Originally published as Genetics Published Articles Ahead of Print on September 9, 2008.

Genetics, Vol. 180, 995-1007, October 2008, Copyright © 2008
doi:10.1534/genetics.108.092742

Genetic Redundancy in Soybean Photoresponses Associated With Duplication of the Phytochrome A Gene

Baohui Liu*, Akira Kanazawa*, Hisakazu Matsumura{dagger}, Ryoji Takahashi{ddagger}, Kyuya Harada§ and Jun Abe*,1

* Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan, {dagger} University of Tsukuba, Tsukuba, Ibaraki 305-8518, Japan, {ddagger} National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan and § National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan

1 Corresponding author: Laboratory of Plant Genetics and Evolution, Research Faculty of Agriculture, Hokkaido University, Kitaku, Kita 9 Nishi 9, Sapporo, Hokkaido 060-8589, Japan.
E-mail: jabe{at}res.agr.hokudai.ac.jp

Gene and genome duplications underlie the origins of evolutionary novelty in plants. Soybean, Glycine max, is considered to be a paleopolyploid species with a complex genome. We found multiple homologs of the phytochrome A gene (phyA) in the soybean genome and determined the DNA sequences of two paralogs designated GmphyA1 and GmphyA2. Analysis of the GmphyA2 gene from the lines carrying a recessive allele at a photoperiod insensitivity locus, E4, revealed that a Ty1/copia-like retrotransposon was inserted in exon 1 of the gene, which resulted in dysfunction of the gene. Mapping studies suggested that GmphyA2 is encoded by E4. The GmphyA1 gene was mapped to a region of linkage group O, which is homeologous to the region harboring E4 in linkage group I. Plants homozygous for the e4 allele were etiolated under continuous far red light, but the de-etiolation occurred partially, indicating that the mutation alone did not cause a complete loss of phyA function. The genetic redundancy suggests that the presence of duplicated copies of phyA genes accounts for the generation of photoperiod insensitivity, while protecting against the deleterious effects of mutation. Thus, this phenomenon provides a link between gene duplication and establishment of an adaptive response of plants to environments.