The carotenoid biosynthetic and catabolic genes in wheat and their association with yellow pigments

Abstract

Background: In plants carotenoids play an important role in the photosynthetic process and photo-oxidative protection, and are the substrate for the synthesis of abscisic acid and strigolactones. In addition to their protective role as antioxidants and precursors of vitamin A, in wheat carotenoids are important as they influence the colour (whiteness vs. yellowness) of the grain. Understanding the genetic basis of grain yellow pigments, and identifying associated markers provide the basis for improving wheat quality by molecular breeding.

Results: Twenty-four candidate genes involved in the biosynthesis and catabolism of carotenoid compounds have been identified in wheat by comparative genomics. Single nucleotide polymorphisms (SNPs) found in the coding sequences of 19 candidate genes allowed their chromosomal location and accurate map position on two reference consensus maps to be determined. The genome-wide association study based on genotyping a tetraploid wheat collection with 81,587 gene-associated SNPs validated quantitative trait loci (QTLs) previously detected in biparental populations and discovered new QTLs for grain colour-related traits. Ten carotenoid genes mapped in chromosome regions underlying pigment content QTLs indicating possible functional relationships between candidate genes and the trait.

Conclusions: The availability of linked, candidate gene-based markers can facilitate breeding wheat cultivars with desirable levels of carotenoids. Identifying QTLs linked to carotenoid pigmentation can contribute to understanding genes underlying carotenoid accumulation in the wheat kernels. Together these outputs can be combined to exploit the genetic variability of colour-related traits for the nutritional and commercial improvement of wheat products.

Keywords: Association mapping; Carotenoids genes; Flour colour; SNP; Wheat; Yellow pigments.

Fig. 1

The carotenoid metabolic/catabolic pathway (modified from Vranova [57])

Fig. 2

Phylogenetic tree of the carotenoid metabolic/catabolic genes from Arabidopsis thaliana, Brachypodium disticum, Zea mays, Oryza sativa and Triticum aestivum

Fig. 3

Schematic representation of wheat genome chromosomes. The map is a representation of A and B genome chromosomes of the durum consensus linkage map [29] and of D chromosomes of the consensus bread wheat map [28], with map positions of carotenoid candidate genes and QTLs for yellow index and yellow pigment content. Each chromosome map is represented by the first and the last SNP marker, and by a SNP marker every about 20 cM. SSR markers have been also inserted every about 20 cM to compare the consensus SNP map with published SSR-based maps. Markers are indicated on the right side and cM distances on the left side of the bar. Solid regions of the chromosome bars indicate regions identified as being significantly associated with YI and YPC in published QTL biparental mapping populations (black regions in at least two different populations, grey regions in one population). QTLs are represented by bars on the right of each chromosome bar. QTL names indicate the trait (YI for yellow index and YPC for yellow pigment content) and the population in which the QTL was detected (Col = whole collection and Dur = durum sub-population); the closest SNP marker is indicated in red. Carotenoid genes are indicated after the corresponding SNP located in the gene sequence (in blue) or in the same map position of the co-migrating SNP marker located in the same contig