Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.)

A. Visioni, A. Tondelli, E. Francia, A. Pswarayi, M. Malosetti, J. Russell, W. Thomas, R. Waugh, N. Pecchioni, I. Romagosa, J. Comadran

Research output: Contribution to journalArticleAcademicpeer-review

45 Citations (Scopus)

Abstract

Background: Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure. Results: GWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress Conclusions: Haplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance
Original languageEnglish
Article number424
Number of pages13
JournalBMC Genomics
Volume14
DOIs
Publication statusPublished - 2013

Fingerprint

Hordeum
Single Nucleotide Polymorphism
Genome
Genome-Wide Association Study
Gene Pool
Linkage Disequilibrium
Spain
Haplotypes
Italy
Population
Chromosomes
Genotype
Economics
Phenotype

Keywords

  • low-temperature tolerance
  • linkage disequilibrium
  • freezing tolerance
  • gene family
  • locus
  • vernalization
  • population
  • winterhardiness
  • components
  • adaptation

Cite this

Visioni, A., Tondelli, A., Francia, E., Pswarayi, A., Malosetti, M., Russell, J., ... Comadran, J. (2013). Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.). BMC Genomics, 14, [424]. https://doi.org/10.1186/1471-2164-14-424
Visioni, A. ; Tondelli, A. ; Francia, E. ; Pswarayi, A. ; Malosetti, M. ; Russell, J. ; Thomas, W. ; Waugh, R. ; Pecchioni, N. ; Romagosa, I. ; Comadran, J. / Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.). In: BMC Genomics. 2013 ; Vol. 14.
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abstract = "Background: Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure. Results: GWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress Conclusions: Haplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance",
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Visioni, A, Tondelli, A, Francia, E, Pswarayi, A, Malosetti, M, Russell, J, Thomas, W, Waugh, R, Pecchioni, N, Romagosa, I & Comadran, J 2013, 'Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.)' BMC Genomics, vol. 14, 424. https://doi.org/10.1186/1471-2164-14-424

Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.). / Visioni, A.; Tondelli, A.; Francia, E.; Pswarayi, A.; Malosetti, M.; Russell, J.; Thomas, W.; Waugh, R.; Pecchioni, N.; Romagosa, I.; Comadran, J.

In: BMC Genomics, Vol. 14, 424, 2013.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.)

AU - Visioni, A.

AU - Tondelli, A.

AU - Francia, E.

AU - Pswarayi, A.

AU - Malosetti, M.

AU - Russell, J.

AU - Thomas, W.

AU - Waugh, R.

AU - Pecchioni, N.

AU - Romagosa, I.

AU - Comadran, J.

PY - 2013

Y1 - 2013

N2 - Background: Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure. Results: GWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress Conclusions: Haplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance

AB - Background: Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure. Results: GWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress Conclusions: Haplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance

KW - low-temperature tolerance

KW - linkage disequilibrium

KW - freezing tolerance

KW - gene family

KW - locus

KW - vernalization

KW - population

KW - winterhardiness

KW - components

KW - adaptation

U2 - 10.1186/1471-2164-14-424

DO - 10.1186/1471-2164-14-424

M3 - Article

VL - 14

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 424

ER -

Visioni A, Tondelli A, Francia E, Pswarayi A, Malosetti M, Russell J et al. Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.). BMC Genomics. 2013;14. 424. https://doi.org/10.1186/1471-2164-14-424