Characterization of phytoene synthase 1 gene (Psy1) located on common wheat chromosome 7A and development of a functional marker

Abstract

Phytoene synthase (Psy), a critical enzyme in the carotenoid biosynthetic pathway, demonstrated high association with the yellow pigment (YP) content in wheat grain. Characterization of Psy genes and the development of functional markers for them are of importance for marker-assisted selection in wheat breeding. In this study, the full-length genomic DNA sequence of a Psy gene (Psy-A1) located on chromosome 7A, was characterized by in silico cloning and experimental validation. The cloned Psy-A1 comprises six exons and five introns, 4,175 bp in total, and an ORF of 1,284 bp. A co-dominant marker, YP7A, was developed based on polymorphisms of two haplotypes of Psy-A1, yielding 194 and 231-bp fragments in cultivars with high and low YP content, respectively. The marker YP7A was mapped on chromosome 7AL using an RIL population from cross PH82-2/Neixing 188, and a set of Chinese Spring nullisomic-tetrasomic lines and ditelosomic line 7AS. Psy-A1, co-segregating with the STS marker YP7A, was linked to SSR marker Xwmc809 on chromosome 7AL with a genetic distance of 5.8 cM, and explained 20-28% of the phenotypic variance for YP content across three environments. A total of 217 Chinese wheat cultivars and advanced lines were used to validate the association between the polymorphic band pattern and grain YP content. The results showed that the functional marker YP7A was closely related to grain YP content and, therefore, could be used in wheat breeding programs targeting of YP content for various wheat-based products.

Association between allelic variation at the Phytoene synthase 1 gene and yellow pigment content in the wheat grain

“…An additional 37-bp insertion in the second exon of PSY-A1 has been recently reported in several Chinese common wheat varieties (He et al 2008). This insertion, which is absent in CS or the durum wheat varieties analyzed here, is associated with reduced levels of GYPC.…”

The colours of durum wheat: a review

“…The genes coding for PSY were mapped to the chromosome 7 groups by Pozniak et al (2007); in particular, the Psy-B1 locus co-segregated with a QTL on chromosome 7B, which demonstrated an association between the position of this gene and part of the phenotypic variation for endosperm colour (Pozniak et al 2007;Roncallo et al 2012). Similarly, Psy-A1, located on chromosome 7A, showed a co-dominant marker based on polymorphisms between two Psy-A1 haplotypes that explained 20-28% of the phenotypic variance for YPC across three environments (He et al 2008). Positive associations were found between YPC and the Psy1-A1o allele in a collection of 93 cultivars of durum wheat and in a recombinant inbred line population (Singh et al 2009), with the Psy-A1t allele in a panel of 30 Australian lines of bread wheat and Psy-A1p allele in the segregating population Ajana  WAWHT2074, in which the locus controls 32-36% of the observed variability for the trait (Howitt et al 2009;Crawford et al 2011).…”

“…The PSY are also considered as the ratelimiting enzymes for this pathway, and the PSY1 enzymes, in particular, are required for carotenoid accumulation by the endosperm (Gallagher et al 2004;Li et al 2008). Almost 50 different alleles have been identified at the Psy-A1 and Psy-B1 loci in different species of wheat (He et al 2008(He et al , 2009aHowitt et al 2009;Singh et al 2009;Wang et al 2009;Crawford et al 2011;Ravel et al 2013) (Table 1). The genes coding for PSY were mapped to the chromosome 7 groups by Pozniak et al (2007); in particular, the Psy-B1 locus co-segregated with a QTL on chromosome 7B, which demonstrated an association between the position of this gene and part of the phenotypic variation for endosperm colour (Pozniak et al 2007;Roncallo et al 2012).…”

Cloning and allelic variation of two novel catalase genes (SoCAT-1andSsCAT-1) inSaccharum officinarumL. andSaccharum spontaneumL.

“…[22] However, some allelic variations occur in introns and have no influence on the protein-coding sequence of the gene. [23] Introns may affect the gene transcript by modulating alternative splicing. [24] In some genes, insertion/deletion changes in introns may result in changes in the enzymatic activity and thus, in the phenotype.…”