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Background  Selecting for low concentration of Na +  in the shoot provides one approach for tackling salinity stress that adversely affects crop production. Novel alleles for Na +  exclusion can be identified and then introduced into elite crop cultivars.    Results  We have identified loci associated with lower Na +  concentration in leaves of durum wheat landraces originating from Afghanistan. Seedlings of two F 2  populations derived from crossings between Australian durum wheat (Jandaroi) and two Afghani landraces (AUS-14740 and AUS-14752) were grown hydroponically and evaluated for Na +  and K +  concentration in the third leaf. High heritability was found for both third leaf Na +  concentration and the K + /Na +  ratio in both populations. Further work focussed on line AUS-14740. Bulk segregant analysis using 9 K SNP markers identified two loci significantly associated with third leaf Na +  concentration. Marker regression analysis showed a strong association between all traits studied and a favourable allele originating from AUS-14740 located on the long arm of chromosome 4B.    Conclusions  The candidate gene in the relevant region of chromosome 4B is likely to be the high affinity K +  transporter B1 ( HKT1;5-B1 ). A second locus associated with third leaf Na +  concentration was located on chromosome 3BL, with the favourable allele originating from Jandaroi; however, no candidate gene can be identified.    Electronic supplementary material  The online version of this article (10.1186/s12870-017-1164-6) contains supplementary material, which is available to authorized users.

Genetics of Na+ exclusion and salinity tolerance in Afghani durum wheat landraces