Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage

Abstract

Background: Adaptation to drought-prone environments requires robust root architecture. Genotypes with a more vigorous root system have the potential to better adapt to soils with limited moisture content. However, root architecture is complex at both, phenotypic and genetic level. Customized mapping panels in combination with efficient screenings methods can resolve the underlying genetic factors of root traits.

Results: A mapping panel of 233 spring barley genotypes was evaluated for root and shoot architecture traits under non-stress and osmotic stress. A genome-wide association study elucidated 65 involved genomic regions. Among them were 34 root-specific loci, eleven hotspots with associations to up to eight traits and twelve stress-specific loci. A list of candidate genes was established based on educated guess. Selected genes were tested for associated polymorphisms. By this, 14 genes were identified as promising candidates, ten remained suggestive and 15 were rejected. The data support the important role of flowering time genes, including HvPpd-H1, HvCry2, HvCO4 and HvPRR73. Moreover, seven root-related genes, HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 are confirmed as promising candidates. For the QTL with the highest allelic effect for root thickness and plant biomass a homologue of the Arabidopsis Trx-m3 was revealed as the most promising candidate.

Conclusions: This study provides a catalogue of hotspots for seedling growth, root and stress-specific genomic regions along with candidate genes for future potential incorporation in breeding attempts for enhanced yield potential, particularly in drought-prone environments. Root architecture is under polygenic control. The co-localization of well-known major genes for barley development and flowering time with QTL hotspots highlights their importance for seedling growth. Association analysis revealed the involvement of HvPpd-H1 in the development of the root system. The co-localization of root QTL with HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 represents a starting point to explore the roles of these genes in barley. Accordingly, the genes HvHOX2, HsfA2b, HvHAK2, and Dhn9, known to be involved in abiotic stress response, were located within stress-specific QTL regions and await future validation.

Keywords: Barley; Candidate genes; Genome-wide association study; Osmotic stress; Root architecture.

Fig. 1

Box plots for root and seedling traits. Centre lines show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots; data points are plotted as open circles. Trait values for Rsc, Rss, Rthc and Rths are transformed by multiplying by 100 for visualizations

Fig. 2

Correlations between root and seedling traits in non-stress or osmotic stress conditions. Correlations are displayed as heatmap and as numerical value. Red = negative correlation, blue = positive correlation. The part above the diagonal presents correlations of traits only within non-stress treatment and below the diagonal only within stress treatment. Along the diagonal correlations between the same trait in both treatment are displayed. Correlations values above 0.2 and below −0.2 are significant (P < 0.01)

Fig. 3

Manhattan plots of 12 out of 21 root and shoot traits. Horizontal axis presents seven chromosomes (1H–7H) of the barley genome. Vertical axis shows -log10(P) values of the marker-trait associations. Horizontal green line shows the threshold value based on FDR (0.05). Additionally, dashed line signifies threshold of -log(p) = 4.0

Fig. 4

Manhattan plots of 9 out of 21 root and shoot traits. Horizontal axis presents seven chromosomes (1H–7H) of the barley genome. Vertical axis shows -log10(P) values of the marker-trait associations. Horizontal green line shows the threshold value based on FDR (0.05). Additionally, dashed line signifies threshold of -log(p) = 4.0

Fig. 5

Genetic positions (cM) of 65 QTL regions for root and shoot seedling architecture placed on a schematic map of the seven barley chromosomes along with the corresponding QTL name (see Additional file 1: Table S5 for all details). QTL-hotspots are highlighted in green, root specific QTL in orange, stress-specific QTL in pink and the remaining non-specific QTL in black. Centromeric regions are indicated by red segments