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Background  Introgression as a means of generating phenotypic novelty, including altered stress tolerance, is increasingly being recognized as common. The underlying basis for  de novo  genesis of phenotypic variation in the introgression lines remains largely unexplored. In this investigation, we used a rice line ( RZ35 ) derived from introgressive hybridization between rice ( Oryza sativa  L.) and wild rice ( Zizania latifolia  Griseb.), along with its rice parental line (cv.  Matsumae ) as the experimental materials. We compared effects of salt stress on growth, ion homeostasis, and relevant gene expression between  RZ35  and  Matsumae , to explore possible mechanisms of heritable alteration in stress tolerance induced by the introgression.    Results  Contrary to our expectation, the results showed that the inhibitory effect of salt stress on growth of  RZ35  was significantly greater than that of  Matsumae . We further found that a major underlying cause for this outcome is that the introgression process weakened the capacity in Na +  exclusion under the salt stress condition, and hence, escalated the injuries of Na +  and Cl -  in shoots of  RZ35 . Accordingly, based on q-RT-PCR analysis, four genes known to be involved in the Na +  exclusion, i.e.,  OsHKT1;5 ,  OsSOS1 ,  OsCIPK24  and  OsCBL4 , were found to be significantly down-regulated in roots of  RZ35  relative to its rice parental line under the salt stress condition, thus implicating a gene expression regulation-based molecular mechanism underlying the difference in salt stress-tolerance between the introgression line and its rice parental line.    Conclusions  We show that introgression represents a potent means for rapidly generating  de novo  heritable variations in physiological traits like stress tolerance in plants, although the direction of the alteration appears unpredictable.    Electronic supplementary material  The online version of this article (doi:10.1186/1939-8433-5-36) contains supplementary material, which is available to authorized users.

Heritable alteration in salt-tolerance in rice induced by introgression from wild rice (Zizania latifolia)