FISH mapping for physical map improvement in the large genome of barley: a case study on chromosome 2H

Abstract

Fluorescence in situ hybridization (FISH) has been an efficient way for integrating physical and genetic maps of various small genomes like rice, sorghum and Brachypodium; whereas in the large genomes like barley, the repetitive nature of the genome complicates the generation and detection of single-copy FISH probes. Here, we used exemplarily physical map contigs of a defined interval of the long arm of barley chromosome 2H to evaluate the potential of FISH-based mapping as a supportive means for genetic anchoring of the physical map and to resolve the linear order of contigs along the respective chromosome. Repeat-free FISH probes corresponding to 8 previously anchored BAC contigs were specifically allocated to chromosome 2H. This represented an almost 90% success rate in single-copy FISH probe development. FISH mapping of contigs located in the subtelomeric region revealed an over-performance of genetic mapping over FISH for physical map anchoring.