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Background  Grain protein content (GPC) is an important quality determinant for barley used as malt, feed as well as food. It is controlled by a complex genetic system. GPC differs greatly among barley genotypes and is also variable across different environments. It is imperative to understand the genetic control of barley GPC and identify the genotypes with less variation under the different environments.    Results  In this study, 59 cultivated and 99 Tibetan wild barley genotypes were used for a genome-wide association study (GWAS) and a multi-platform candidate gene-based association analysis, in order to identify the molecular markers associated with GPC. Tibetan wild barley had higher GPC than cultivated barley. The significant correlation between GPC and diastatic power (DP), and malt extract confirmed the importance of GPC in determining malt quality. Diversity arrays technology (DArT) markers associated with barley GPC were detected by GWAS. In addition, GWAS revealed two  HvNAM  genes as the candidate genes controlling GPC. No association was detected between  HvNAM1  polymorphism and GPC, while a single nucleotide polymorphism (SNP) (798, P < 0.01), located within the second intron of  HvNAM2 , was associated with GPC. There was a significant correlation between haplotypes of  HvNAM1 ,  HvNAM2  and GPC in barley.    Conclusions  The GWAS and candidate gene based-association study may be effectively used to determine the genetic variation of GPC in barley. The DArT markers and the polymorphism of  HvNAM  genes identified in this study are useful in developing high quality barley cultivars in the future.  HvNAM  genes could play a role in controlling barley GPC.

Grain protein content variation and its association analysis in barley