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Background  Leaf color variations are common in plants. Herein we describe a natural mutant of barley cultivar Edamai No.6,  whs18 , whose leaf color showed stable and inheritable stage-green-revertible-albino under field condition.    Methods  Bulked Segregant Analysis (BSA) based on SSR assay and Specific Length Amplified Fragment Sequencing (SLAF-seq) was used to map the candidate gene for this trait.    Results  We found that leaf color of  whs18  was green at seedling stage, while the seventh or eighth leaf began to show etiolation, and albino leaves emerged after a short period. The newly emerged leaves began to show stripe white before jointing stage, and normal green leaves emerged gradually. The duration of  whs18  with abnormal leaf color lasted for about 3 months, which had some negative impacts on yield-related-traits. Further investigations showed that the variation was associated with changes in chlorophyII content and chloroplast development. Genetic analysis revealed that the trait was controlled by a single recessive nuclear gene, and was designed as  HvSGRA  in this study. Based on the F 2  population derived from Edamai No.9706 and  whs18 , we initially mapped the  HvSGRA  gene on the short arm of chromosome 2H using SSR and BSA.  GBMS247  on 2HS showed co-segregation with  HvSGRA . The genetic distance between the other marker  GBM1187  and  HvSGRA  was 1.2 cM. Further analysis using BSA with SLAF-seq also identified this region as candidate region. Finally,  HvSGRA  interval was narrowed to 0.4 cM between morex_contig_160447 and morex_contig_92239, which were anchored to two adjacent FP contigs, contig_34437 and contig_46434, respectively. Furthermore, six putative genes with high-confidence in this interval were identified by POPSEQ. Further analysis showed that the substitution from C to A in the third exon of fructokinase-1-like gene generated a premature stop codon in  whs18 , which may lead to loss function of this gene.    Conclusions  Using SSR and SLAF-seq in conjunction with BSA, we mapped  HvSGRA  within two adjacent FP contigs of barley. The mutation of fructokinase-1-like gene in  whs18  may cause the stage green-revertible albino of barley. The current study lays foundation for hierarchical map-based cloning of  HvSGRA  and utilizing the gene/trait as a visualized maker in molecular breeding in future.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2015-1) contains supplementary material, which is available to authorized users.

bmc genomics

Characterization and fine mapping of a novel barley Stage Green-Revertible Albino Gene (HvSGRA) by Bulked Segregant Analysis based on SSR assay and Specific Length Amplified Fragment Sequencing