A tiered approach to genome-wide association analysis for the adherence of hulls to the caryopsis of barley seeds reveals footprints of selection

BackgroundSeeds of domesticated barley are grouped into two distinct types, which differ in morphology. Caryopses covered by adaxial (palea) and abaxial (lemma) hulls that tightly adhere to the pericarp at maturity give rise to hulled seeds whereas caryopses without adhering hulls give rise to naked seeds. The naked caryopsis character is an essential trait regarding the end use of barley.ResultsTo uncover the genetic basis of the trait, a genome-wide association study (GWAS) has been performed in a panel comprising 222 2-rowed and 303 6-rowed spring barley landrace accessions. In addition to the well-described Nud locus on chromosome 7H, three novel loci showed strong associations with the trait: the first locus on 2H was specifically detected in 6-rowed accessions, the second locus on 3H was found in 2-rowed accessions from Eurasia and the third locus on 6H was revealed in 6-rowed accessions from Ethiopia. PCR analysis of naked accessions also confirmed the absence of a 17kb region harboring the Nud gene on chromosome 7H for all but one naked accession. The latter was characterized by a slightly variant phenotype of the caryopsis.ConclusionOur findings provide evidence of the pervasiveness of the 17kb deletion in spring barley from different geographic regions and at the same time reveal genomic footprints of selection in naked barley, which follow both geographic and morphological patterns.