An improved consensus linkage map of barley based on flow-sorted chromosomes and SNP markers

Authors: MUNOZ-AMATRIAIN, MARIA - University Of Minnesota; MOSCOU, MATTHEW - Sainsbury Laboratory; BHAT, PRASANNA - University Of California; SVENSSON, JAN - University Of California; BARTOS, JAN - Academy Of Science Of Czech Republic; SUCHANKOVA, PAVLA - Academy Of Science Of Czech Republic; SIMKOVA, HANA - Palacky University; ENDO, TAKASHI - Kyoto University; FENTON, RAYMOND - University Of California; LONARDI, STEFANO - University Of California; CASTILLO, ANA - Consejo Superior De Investigaciones Cientificas (CSIC); Chao, Shiaoman; CISTUE, LUIS - Oregon State University; CUESTA-MARCOS, ALFONSO - Oregon State University; FORREST, KERRIE - Department Of Primary Industries; HAYDEN, MATTHEW - Department Of Primary Industries; HAYES, PATRICK - Oregon State University; HORSLEY, RICHARD - North Dakota State University; MOODY, DAVID - Intergrain Pty Ltd; SATO, KAZUHIRO - Okayama University; VALLES, MARIA - Consejo Superior De Investigaciones Cientificas (CSIC); WULFF, BRANDE - Sainsbury Laboratory; MUEHLBAUER, GARY - University Of Minnesota; DOLEZEL, JAROSLAV - Academy Of Science Of Czech Republic; CLOSE, TIMOTHY - University Of California

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/25/2011
Publication Date: 11/21/2011
Citation: Munoz-Amatriain, M., Moscou, M.J., Bhat, P.R., Svensson, J.T., Bartos, J., Suchankova, P., Simkova, H., Endo, T.R., Fenton, R.D., Lonardi, S., Castillo, A.M., Chao, S., Cistue, L., Cuesta-Marcos, A., Forrest, K., Hayden, M.J., Hayes, P.M., Horsley, R.D., Moody, D., Sato, K., Valles, M.P., Wulff, B.B., Muehlbauer, G.J., Dolezel, J., Close, T.J. 2011. An improved consensus linkage map of barley based on flow-sorted chromosomes and SNP markers. The Plant Genome. 4:238-239.

Interpretive Summary: Recent advances in high-throughput genotyping capable of assaying high density DNA markers have made it easier to combine information obtained from different genetic mapping studies. Using the same high density genotyping platform, individual genetic maps generated in different studies utilizing different genetic materials can be merged into consensus genetic maps, which provide increased DNA marker density and genome-wide marker coverage as compared to individual maps. Previously, a high density genotyping platform that assays thousands of genetic variants at single nucleotide positions, known as single nucleotide polymorphisms (SNPs), was developed and used to assay 373 individuals derived from four mapping populations in barley (Hordeum vulgare L.). This led to the construction of a consensus genetic map with 2,943 SNPs anchored on all seven barley chromosomes. In this work, we add data from six additional populations and more individuals from one of the original populations to develop an improved consensus map based on 1,133 individuals. A stringent and systematic data analysis of each of the ten populations was performed to achieve uniformity. This involved re-examination of the four populations included in the previous map. As a consequence, we present a robust genetic consensus map containing 2,994 SNP positions partitioned into 1,163 distinct genetic loci. To further confirm the physical locations of these genetically mapped SNP markers, we used flow-sorting techniques that sort and separate individual barley chromosomes and chromosome arms. The availability of wheat-barley addition line stocks each having a single barley chromosome or chromosome arm added to the wheat background readily facilitated such a flow-sorting task. Results from genotyping these sorted chromosome arms using the same high density SNP marker platform have assigned 2,930 SNP positions, and confirmed the chromosome or arm position of 2,545 genetically mapped SNP positions. The new consensus map has improved marker order and increased map resolution by almost 20 percent. The outcomes of increased precision will enable more optimized SNP marker selection for various genetic and breeding applications.

Technical Abstract: Recent advances in high-throughput genotyping have made it easier to combine information from different mapping populations into consensus genetic maps, which provide increased marker density and genome coverage compared to individual maps. Previously, a SNP-based genotyping platform was developed and used to genotype 373 individuals in four barley (Hordeum vulgare L.) mapping populations. This led to a 2,943-SNP consensus genetic map with 975 unique positions. In this work, we add data from six additional populations and more individuals from one of the original populations to develop an improved consensus map from 1,133 individuals. A stringent and systematic analysis of each of the ten populations was performed to achieve uniformity. This involved re-examination of the four populations included in the previous map. As a consequence, we present a robust genetic consensus map that contains 2,994 SNP loci mapped to 1,163 unique positions. The map spans 1,137.3 cM with an average density of one marker bin per 0.99 cM. A novel application of the genotyping platform to gene detection assigned 2,815 genes to flow-sorted chromosomes or arms, confirmed the position of 2,513 SNP-mapped loci, added chromosome or arm allocations to an additional 300 SNP loci and delineated peri-centromeric regions for chromosomes 2H-7H. Marker order has been improved and map resolution has been increased by almost 20 percent. These increased-precision outcomes enable more optimized SNP selection for marker-assisted breeding, buttress association genetic analysis, assist map-based cloning and will improve the anchoring of DNA sequence scaffolds and the barley physical map to the genetic map.