An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

María Muñoz-Amatriaín; Matthew J. Moscou; Prasanna R. Bhat; Jan T. Svensson; Jan Bartoš; Pavla Suchánková; Hana Šimková; Takashi R. Endo; Raymond D. Fenton; Stefano Lonardi; Ana M. Castillo; Shiaoman Chao; Luis Cistué; Alfonso Cuesta-Marcos; Kerrie L. Forrest; Matthew J. Hayden; Patrick M. Hayes; Richard D. Horsley; Kihara Makoto; David Moody; Kazuhiro Sato; María P. Vallés; Brande B.H. Wulff; Gary J. Muehlbauer; Jaroslav Doležel; Timothy J. Close

doi:10.3835/plantgenome2011.08.0023

An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

María Muñoz-Amatriaín, Matthew J. Moscou, Prasanna R. Bhat, Jan T. Svensson, Jan Bartoš, Pavla Suchánková, Hana Šimková, Takashi R. Endo, Raymond D. Fenton, Stefano Lonardi, Ana M. Castillo, Shiaoman Chao, Luis Cistué, Alfonso Cuesta-Marcos, Kerrie L. Forrest, Matthew J. Hayden, Patrick M. Hayes, Richard D. Horsley, Kihara Makoto, David MoodyKazuhiro Sato, María P. Vallés, Brande B.H. Wulff, Gary J. Muehlbauer, Jaroslav Doležel, Timothy J. Close^*

^*Corresponding author for this work

Plant Science

Research output: Contribution to journal › Article › peer-review

115 Scopus citations

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 single nucleotide polymorphism (SNP)-based genotyping platform was developed and used to genotype 373 individuals in four barley (Hordeum vulgare L.) mapping populations. This led to a 2943 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 1133 individuals. A stringent and systematic analysis of each of the 10 populations was performed to achieve uniformity. This involved reexamination of the four populations included in the previous map. As a consequence, we present a robust consensus genetic map that contains 2994 SNP loci mapped to 1163 unique positions. The map spans 1137.3 cM with an average density of one marker bin per 0.99 cM. A novel application of the genotyping platform for gene detection allowed the assignment of 2930 genes to flow-sorted chromosomes or arms, confirmed the position of 2545 SNP-mapped loci, added chromosome or arm allocations to an additional 370 SNP loci, and delineated pericentromeric regions for chromosomes 2H to 7H. Marker order has been improved and map resolution has been increased by almost 20%. These increased precision outcomes enable more optimized SNP selection for marker-assisted breeding and support association genetic analysis and map-based cloning. It will also improve the anchoring of DNA sequence scaffolds and the barley physical map to the genetic map.

Original language	English (US)
Article number	PLANTGENOME2011080023
Journal	Plant Genome
Volume	4
Issue number	3
DOIs	https://doi.org/10.3835/plantgenome2011.08.0023
State	Published - Nov 2011

ASJC Scopus subject areas

Genetics
Agronomy and Crop Science
Plant Science

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Muñoz-Amatriaín, M., Moscou, M. J., Bhat, P. R., Svensson, J. T., Bartoš, J., Suchánková, P., Šimková, H., Endo, T. R., Fenton, R. D., Lonardi, S., Castillo, A. M., Chao, S., Cistué, L., Cuesta-Marcos, A., Forrest, K. L., Hayden, M. J., Hayes, P. M., Horsley, R. D., Makoto, K., ... Close, T. J. (2011). An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers. Plant Genome, 4(3), Article PLANTGENOME2011080023. https://doi.org/10.3835/plantgenome2011.08.0023

