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

Abstract

Background: Seeds 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.

Results: To 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 17 kb 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.

Conclusion: Our findings provide evidence of the pervasiveness of the 17 kb 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.

Keywords: Domestication; GWAS; Naked caryopsis; Nud; Seed protein content.

Fig. 1

Barley seeds. Top panel: dorsal side of hulled seeds (left) and naked seeds (right); lower panel; ventral side of hulled seeds (left) and naked seeds (right)

Fig. 2

PCA for the entire Lr_all panel of 525 spring barley landrace accessions (both 2- and 6-rowed) based on iSelect SNP data. The unique grouping of accessions from Ethiopia (naked 2- and 6-rowed together with hulled 6-rowed accessions) is indicated by brackets

Fig. 3

Circular Manhattan plots of genome-wide association scans for seed morphotype (covered/naked) in (a) the combined panel of 2- and 6-rowed barley landraces (Lr_all), b) the subpopulation of 2-rowed (Lr_2), and c) the subpopulation of 6-rowed accessions (Lr_6). The significance level of marker-trait associations (−logP values) is represented by the vertical scale bar. Individual chromosomes are represented on the outer circle and separated from each other by white borders. FDR thresholds (0.05) are indicated by dashed circles. Genomic regions of detected QTL on the respective chromosomes are coloured in red (outer circle). Owing to the limited resolution of the figure single dots can represent multiple SNPs, especially if they have the same or very similar -logP values

Fig. 4

Circular Manhattan plots of GWAS for the seed morphotype in a) the 2-rowed panel including naked barleys only from Ethiopia (Lr_2Eth), b) 6-rowed naked barleys only from Ethiopia (Lr_6Eth), c) 2-rowed panel including naked barleys only from Europe and Asia (Lr_2Eur) and d) 6-rowed panel including naked barley only from Europe and Asia (Lr_6Eur). The significance level of SNPs (−logP values) is indicated on the vertical scale bar. Individual chromosomes are represented on the outer circle and separated from each other by white borders. Threshold for the FDR (0.05) is indicated by solid circular dash lines. Genomic regions of detected QTL on the respective chromosomes are coloured in red (outer circle). Owing to the limited resolution of the figure single dots can represent multiple SNPs, especially if they have the same or very similar -logP values

Fig. 5

Gel analysis of 2- and 6-rowed accessions. An approximate 900 bp amplicon size was detected for both 2-and 6–rowed hulled accessions as well as for Entry 1365 (naked 2-rowed accession), while all naked barley detected an amplicon size of approximately 800 bp. Size standard (left, right, middle) 100 bp ladder

Fig. 6

Morphotype of different naked barley accessions after threshing. A marked difference can be seen with Entry 1365 where majority of seeds still remain partially enclosed in the hulls