BackgroundHigh temperature (heat) stress during grain filling is a major problem in most of the wheat growing areas. Developing heat tolerant cultivars has become a principal breeding goal in the Southern and Central Great Plain areas of the USA. Traits associated with high temperature tolerance can be used to develop heat tolerant cultivars in wheat. The present study was conducted to identify chromosomal regions associated with thylakoid membrane damage (TMD), plasmamembrane damage (PMD), and SPAD chlorophyll content (SCC), which are indicative of high temperature tolerance.ResultsIn this study we have reported one of the first linkage maps in wheat using genotype by sequencing SNP (GBS-SNP) markers to extreme response to post anthesis heat stress conditions. The linkage map was comprised of 972 molecular markers (538 Bin, 258 AFLPs, 175 SSRs, and an EST). The genotypes of the RIL population showed strong variation for TMD, SCC and PMD in both generations (F10 and F9). Composite interval mapping identified five QTL regions significantly associated with response to heat stress. Associations were identified for PMD on chromosomes 7A, 2B and 1D, SCC on 6A, 7A, 1B and 1D and TMD on 6A, 7A and 1D. The variability (R2) explained by these QTL ranged from 11.9 to 30.6% for TMD, 11.4 to 30.8% for SCC, and 10.5 to 33.5% for PMD. Molecular markers Xbarc113 and AFLP AGCTCG-347 on chromosome 6A, Xbarc121 and Xbarc49 on 7A, gwm18 and Bin1130 on 1B, Bin178 and Bin81 on 2B and Bin747 and Bin1546 on 1D were associated with these QTL.ConclusionThe identified QTL can be used for marker assisted selection in breeding wheat for improved heat tolerance in Ventnor or Karl 92 genetic background.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0097-4) contains supplementary material, which is available to authorized users.