The present invention includes modified phytochrome A (PHYA) nucleic acid molecules in which Pr absorption spectra have been shifted to longer wavelength (i.e. bathochromism or red-shift). The plants with the bathochromic phytochromes are expected to respond to canopy and shade conditions for growth and development with greater efficiency than the plants with wild-type phytochrome (i.e. suppression of shade avoidance reactions in plants). Since the shade avoidance reactions in plants induce a rapid and dramatic increase in the extension growth of stems and petioles at the expense of leaf growth, storage organ production, and reproductive development, it causes significant losses of crop yields. Thus, the bathochromic phytochromes that utilize the shade light efficiently would suppress the shade avoidance reactions in plants, giving plants the tolerance to shade. In this invention, several bathochromic phytochromes were generated by site-directed mutagenesis in the region of bilin lyase domain in plant PHYA, and their ability to suppress the shade avoidance reactions were examined by transforming the bathochromic phytochromes into PHYA deficient Arabidopsis thaliana (ecotype col-0). The transgenic plants with the bathochromic phytochromes showed significantly increased shade tolerance compared to wild-type plants and transgenic plants with wild-type phytochromes. Therefore, the present invention can be utilized to suppress plants' shade avoidance that is one of major causes to induce crop-yield losses, and ultimately to generate shade tolerant plants with higher yields. The invention also includes plants having at least one cell expressing the modified PHYA, vectors comprising at least one portion of the modified PHYA nucleic acids, and methods using such vectors for producing plants with shade tolerance.


> Parallel Polymer Sequencing Methods

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