@article{2f0ffbfbaac74151898b0bd4ce9cfbb6,

title = "An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers",

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 single nucleotide polymorphism (SNP)-based genotyping platform was developed and used to genotype 373 individuals in four barley (Hordeum vulgare L.) mapping populations. This led to a 2943 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 1133 individuals. A stringent and systematic analysis of each of the 10 populations was performed to achieve uniformity. This involved reexamination of the four populations included in the previous map. As a consequence, we present a robust consensus genetic map that contains 2994 SNP loci mapped to 1163 unique positions. The map spans 1137.3 cM with an average density of one marker bin per 0.99 cM. A novel application of the genotyping platform for gene detection allowed the assignment of 2930 genes to flow-sorted chromosomes or arms, confirmed the position of 2545 SNP-mapped loci, added chromosome or arm allocations to an additional 370 SNP loci, and delineated pericentromeric regions for chromosomes 2H to 7H. Marker order has been improved and map resolution has been increased by almost 20%. These increased precision outcomes enable more optimized SNP selection for marker-assisted breeding and support association genetic analysis and map-based cloning. It will also improve the anchoring of DNA sequence scaffolds and the barley physical map to the genetic map.",

author = "Mar{\'i}a Mu{\~n}oz-Amatria{\'i}n and Moscou, {Matthew J.} and Bhat, {Prasanna R.} and Svensson, {Jan T.} and Jan Barto{\v s} and Pavla Such{\'a}nkov{\'a} and Hana {\v S}imkov{\'a} and Endo, {Takashi R.} and Fenton, {Raymond D.} and Stefano Lonardi and Castillo, {Ana M.} and Shiaoman Chao and Luis Cistu{\'e} and Alfonso Cuesta-Marcos and Forrest, {Kerrie L.} and Hayden, {Matthew J.} and Hayes, {Patrick M.} and Horsley, {Richard D.} and Kihara Makoto and David Moody and Kazuhiro Sato and Vall{\'e}s, {Mar{\'i}a P.} and Wulff, {Brande B.H.} and Muehlbauer, {Gary J.} and Jaroslav Dole{\v z}el and Close, {Timothy J.}",

note = "Funding Information: This work was supported by the USA National Science Foundation (DBI‐0321756 to TJC and SL), the Human Frontier Science Program (LT000218/2011‐L to MJM) and Gatsby Charitable Foundation (MJM and BBHW), the Czech Ministry of Education Youth and Sports and the European Regional Development Fund (LC06004 and CZ.1.05/2.1.00/01.0007 to JD, JB, H{\v S} and PS), the Ministry of Science and Innovation of Spain (AGL2007‐62930/AGR and GEN2006‐28560), and the Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA's Cooperative State Research and Extension Service (2009‐65300‐05645 to TJC, SL and GJM). Authors thank Dr. Adam J. Lukaszewski for seeds of wheat‐barley addition lines. Publisher Copyright: {\textcopyright} 2011 The Authors.",

year = "2011",

month = nov,

doi = "10.3835/plantgenome2011.08.0023",

language = "English (US)",

volume = "4",

journal = "Plant Genome",

issn = "1940-3372",

publisher = "Crop Science Society of America",

number = "3",

}

Muñoz-Amatriaín, M, Moscou, MJ, Bhat, PR, Svensson, JT, Bartoš, J, Suchánková, P, Šimková, H, Endo, TR, Fenton, RD, Lonardi, S, Castillo, AM, Chao, S, Cistué, L, Cuesta-Marcos, A, Forrest, KL, Hayden, MJ, Hayes, PM, Horsley, RD, Makoto, K, Moody, D, Sato, K, Vallés, MP, Wulff, BBH, Muehlbauer, GJ, Doležel, J & Close, TJ 2011, 'An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers', Plant Genome, vol. 4, no. 3, PLANTGENOME2011080023. https://doi.org/10.3835/plantgenome2011.08.0023

TY - JOUR

T1 - An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

AU - Muñoz-Amatriaín, María

AU - Moscou, Matthew J.

AU - Bhat, Prasanna R.

AU - Svensson, Jan T.

AU - Bartoš, Jan

AU - Suchánková, Pavla

AU - Šimková, Hana

AU - Endo, Takashi R.

AU - Fenton, Raymond D.

AU - Lonardi, Stefano

AU - Castillo, Ana M.

