A major QTL on chromosome 7HS controls the response of barley seedling to salt stress in the Nure × Tremois population

BACKGROUND: Seedling establishment is a crucial and vulnerable stage in the crop life cycle which determines further plant growth. While many studies are available on salt tolerance at the vegetative stage, the mechanisms and genetic bases of salt tolerance during seedling establishment have been poorly investigated. Here, a novel and accurate phenotyping protocol was applied to characterize the response of seedlings to salt stress in two barley cultivars (Nure and Tremois) and their double-haploid population. RESULTS: The combined phenotypic data and existing genetic map led to the identification of a new major QTL for root elongation under salt stress on chromosome 7HS, with the parent Nure carrying the favourable allele. Gene-based markers were developed from the rice syntenic genomic region to restrict the QTL interval to Bin2.1 of barley chromosome 7HS. Furthermore, doubled haploid lines with contrasting responses to salt stress revealed different root morphological responses to stress, with the susceptible genotypes exhibiting an overall reduction in root length and volume but an increase in root diameter and root hair density. CONCLUSIONS: Salt tolerance at the seedling stage was studied in barley through a comprehensive phenotyping protocol that allowed the detection of a new major QTL on chromosome 7HS. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-017-0545-z) contains supplementary material, which is available to authorized users.