Radiation hybrid map of barley chromosome 3H

Authors: MAZAHERI, MONA - North Dakota State University; KIANIAN, PENNY - University Of Minnesota; KUMAR, AJAY - North Dakota State University; MERGOUM, MOHAMED - North Dakota State University; SEETAN, RAED - North Dakota State University; SOLTANI, ALI - North Dakota State University; LUND, LUCY - North Dakota State University; PIRSEYEDI, SEYED - North Dakota State University; DENTON, ANNE - North Dakota State University; Kianian, Shahryar

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/26/2015
Publication Date: 7/10/2015
Publication URL: http://doi: 10.3835/plantgenome2015.02.0005
Citation: Mazaheri, M., Kianian, P., Kumar, A., Mergoum, M., Seetan, R., Soltani, A., Lund, L., Pirseyedi, S., Denton, A., Kianian, S. 2015. Radiation hybrid map of barley chromosome 3H. The Plant Genome. 8(2):1-11.

Interpretive Summary: Barley is a model plant in genomic studies of Triticeae species. Assembly of the barley genome is complicated by its large size and proportion of repetitive elements. This process is facilitated by high resolution maps for aligning BAC contigs along chromosomes. Available genetic maps; however, do not provide accurate information on the physical position of a large portion of the genome located in recombination-poor regions. Radiation hybrid (RH) mapping is an alternative approach. In this approach a chromosome is broken into random fragments using radiation. Then, the presence or absence of a marker is screened to generate a radiation hybrid population. Markers can be genes or any simple short fragments of DeoxyriboNucleic Acid (DNA) sequence that appear only once in the genome. In this manuscript we describe the development of a RH map for chromosome 3 of barley (3H), which had a total of 9.53X higher resolution than an analogous genetic map, reaching a maximum of >262.40X resolution in regions around the centromere. It was estimated that the map resolution can be improved to an average of 30.34 Kb by saturating the 3H-RH map with molecular markers. The generated RH panel enabled alignment of BAC and sequence contigs as small as 1.50 Kb in size. The high resolution and the coverage of poor-recombination regions make RH maps an ideal resource for barley genome assembly, as well as other genetic studies.

Technical Abstract: Assembly of the barley genome is complicated by its large size (5.1 Gb) and proportion of repetitive elements (84%). This process is facilitated by high resolution maps for aligning BAC contigs along chromosomes. Available genetic maps; however, do not provide accurate information on the physical position of a large portion of the genome located in recombination-poor regions. Radiation hybrid (RH) mapping is an alternative approach, which is based on radiation-induced deletions along the length of chromosomes. In this study, the first RH map for barley chromosome 3H was developed. In total 373 in vivo RH lines were generated by irradiating wheat-barley chromosome 3H addition lines and crossing them to a normal wheat cultivar. Each RH informative line (containing deletions) had on average three deletions. The induced deletion size varied from 36.58 Kb to 576.00 Mb, with an average length of 52.42 Mb. This initial 3H-RH map had a total of 9.53X higher resolution than an analogous genetic map, reaching a maximum of >262.40X resolution in regions around the centromere. The final RH map was 3,066.1 cR in length, with a 0.76 Mb resolution. It was estimated that the map resolution can be improved to an average of 30.34 Kb by saturating the 3H-RH map with molecular markers. The generated RH panel enabled alignment of BAC and sequence contigs as small as 1.50 Kb in size. The high resolution and the coverage of poor-recombination regions make RH maps an ideal resource for barley genome assembly, as well as other genetic studies.