within 4cM. The analysis of population structure (Q) identified four subpopulations in the collection, but no obvious relative kinship (K) was found. The Q model was the best to describe associations between SSR and traits, compared to the simple linear, K, and Q + K models. Fifteen SSR markers were associated with a reduction in leaf color, F(v)/F(m), HT, and RGR under submergence stress using the Q model. These markers can be used for genetic improvement of submergence tolerance of perennial ryegrass after further validation. The diverse populations of perennial ryegrass is a valuable resource for association mapping of stress tolerance-related physiological traits.
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