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

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.