Structure, organization and evolution around the Hd1 quantitative trait locus controlling heading date in Oryza
Abstract
We sequenced an orthologous Hd1 QTL region in 10 Oryza species in order to determine the evolutionary forces acting on this region in a relatively short time frame (∼22 MY). Our observations reveal high gene colinearity among the species despite length differences of the overall region due mostly to LTR-retrotransposons. These observations are well supported by parallel observations by others at the adh1/adh2, and sh2/a1 loci in grass species. Unexpectedly, the gene underlying the Hd1 QTL in at least one species was transposed leading to questions about its function in that species. In two of the species, mutations in the Hd1 gene suggested an inactive protein or the possibility of an alternative protein form in these species. Further tests need to be done to determine if these are functional Hd1 alleles that contribute to flowering time. In addition to the dynamics of Hd1, a possible gene duplication and truncation event predating the divergence within the Oryza was found in this region. A low Ka/Ks ratio for all the genes in this region indicated that the Hd1 region was under strong purifying selection. Overall, these results suggest that if other genomic regions are similar in the conservation of genes across the Oryza genomes, then this is an exceptional system for the study of genetic variation at specific loci across species. This platform can then be quickly launched to clone and/or introgress potentially valuable agricultural genes.
Degree
Ph.D.
Advisors
Jackson, Purdue University.
Subject Area
Plant sciences|Bioinformatics
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