ARS | Publication request: Nucelotide Diversity and Molecular Evolution of the PSY1 Gene in Zea mays Compared to some Other Grass Species

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 10, 2009
Publication Date: January 1, 2010
Citation: Fu, Z.Y., Yan, J.B., Zheng, Y.P., Warburton, M.L., Crouch, J.H., Li, J.S. 2010. Nucelotide Diversity and Molecular Evolution of the PSY1 Gene in Zea mays Compared to some Other Grass Species. Theoretical and Applied Genetics. 120:709-720.

Interpretive Summary: The PSY1 gene encodes and enzyme, phytoene synthase,is known to be important in the production of plant carotenoids, including the necessary components of Vitamin A biosynthesis in the human body. To improve the nutritional quality of cereal grains,we wished to understand the structure of the DNA sequence of this gene in various grass species, especially the most economically important, maize, including its wild ancestor, teosinte, the wild related grasses tripsacum and coix, and other economically important species including sorghum and rice. The evolution of the gene in these different species is explained in this paper.

Technical Abstract: Phytoene synthase is the first rate-limiting enzyme in the plant carotenoid biosynthetic pathway, and is encoded by the phytoene synthase 1 (PSY1) gene. To examine the genetic diversity and pattern of evolution of PSY1 within the Andropogoneae, sequences of 76 accessions from 5 species (including maize, teosinte, tripsacum, coix, and sorghum) of the Andropogoneae were analyzed, along with 4 accessions of rice (Oryza sativa L.) included as outliers. Both number and order of exons and introns were relatively conserved, with six exons and five introns. Three conserved domains were identified in the Andropogoneae coding sequence, including a signal peptide (SP), phytoene synthase (PSY), and a highly conserved squalene synthase (SQS) domain. Although no positive selection signal was detected on an overall coding level, the SP domain and the region upstream of the SQS-PSY domain has undergone rapid positive evolution, as evidenced by a high (>1.0) dN/dS ratio. On the nucleotide level, only yellow maize has significant values for Tajima’s D (-2.35) and HKA (P=0.0000), showing strong selection on the PSY1 gene, especially in the 5’ untranslated region. Tajima’s D test for distinct regions indicates that selection has occurred on regulatory regions and the 3’ untranslated region of white maize, possibly caused by balancing selection. The full length of PSY1-like sequences was used to construct a phylogenetic tree, which supports the theory that the Andropogoneae is monophyletic and Zea has a much closer relationship with Tripsacum than with the other Andropogoneae. Coix, which has been theorized to have a closer relationship with maize due to similarities in morphology and chromosome number, has been shown in this study to have diverged relatively early from the other Andropogoneae, including maize.