Abstract
Violaxanthin de-epoxidase (VDE) has a critical role in the carotenoid biosynthesis pathway, which is involved in protecting the photosynthesis apparatus from damage caused by excessive light. Here, a VDE gene in maize, ZmVDE1, was cloned and shown to have functional domains in common with the gramineous VDE protein. Candidate gene association analysis indicated that no polymorphic sites in ZmVDE1 were significant association with any of the examined carotenoid-related traits at P = 0.05 in an association panel containing 155 maize inbred lines. Nucleotide diversity analysis of VDE1 in maize and teosinte indicated that its exon had less genetic variation, consistent with the conserved function of VDE1 in plants. In addition, dramatically reduced nucleotide diversity, fewer haplotypes and a significantly negative parameter deviation for Tajima’s D test of ZmVDE1 in maize and teosinte suggested that a potential selective force had acted across the ZmVDE1 locus. We further identified a 4.2 Mb selective sweep with low recombination surrounding the ZmVDE1 locus that resulted in severely reduced nucleotide diversity on chromosome 2. Collectively, natural selection and the conserved domains of ZmVDE1 might show an important role in the xanthophyll cycle of the carotenoid biosynthesis pathway.
Highlights
Crop domestication and breeding, which have been ongoing for > 10,000 years, represent evolutionary experiments that have radically altered wild species to meet human needs (Hufford et al, 2012)
To determine the expression level of ZmVDE1, 557,955 polymorphic sites with a minor allele frequency (MAF) ≥0.05 and missing rate
Using the expression levels of ZmVDE1, we looked for expression quantitative trait loci (QTL) and analyzed their correlations with carotenoid content
Summary
Crop domestication and breeding, which have been ongoing for > 10,000 years, represent evolutionary experiments that have radically altered wild species to meet human needs (Hufford et al, 2012). The dramatic morphological changes from teosinte to maize likely involved alterations in only a few significant genes with large effects (Tian et al, 2009). Teosinte branched (tb1), which was a major contributor to the increase in apical dominance during maize domestication, has been successfully cloned (Doebley et al, 1995, 1997; Wang et al, 1999). A few genes underwent a process of genetic modification to meet the needs of humans, including an increase in harvestable yield and better kernel quality (Tian et al, 2009). Four of the six genes involved in the starch biosynthesis pathway show evidence of selection (Whitt et al, 2002)
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