Plants acquire thermotolerance to lethal high temperatures if first exposed to moderately high temperature or if temperature is increased gradually to an otherwise lethal temperature. We have taken a genetic approach to dissecting acquired thermotolerance by characterizing loss-of-function thermotolerance mutants in Arabidopsis. In previous work, we identified single recessive alleles of four loci required for thermotolerance of hypocotyl elongation, hot1-1, hot2-1, hot3-1, and hot4-1. Completed screening of M 2 progeny from approximately 2500 M 1 plants has now identified new alleles of three of these original loci, along with three new loci. The low mutant frequency suggests that a relatively small number of genes make a major contribution to this phenotype or that other thermotolerance genes encode essential or redundant functions. Further analysis of the original four loci was performed to define the nature of their thermotolerance defects. Although the HOT1 locus was shown previously to encode a major heat shock protein (Hsp), Hsp101, chromosomal map positions indicate that HOT2, 3, and 4 do not correspond to major Hsp or heat shock transcription factor genes. Measurement of thermotolerance at different growth stages reveals that the mutants have growth stage-specific heat sensitivity. Analysis of Hsp accumulation shows that hot2 and hot4 produce normal levels of Hsps, whereas hot3 shows reduced accumulation. Thermotolerance of luciferase activity and of ion leakage also varies in the mutants. These data provide the first direct genetic evidence, to our knowledge, that distinct functions, independent of Hsp synthesis, are required for thermotolerance, including protection of membrane integrity and recovery of protein activity/synthesis.Plants have many different mechanisms for surviving high temperatures in their environment, including long-term evolutionary adaptations of life history and morphology and shorter term avoidance or acclimation mechanisms involving, for example, leaf orientation, transpirational cooling, or alterations of membrane lipid composition (Berry, 1975; Turner and Kramer, 1980;Radin et al., 1994). It has also long been known that plants, like other organisms, have the ability to acquire thermotolerance rapidly, within hours, to otherwise normally lethal high temperatures (Alexandrov, 1961;Lin et al., 1984;Neumann et al., 1989; Vierling, 1991). The acquisition of thermotolerance is a cell autonomous phenomenon and results from prior exposure to a conditioning pretreatment, which can be a short, sublethal high temperature or other moderate stress treatments (Lindquist, 1986). Thermotolerance can also be induced by a gradual increase to the normally lethal temperature (Vierling, 1991), as would be experienced in the natural environment (Ansari and Loomis, 1959;Ehler, 1973). Even plants growing in their natural distribution range may experience high temperatures that would be lethal in the absence of this rapid acclimation; thus, ability to acquire thermotolerance is likely of significa...