Molecular mapping, chromosomal assignment, and genetic diversity analysis of phytochrome loci in barley (Hordeum vulgare)

Phytochromes belong to a family of photoreceptors that perceive, interpret, and translate light signals that effect plant growth and development. The objectives of this study were to use a heterologous phytochrome cDNA probe from oat to (1) identify phytochrome loci in barley, (2) determine the chromosomal and genomic location of phytochrome gene(s) in barley, and (3) assess the extent of genetic variation at phytochrome loci in cultivated barley (Hordeum vulgare). Restriction fragment length polymorphism (RFLP) analysis detected four distinct phytochrome loci in barley, arbitrarily designated phy1, phy2, phy3, and phy4. Wheat-barley addition line analysis indicated that phy1, phy2, and phy3 are located on barley chromosomes 7, 4, and 5, respectively, while phy4 represents duplicate loci located on barley chromosomes 2 and 7. Linkage mapping confirmed our results using wheat-barley addition line analysis and located the phy1 and phy3 loci to the short arm of barley chromosome 7 and to the centromeric region of barley chromosome 5, respectively. Two to three alleles were detected at each of the five phytochrome loci examined. Genetic diversity values for the phytochrome loci were near previous estimates for RFLPs. Division of the barley samples based on spike morphology indicated that the revel of diversity in two- and six-rowed barley is about equal, although significant differences in allelic frequencies were detected between the subgroups.