Natural variation of salinity response,population structure and candidate genes associated with salinity tolerance in perennial ryegrass accessions

Natural variation in salinity response, effects of population structure on growth and physiological traits and gene–trait association were examined in 56 global collections of diverse perennial ryegrass (Lolium perenne L.) accessions. Three population structure groups were identified with 66 simple sequence repeat markers, which on average accounted for 9 and 11% of phenotypic variation for the control and salinity treatment at 300 mm NaCl. Group 1 (10 accessions) had greater plant height, leaf dry weight and water content, chlorophyll index, K⁺ concentration and K⁺/Na⁺ than group 2 (39 accessions) and group 3 (7 accessions) under salinity stress, while group 3 had higher Na⁺ than groups 1 and 2. Eighty‐seven single nucleotide polymorphisms were detected from four partial candidate genes encoding aquaporin and Na⁺/H⁺ antiporter in both plasma and tonoplast membranes. Overall, rapid decay of linkage disequilibrium was observed within 500 bp. Significant associations were found between the putative LpTIP1 and Na⁺ for the control and between the putative LpNHX1 and K⁺/Na⁺ under the control and salinity treatments after controlling population structure. These results indicate that population structure influenced phenotypic traits, and allelic variation in LpNHX1 may affect salinity tolerance of perennial ryegrass.