Subfunctionalization, neofunctionalization, and nonfunctionalization of the four soybean phytochrome A genes.

Gene duplication generates new genes, which retain their original function or undergo subfunctionalization, neofunctionalization, or nonfunctionalization. The phytochrome A (PHYA) genes in soybean (Glycine max) have undergone duplication to produce GmPHYA1, GmPHYA2 (E4), GmPHYA3 (E3), and GmPHYA4, each with distinct evolutionary fates. Using genetic and biochemical analyses, we discovered that GmPHYA1 has undergone subfunctionalization and is essential for regulating photomorphogenesis and plant height in soybean. GmPHYA2 has experienced both subfunctionalization and neofunctionalization, as it regulates flowering time under far red-enriched light and red-enriched light. GmPHYA3 has undergone neofunctionalization; despite losing some ancestral functions, it has gained two characteristics not observed in Arabidopsis thaliana PHYA: protein stability in red light and regulation of flowering-time under red-enriched light. GmPHYA4, which lacks a key phyA domain and has lost all functionality, is considered a pseudogene. These findings demonstrate the varied outcomes of the duplication of soybean GmPHYA genes.