AU - Chao, Shiaoman

AU - Cistué, Luis

AU - Cuesta-Marcos, Alfonso

AU - Forrest, Kerrie L.

AU - Hayden, Matthew J.

AU - Hayes, Patrick M.

AU - Horsley, Richard D.

AU - Makoto, Kihara

AU - Moody, David

AU - Sato, Kazuhiro

AU - Vallés, María P.

AU - Wulff, Brande B.H.

AU - Muehlbauer, Gary J.

AU - Doležel, Jaroslav

AU - Close, Timothy J.

N1 - Funding Information: This work was supported by the USA National Science Foundation (DBI‐0321756 to TJC and SL), the Human Frontier Science Program (LT000218/2011‐L to MJM) and Gatsby Charitable Foundation (MJM and BBHW), the Czech Ministry of Education Youth and Sports and the European Regional Development Fund (LC06004 and CZ.1.05/2.1.00/01.0007 to JD, JB, HŠ and PS), the Ministry of Science and Innovation of Spain (AGL2007‐62930/AGR and GEN2006‐28560), and the Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA's Cooperative State Research and Extension Service (2009‐65300‐05645 to TJC, SL and GJM). Authors thank Dr. Adam J. Lukaszewski for seeds of wheat‐barley addition lines. Publisher Copyright: © 2011 The Authors.

PY - 2011/11

Y1 - 2011/11

N2 - 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 single nucleotide polymorphism (SNP)-based genotyping platform was developed and used to genotype 373 individuals in four barley (Hordeum vulgare L.) mapping populations. This led to a 2943 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 1133 individuals. A stringent and systematic analysis of each of the 10 populations was performed to achieve uniformity. This involved reexamination of the four populations included in the previous map. As a consequence, we present a robust consensus genetic map that contains 2994 SNP loci mapped to 1163 unique positions. The map spans 1137.3 cM with an average density of one marker bin per 0.99 cM. A novel application of the genotyping platform for gene detection allowed the assignment of 2930 genes to flow-sorted chromosomes or arms, confirmed the position of 2545 SNP-mapped loci, added chromosome or arm allocations to an additional 370 SNP loci, and delineated pericentromeric regions for chromosomes 2H to 7H. Marker order has been improved and map resolution has been increased by almost 20%. These increased precision outcomes enable more optimized SNP selection for marker-assisted breeding and support association genetic analysis and map-based cloning. It will also improve the anchoring of DNA sequence scaffolds and the barley physical map to the genetic map.

AB - 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 single nucleotide polymorphism (SNP)-based genotyping platform was developed and used to genotype 373 individuals in four barley (Hordeum vulgare L.) mapping populations. This led to a 2943 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 1133 individuals. A stringent and systematic analysis of each of the 10 populations was performed to achieve uniformity. This involved reexamination of the four populations included in the previous map. As a consequence, we present a robust consensus genetic map that contains 2994 SNP loci mapped to 1163 unique positions. The map spans 1137.3 cM with an average density of one marker bin per 0.99 cM. A novel application of the genotyping platform for gene detection allowed the assignment of 2930 genes to flow-sorted chromosomes or arms, confirmed the position of 2545 SNP-mapped loci, added chromosome or arm allocations to an additional 370 SNP loci, and delineated pericentromeric regions for chromosomes 2H to 7H. Marker order has been improved and map resolution has been increased by almost 20%. These increased precision outcomes enable more optimized SNP selection for marker-assisted breeding and support association genetic analysis and map-based cloning. It will also improve the anchoring of DNA sequence scaffolds and the barley physical map to the genetic map.

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U2 - 10.3835/plantgenome2011.08.0023

DO - 10.3835/plantgenome2011.08.0023

M3 - Article

AN - SCOPUS:85167516304

SN - 1940-3372

VL - 4

JO - Plant Genome

JF - Plant Genome

IS - 3

M1 - PLANTGENOME2011080023

ER -

An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers

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