Genome-wide association analysis of grain yield-associated traits in a pan-European barley cultivar collection

Xin Xu; Rajiv Sharma; Allessandro Tondelli; Joanne Russell; Jordi Comadran; Klaus Pillen; Florian Schnaithmann; Benjamin Kilian; Luigi Cattivelli; William T. B. Thomas; Andrew J. Flavell

doi:10.3835/plantgenome2017.08.0073

Genome-wide association analysis of grain yield-associated traits in a pan-European barley cultivar collection

Xin Xu, Rajiv Sharma, Allessandro Tondelli, Joanne Russell, Jordi Comadran, Klaus Pillen, Florian Schnaithmann, Benjamin Kilian, Luigi Cattivelli, William T. B. Thomas, Andrew J. Flavell (Lead / Corresponding author)

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Abstract

A collection of 379 Hordeum vulgare cultivars, comprising all combinations of spring and winter growth habits with 2 and 6 row ear type, was screened by genome wide association analysis to discover alleles controlling traits related to grain yield. Genotypes were obtained at 6810 segregating gene-based SNP loci and corresponding field trial data were obtained for ten traits related to grain yield at four European sites in three countries over two growth years. The combined data were analysed and statistically significant associations between the traits and regions of the barley genomes were obtained. Combining this information with the high resolution gene map for barley allowed the identification of candidate genes underlying all scored traits and superposition of this information with the known genomics of grain trait genes in rice resulted in the assignation of 13 putative barley genes controlling grain traits in European cultivated barley. Several of these genes are associated with grain traits in both winter and spring barley.

Original language	English
Article number	170073
Pages (from-to)	1-11
Number of pages	11
Journal	Plant Genome
Volume	11
Issue number	1
DOIs	https://doi.org/10.3835/plantgenome2017.08.0073
Publication status	Published - 25 Jan 2018

Keywords

Europe
Genome-Wide Association Study
Genotype
Hordeum/genetics
Plant Proteins/genetics
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Seeds/genetics

ASJC Scopus subject areas

Genetics
Agronomy and Crop Science
Plant Science

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10.3835/plantgenome2017.08.0073Licence: CC BY

Final Published Version
© Crop Science Society of America. This is an open access article distributed under the CC BY license (https://creativecommons.org/licenses/by/4.0/).
Final published version, 1.13 MBLicence: CC BY

Cite this

@article{5f6618fe60684db0be2a613bb314f834,

title = "Genome-wide association analysis of grain yield-associated traits in a pan-European barley cultivar collection",

abstract = "A collection of 379 Hordeum vulgare cultivars, comprising all combinations of spring and winter growth habits with 2 and 6 row ear type, was screened by genome wide association analysis to discover alleles controlling traits related to grain yield. Genotypes were obtained at 6810 segregating gene-based SNP loci and corresponding field trial data were obtained for ten traits related to grain yield at four European sites in three countries over two growth years. The combined data were analysed and statistically significant associations between the traits and regions of the barley genomes were obtained. Combining this information with the high resolution gene map for barley allowed the identification of candidate genes underlying all scored traits and superposition of this information with the known genomics of grain trait genes in rice resulted in the assignation of 13 putative barley genes controlling grain traits in European cultivated barley. Several of these genes are associated with grain traits in both winter and spring barley.",

keywords = "Europe, Genome-Wide Association Study, Genotype, Hordeum/genetics, Plant Proteins/genetics, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Seeds/genetics",

author = "Xin Xu and Rajiv Sharma and Allessandro Tondelli and Joanne Russell and Jordi Comadran and Klaus Pillen and Florian Schnaithmann and Benjamin Kilian and Luigi Cattivelli and Thomas, {William T. B.} and Flavell, {Andrew J.}",

note = "This work was supported by ERA-PG-funded project Exbardiv (Genomics-Assisted Analysis and Exploitation of Barley Diversity; http://www.erapg.org) and ERA-CAPS project Barley-NAM (Locating exotic genes that control agronomic traits under stress in a wild barley nested association mapping (NAM) population; http://www.eracaps.org). We thank the following persons for excellent technical assistance: Hazel Bull, Birgit Dubsky, Nadia Faccini, Heike Harms, Christiane Kehler, Richard Keith, Ute Krajewski, Leena Lohermaa, Marja-Leena Manninen, Marita Nix, Donata Pagani, Peter Schreiber, Kerstin Wolf, and the “Experimental Fields and Nurseries” and “Genome Diversity” group at IPK. We are also grateful to the following for support and discussions: Christine Hackett, Andreas Graner, Raj K. Pasam, Kerstin Neumann, and Michele Stanca. The authors declare no conflicts of interest.",

