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Background  Climate change models predict more frequent incidents of heat stress worldwide. This trend will contribute to food insecurity, particularly for some of the most vulnerable regions, by limiting the productivity of crops. Despite its great importance, there is a limited understanding of the underlying mechanisms of variation in heat tolerance within plant species. Common bean,  Phaseolus vulgaris , is relatively susceptible to heat stress, which is of concern given its critical role in global food security. Here, we evaluated three genotypes of  P. vulgaris  belonging to kidney market class under heat and control conditions. The Sacramento and NY-105 genotypes were previously reported to be heat tolerant, while Redhawk is heat susceptible.    Results  We quantified several morpho-physiological traits for leaves and found that photosynthetic rate, stomatal conductance, and leaf area all increased under elevated temperatures. Leaf area expansion under heat stress was greatest for the most susceptible genotype, Redhawk. To understand gene regulatory responses among the genotypes, total RNA was extracted from the fourth trifoliate leaves for RNA-sequencing. Several genes involved in the protection of PSII ( HSP21 ,  ABA4 , and  LHCB4.3 ) exhibited increased expression under heat stress, indicating the importance of photoprotection of PSII. Furthermore, expression of the gene  SUT2  was reduced in heat. SUT2 is involved in the phloem loading of sucrose and its distal translocation to sinks. We also detected an almost four-fold reduction in the concentration of free hexoses in heat-treated beans. This reduction was more drastic in the susceptible genotype.    Conclusions  Overall, our data suggests that while moderate heat stress does not negatively affect photosynthesis, it likely interrupts intricate source-sink relationships. These results collectively suggest a physiological mechanism for why pollen fertility and seed set are negatively impacted by elevated temperatures. Identifying the physiological and transcriptome dynamics of bean genotypes in response to heat stress will likely facilitate the development of varieties that can better tolerate a future of elevated temperatures.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5669-2) contains supplementary material, which is available to authorized users.

Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships