Abstract
An oligo-nucleotide pooled assay (OPA) for high-throughput single nucleotide polymorphism (SNP) genotyping was used for genetic map development in order to coordinate marker information from multiple mapping resources in barley. A doubled haploid (DH) population derived from the cross between barley cultivar “Haruna Nijo” (Hordeum vulgare ssp. vulgare) and wild barley strain “H602” (H. vulgare ssp. spontaneum) was genotyped with 1,448 unigene-derived OPA-SNPs. Of these, 732 markers showed polymorphisms and 384 were cross-referenced with EST markers on our high-density transcript map. The OPA-SNP markers were well distributed on barley chromosomes as follows: 1H (93), 2H (131), 3H (123), 4H (97), 5H (108), 6H (92) and 7H (88). Using a cMAP platform, it was possible to integrate EST marker positions across high-density EST maps. The OPA-SNPs were used to genotype 99 BC3F5 recombinant chromosome substitution lines (RCSLs) from the same cross (Haruna Nijo/H602). These data were used to create graphical genotypes for each line and thus estimate the location, extent, and total number of introgressions from the wild barley parent. The RCSLs sampled most of the wild barley genome, with only a few missing segments. With the resources we have developed, all QTL alleles segregating in this germplasm are now potential targets for map-based cloning.
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Acknowledgments
We would like to thank Dr. Joe Deyong, Southern California Genotyping Consortium, Illumina BeadLab, UCLA for the OPA-SNP assay; Drs. Timothy J. Close, Prasanna Bhat, Department of Botany & Plant Sciences, University of California, Riverside for basecalling of OPA assay; Drs. Hans Harudrup and Heidi Jaiser (Pajbjergfonden, Denmark) for producing the doubled haploid population; and Dr. Yukiko Yamazaki (National Institute of Genetics, Japan) for developing the cMAP resource. The project was supported by a grant from the Program of Promotion of Basic Research Activities for Innovative Biosciences.
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Communicated by A. Graner.
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122_2009_1071_MOESM1_ESM.xls
Table 1 Marker information and SNP genotypes of doubled haploid population derived form the cross between Haruna Nijo (A) and H602 (B (XLS 1633 kb)
122_2009_1071_MOESM2_ESM.xls
Table 2 SNP genotypes of a minimum set of 36 RCSLs representing H602 wild barley substituted allele (B) on the background of cv. Harun Nijo (A) (XLS 427 kb)
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Sato, K., Takeda, K. An application of high-throughput SNP genotyping for barley genome mapping and characterization of recombinant chromosome substitution lines. Theor Appl Genet 119, 613–619 (2009). https://doi.org/10.1007/s00122-009-1071-9
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DOI: https://doi.org/10.1007/s00122-009-1071-9