A large-scale pedigree resource of wheat reveals evidence for adaptation and selection by breeders

Nick Fradgley, Keith Gardner, James Cockram, James Elderfield, John Hickey, Phil Howell, Rob Jackson, IM Mackay

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Information on crop pedigrees can be used to help maximise genetic gain in crop breeding and allow efficient management of genetic resources. We present a pedigree resource of 2,657 wheat (Triticum aestivum L.) genotypes originating from 38 countries, representing more than a century of breeding and variety development. Visualisation of the pedigree enables illustration of the key developments in United Kingdom wheat breeding, highlights the wide genetic background of the UK wheat gene pool, and facilitates tracing the origin of beneficial alleles. A relatively high correlation between pedigree- and marker-based kinship coefficients was found, which validated the pedigree and enabled identification of errors in the pedigree or marker data. Using simulations with a combination of pedigree and genotype data, we found evidence for significant effects of selection by breeders. Within crosses, genotypes are often more closely related than expected by simulations to one of the parents, which indicates selection for favourable alleles during the breeding process. Selection across the pedigree was demonstrated on a subset of the pedigree in which 110 genotyped varieties released before the year 2000 were used to simulate the distribution of marker alleles of 45 genotyped varieties released after the year 2000, in the absence of selection. Allelic diversity in the 45 varieties was found to deviate significantly from the simulated distributions at a number of loci, indicating regions under selection over this period. The identification of one of these regions as coinciding with a strong yield component quantitative trait locus (QTL) highlights both the potential of the remaining loci as wheat breeding targets for further investigation, as well as the utility of this pedigree-based methodology to identify important breeding targets in other crops. Further evidence for selection was found as greater linkage disequilibrium (LD) for observed versus simulated genotypes within all chromosomes. This difference was greater at shorter genetic distances, indicating that breeder selections have conserved beneficial linkage blocks. Collectively, this work highlights the benefits of generating detailed pedigree resources for crop species. The wheat pedigree database developed here represents a valuable community resource and will be updated as new varieties are released at https://www.niab.com/pages/id/501/UK_Wheat_varieties_Pedigree.
Original languageEnglish
Article numbere3000071
Number of pages20
JournalPLoS Biology
Volume17
Issue number2
Early online date28 Feb 2019
DOIs
Publication statusFirst published - 28 Feb 2019
Externally publishedYes

Fingerprint

Pedigree
pedigree
Triticum
Crops
wheat
Breeding
Chromosomes
Genotype
breeding
Visualization
Genes
genotype
Alleles
alleles
crops
Gene Pool
loci
Quantitative Trait Loci
kinship
Linkage Disequilibrium

Keywords

  • pedigree
  • wheat
  • plant breeding

Cite this

Fradgley, Nick ; Gardner, Keith ; Cockram, James ; Elderfield, James ; Hickey, John ; Howell, Phil ; Jackson, Rob ; Mackay, IM. / A large-scale pedigree resource of wheat reveals evidence for adaptation and selection by breeders. In: PLoS Biology. 2019 ; Vol. 17, No. 2.
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abstract = "Information on crop pedigrees can be used to help maximise genetic gain in crop breeding and allow efficient management of genetic resources. We present a pedigree resource of 2,657 wheat (Triticum aestivum L.) genotypes originating from 38 countries, representing more than a century of breeding and variety development. Visualisation of the pedigree enables illustration of the key developments in United Kingdom wheat breeding, highlights the wide genetic background of the UK wheat gene pool, and facilitates tracing the origin of beneficial alleles. A relatively high correlation between pedigree- and marker-based kinship coefficients was found, which validated the pedigree and enabled identification of errors in the pedigree or marker data. Using simulations with a combination of pedigree and genotype data, we found evidence for significant effects of selection by breeders. Within crosses, genotypes are often more closely related than expected by simulations to one of the parents, which indicates selection for favourable alleles during the breeding process. Selection across the pedigree was demonstrated on a subset of the pedigree in which 110 genotyped varieties released before the year 2000 were used to simulate the distribution of marker alleles of 45 genotyped varieties released after the year 2000, in the absence of selection. Allelic diversity in the 45 varieties was found to deviate significantly from the simulated distributions at a number of loci, indicating regions under selection over this period. The identification of one of these regions as coinciding with a strong yield component quantitative trait locus (QTL) highlights both the potential of the remaining loci as wheat breeding targets for further investigation, as well as the utility of this pedigree-based methodology to identify important breeding targets in other crops. Further evidence for selection was found as greater linkage disequilibrium (LD) for observed versus simulated genotypes within all chromosomes. This difference was greater at shorter genetic distances, indicating that breeder selections have conserved beneficial linkage blocks. Collectively, this work highlights the benefits of generating detailed pedigree resources for crop species. The wheat pedigree database developed here represents a valuable community resource and will be updated as new varieties are released at https://www.niab.com/pages/id/501/UK_Wheat_varieties_Pedigree.",
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Fradgley, N, Gardner, K, Cockram, J, Elderfield, J, Hickey, J, Howell, P, Jackson, R & Mackay, IM 2019, 'A large-scale pedigree resource of wheat reveals evidence for adaptation and selection by breeders', PLoS Biology, vol. 17, no. 2, e3000071. https://doi.org/10.1371/journal.pbio.3000071

A large-scale pedigree resource of wheat reveals evidence for adaptation and selection by breeders. / Fradgley, Nick; Gardner, Keith; Cockram, James; Elderfield, James; Hickey, John; Howell, Phil; Jackson, Rob; Mackay, IM.

In: PLoS Biology, Vol. 17, No. 2, e3000071, 28.02.2019.

Research output: Contribution to journalArticleResearchpeer-review

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Fradgley N, Gardner K, Cockram J, Elderfield J, Hickey J, Howell P et al. A large-scale pedigree resource of wheat reveals evidence for adaptation and selection by breeders. PLoS Biology. 2019 Feb 28;17(2). e3000071. https://doi.org/10.1371/journal.pbio.3000071