Molecular Breeding

, 35:11 | Cite as

Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information

  • Ernesto Igartua
  • Elsayed Mansour
  • Carlos P. Cantalapiedra
  • Bruno Contreras-Moreira
  • M. Pilar Gracia
  • Prudencio Fuster
  • Juan Escribano
  • José Luis Molina-Cano
  • Marian Moralejo
  • Francisco J. Ciudad
  • William T. B. Thomas
  • Ildikó Karsai
  • Ana M. Casas


This study is a retrospective analysis of an elite cross from the Spanish National Barley Breeding Program. This was the most successful cross produced in the breeding program in the past 20 years. The progeny from this cross has been investigated at two points in the program, before and after selection, through the analysis of allelic frequencies at a number of genetic loci with molecular markers. Shifts in allelic frequencies after selection allowed the identification of genomic regions with selection footprints likely due to the breeding process. The cross was replicated in three different years, and therefore, the three progenies represent different selection histories but, in all cases, were preferentially selected compared to the lines from other crosses used in the program. The progenies were sampled at two generations, before conscious selection (F2) and after six generations of selection (F8). The F2 plants were genotyped with microsatellites, whereas 31 F8 lines were surveyed for SNP and presence/absence variation polymorphisms using a genotyping-by-sequencing system (DArTseq). The DArTseq markers were aligned to the barley physical map, and, after curation, over 3,000 were still available for the analysis. Overall, 15 genomic regions in the F8 lines had allele frequencies beyond chosen thresholds, indicating selection, eight toward parent Orria and seven toward Plaisant. These selection footprints partially validated QTLs detected through classical linkage mapping in a RIL population of the same cross. These validated selection footprints convey useful information for barley breeding, either through marker-assisted selection or through genomic selection.


Barley Breeding Selection footprint Genotyping-by-sequencing 





Single nucleotide polymorphism


Presence–absence variation


Quantitative trait locus



This work was supported by the Spanish Ministry of Science and Innovation (MICINN), who funded this work with the scholarship BES-2008-009623 (EM), and the projects AGL2010-21929, RTA03-028-C4, RTA2006-00020-C04 and RTA2009-00006-C04, and by Grant A06 from the Aragon Government. Genotype by sequencing was funded by DGA—Obra Social La Caixa (Grant Number GA-LC-059-2011). WTBT acknowledges funding by the Scottish Government’s Rural and Environment Science and Analytical Services Division.

Supplementary material

11032_2015_194_MOESM1_ESM.docx (114 kb)
Supplementary material 1 (DOCX 114 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Ernesto Igartua
    • 1
  • Elsayed Mansour
    • 1
    • 2
  • Carlos P. Cantalapiedra
    • 1
  • Bruno Contreras-Moreira
    • 1
    • 3
  • M. Pilar Gracia
    • 1
  • Prudencio Fuster
    • 4
  • Juan Escribano
    • 4
  • José Luis Molina-Cano
    • 5
  • Marian Moralejo
    • 6
  • Francisco J. Ciudad
    • 7
  • William T. B. Thomas
    • 8
  • Ildikó Karsai
    • 9
  • Ana M. Casas
    • 1
  1. 1.Estación Experimental de Aula DeiEEAD-CSICZaragozaSpain
  2. 2.Agronomy Department, Faculty of AgricultureZagazig UniversityZagazigEgypt
  3. 3.Fundación ARAIDZaragozaSpain
  4. 4.Instituto Técnico Agrónomico Provincial de Albacete (ITAP)AlbaceteSpain
  5. 5.Institut de Recerca i Tecnología Agroalimentàries (UdL-IRTA)LleidaSpain
  6. 6.Universitat de Lleida (UdL)LleidaSpain
  7. 7.Instituto de Tecnología Agraria, Junta de Castilla y León (ITACyL)ValladolidSpain
  8. 8.The James Hutton InstituteDundeeUK
  9. 9.Centre for Agricultural ResearchHungarian Academy of SciencesMartonvásárHungary

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