year = "2018",

month = jan,

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doi = "10.3835/plantgenome2017.08.0073",

language = "English",

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journal = "Plant Genome",

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T1 - Genome-wide association analysis of grain yield-associated traits in a pan-European barley cultivar collection

AU - Xu, Xin

AU - Sharma, Rajiv

AU - Tondelli, Allessandro

AU - Russell, Joanne

AU - Comadran, Jordi

AU - Pillen, Klaus

AU - Schnaithmann, Florian

AU - Kilian, Benjamin

AU - Cattivelli, Luigi

AU - Thomas, William T. B.

AU - Flavell, Andrew J.

N1 - This work was supported by ERA-PG-funded project Exbardiv (Genomics-Assisted Analysis and Exploitation of Barley Diversity; http://www.erapg.org) and ERA-CAPS project Barley-NAM (Locating exotic genes that control agronomic traits under stress in a wild barley nested association mapping (NAM) population; http://www.eracaps.org). We thank the following persons for excellent technical assistance: Hazel Bull, Birgit Dubsky, Nadia Faccini, Heike Harms, Christiane Kehler, Richard Keith, Ute Krajewski, Leena Lohermaa, Marja-Leena Manninen, Marita Nix, Donata Pagani, Peter Schreiber, Kerstin Wolf, and the “Experimental Fields and Nurseries” and “Genome Diversity” group at IPK. We are also grateful to the following for support and discussions: Christine Hackett, Andreas Graner, Raj K. Pasam, Kerstin Neumann, and Michele Stanca. The authors declare no conflicts of interest.

PY - 2018/1/25

Y1 - 2018/1/25

N2 - A collection of 379 Hordeum vulgare cultivars, comprising all combinations of spring and winter growth habits with 2 and 6 row ear type, was screened by genome wide association analysis to discover alleles controlling traits related to grain yield. Genotypes were obtained at 6810 segregating gene-based SNP loci and corresponding field trial data were obtained for ten traits related to grain yield at four European sites in three countries over two growth years. The combined data were analysed and statistically significant associations between the traits and regions of the barley genomes were obtained. Combining this information with the high resolution gene map for barley allowed the identification of candidate genes underlying all scored traits and superposition of this information with the known genomics of grain trait genes in rice resulted in the assignation of 13 putative barley genes controlling grain traits in European cultivated barley. Several of these genes are associated with grain traits in both winter and spring barley.

AB - A collection of 379 Hordeum vulgare cultivars, comprising all combinations of spring and winter growth habits with 2 and 6 row ear type, was screened by genome wide association analysis to discover alleles controlling traits related to grain yield. Genotypes were obtained at 6810 segregating gene-based SNP loci and corresponding field trial data were obtained for ten traits related to grain yield at four European sites in three countries over two growth years. The combined data were analysed and statistically significant associations between the traits and regions of the barley genomes were obtained. Combining this information with the high resolution gene map for barley allowed the identification of candidate genes underlying all scored traits and superposition of this information with the known genomics of grain trait genes in rice resulted in the assignation of 13 putative barley genes controlling grain traits in European cultivated barley. Several of these genes are associated with grain traits in both winter and spring barley.

KW - Europe

KW - Genome-Wide Association Study

KW - Genotype

KW - Hordeum/genetics

KW - Plant Proteins/genetics

KW - Polymorphism, Single Nucleotide

KW - Quantitative Trait Loci

KW - Seeds/genetics

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U2 - 10.3835/plantgenome2017.08.0073

DO - 10.3835/plantgenome2017.08.0073

M3 - Article

C2 - 29505630

SN - 1940-3372

VL - 11

SP - 1

EP - 11

JO - Plant Genome

JF - Plant Genome

IS - 1

M1 - 170073

ER -

Genome-wide association analysis of grain yield-associated traits in a pan-European barley cultivar collection

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