Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding

Rajiv Sharma, Fulvia Draicchio, Hazel Bull, Paul Herzig, Andreas Maurer, Klaus Pillen, William T.B. Thomas, Andrew J. Flavell

Research output: Contribution to journalArticle

7 Citations (Scopus)
67 Downloads (Pure)

Abstract

To explore wild barley as a source of useful alleles for yield improvement in breeding, we have carried out a genome-wide association scan using the nested association mapping population HEB-25, which contains 25 diverse exotic barley genomes superimposed on an ∼70% genetic background of cultivated barley. A total of 1420 HEB-25 lines were trialled for nine yield-related grain traits for 2 years in Germany and Scotland, with varying N fertilizer application. The phenotypic data were related to genotype scores for 5398 gene-based single nucleotide polymorphism (SNP) markers. A total of 96 quantitative trait locus (QTL) regions were identified across all measured traits, the majority of which co-localize with known major genes controlling flowering time (Ppd-H2, HvCEN, HvGI, VRN-H1, and VRN-H3) and spike morphology (VRS3, VRS1, VRS4, and INT-C) in barley. Fourteen QTL hotspots, with at least three traits coinciding, were also identified, several of which co-localize with barley orthologues of genes controlling grain dimensions in rice. Most of the allele effects are specific to geographical location and/or exotic parental genotype. This study shows the existence of beneficial alleles for yield-related traits in exotic barley germplasm and provides candidate alleles for future improvement of these traits by the breeder.

Original languageEnglish
Pages (from-to)3811-3822
Number of pages12
JournalJournal of Experimental Botany
Volume69
Issue number16
DOIs
Publication statusPublished - 20 Jul 2018

Fingerprint

Hordeum
chromosome mapping
Breeding
barley
Genome
genome
breeding
Alleles
Population
Genes
alleles
genes
Quantitative Trait Loci
quantitative trait loci
Genotype
genotype
Genome-Wide Association Study
Fertilizers
Geographical Locations
Scotland

Keywords

  • Genome-wide association scans (GWAS)
  • nested association mapping (NAM)
  • quantitative trait locus hotspot (QTL hotspot)
  • yield-related grain traits

Cite this

Sharma, Rajiv ; Draicchio, Fulvia ; Bull, Hazel ; Herzig, Paul ; Maurer, Andreas ; Pillen, Klaus ; Thomas, William T.B. ; Flavell, Andrew J. / Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding. In: Journal of Experimental Botany. 2018 ; Vol. 69, No. 16. pp. 3811-3822.
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Sharma, R, Draicchio, F, Bull, H, Herzig, P, Maurer, A, Pillen, K, Thomas, WTB & Flavell, AJ 2018, 'Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding', Journal of Experimental Botany, vol. 69, no. 16, pp. 3811-3822. https://doi.org/10.1093/jxb/ery178

Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding. / Sharma, Rajiv; Draicchio, Fulvia; Bull, Hazel; Herzig, Paul; Maurer, Andreas; Pillen, Klaus; Thomas, William T.B.; Flavell, Andrew J.

In: Journal of Experimental Botany, Vol. 69, No. 16, 20.07.2018, p. 3811-3822.

Research output: Contribution to journalArticle

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AU - Sharma, Rajiv

AU - Draicchio, Fulvia

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AU - Herzig, Paul

AU - Maurer, Andreas

AU - Pillen, Klaus

AU - Thomas, William T.B.

AU - Flavell, Andrew J.

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N2 - To explore wild barley as a source of useful alleles for yield improvement in breeding, we have carried out a genome-wide association scan using the nested association mapping population HEB-25, which contains 25 diverse exotic barley genomes superimposed on an ∼70% genetic background of cultivated barley. A total of 1420 HEB-25 lines were trialled for nine yield-related grain traits for 2 years in Germany and Scotland, with varying N fertilizer application. The phenotypic data were related to genotype scores for 5398 gene-based single nucleotide polymorphism (SNP) markers. A total of 96 quantitative trait locus (QTL) regions were identified across all measured traits, the majority of which co-localize with known major genes controlling flowering time (Ppd-H2, HvCEN, HvGI, VRN-H1, and VRN-H3) and spike morphology (VRS3, VRS1, VRS4, and INT-C) in barley. Fourteen QTL hotspots, with at least three traits coinciding, were also identified, several of which co-localize with barley orthologues of genes controlling grain dimensions in rice. Most of the allele effects are specific to geographical location and/or exotic parental genotype. This study shows the existence of beneficial alleles for yield-related traits in exotic barley germplasm and provides candidate alleles for future improvement of these traits by the breeder.

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