PHENOTYPE-BASED CLONING IN BARLEY: COMING OF AGE

¹ Dept. Crop and Soil Sciences & School of Molecular Biosciences, Washington State University, Pullman, WA, 99164-6420, USA

Map-based cloning in barley has a brief and recent history. The published work will be reviewed. In my laboratory, the traditional high-resolution genetic mapping and BAC contig development resulted in cloning of the stem rust resistance gene Rpg1 and the candidate genes for rpg4 and RpgQ. Synteny with rice provided valuable markers, but chromosome walking was required to close the BAC contig (Druka poster). A saturation mapping approach, employing low-resolution genetic mapping combined with physical mapping, was attempted. Synteny with rice was again used. While the region of interest was highly saturated with genetic markers, the identified BAC clones failed to form a contig around the gene of interest, in this case the spot blotch resistance gene Rcs5. Chromosome walking was employed to close the contig (K. Johnson poster). The examples of barley genes cloned by the map-based approach indicate feasibility, but required extensive work and a bit of luck. They also illustrate the usefulness and limitations of rice synteny. A third approach was opened by the development of the 22,700-gene Affymetrix Barley1 gene chip. We used the Barley1 chip to compare gene expression levels in a fast neutron induced mutant and its parent cultivar Morex (L. Zhang poster). Three candidate genes were identified by highly down-regulated gene expression. Low-resolution mapping should differentiate among genes down-regulated because of limited transcription of the gene of interest and chance mutations elsewhere in the genome or down-stream effects. Future prospects and limitations of phenotype-based cloning in barley will be discussed.