Marker-Trait Associations for Total Carotenoid Content and Individual Carotenoids in Durum Wheat Identified by Genome-Wide Association Analysis

Abstract

Yellow pigment content is one of the main traits considered for grain quality in durum wheat (Triticum turgidum L.). The yellow color is mostly determined by carotenoid pigments, lutein being the most abundant in wheat endosperm, although zeaxanthin, α-carotene and β-carotene are present in minor quantities. Due to the importance of carotenoids in human health and grain quality, modifying the carotenoid content and profile has been a classic target. Landraces are then a potential source for the variability needed for wheat breeding. In this work, 158 accessions of the Spanish durum wheat collection were characterized for carotenoid content and profile and genotyped using the DArTSeq platform for association analysis. A total of 28 marker-trait associations were identified and their co-location with previously described QTLs and candidate genes was studied. The results obtained confirm the importance of the widely described QTL in 7B and validate the QTL regions recently identified by haplotype analysis for the semolina pigment. Additionally, copies of the Zds and Psy genes on chromosomes 7B and 5B, respectively, may have a putative role in determining zeaxanthin content. Finally, genes for the methylerythritol 4-phosphate (MEP) and isopentenyl diphosphate (IPPI) carotenoid precursor pathways were revealed as additional sources of untapped variation for carotenoid improvement.

Keywords: GWAS; Triticum turgidum; grain quality; landraces.

Figure 5

Co-localization of marker-trait associations identified in this work with previous QTLs for yellow pigment content (YPC) and semolina yellowness (YI). Regions identified as ‘QTL’ were depicted according to their position at the ‘Svevo’ genome browser [37]. Haplotype regions associated to semolina pigment [44] were identified as ‘hap’ regions. The MTA between wPt-2724-2B and Yellow index was reported by [45]. Trait abbreviations: Tlut: Total lutein; Flut: Free lutein; Tcar: Total carotenoids; Zeax: Zeaxanthin; Pbb: Relative proportion of carotenoids from the β,β-branch relative to the total carotenoid pool.

Figure 1

Marker distribution along ‘Svevo’ genome.

Figure 2

Pearson correlations between seasons and density functions, showing the distribution of traits in both seasons (BLUEs values). *** p < 0.001.

Figure 2

Pearson correlations between seasons and density functions, showing the distribution of traits in both seasons (BLUEs values). *** p < 0.001.

Figure 3

Pearson correlations and density functions showing the distribution of traits (mean values of both seasons). *** p < 0.001.

Figure 4

Manhattan plots from the GWAS analyses. For each trait, a suggestive (FDR) threshold by Benjamini and Hochberg [36] at α = 0.2 is shown (blue horizontal line). The significance of each MTA calculated with the same FDR approach is shown in Table 1.