Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information
Igartua E, Mansour E, Cantalapiedra CP, Contreras-Moreira B, Gracia MP, Fuster P, Escribano J, Molina-Cano JL, Moralejo M, Ciudad FJ, Thomas WTB, Karsai I and Casas A (2015) Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information. Molecular Breeding, 35:11
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 6 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 3000 were still available for the analysis. Overall, 15 genomic regions in the F8 lines had allele frequencies beyond chosen thresholds, indicating selection, 8 towards parent Orria and 7 towards Plaisant. These selection footprints partially validated QTLs detected though 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 genomic selection.
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 6 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 3000 were still available for the analysis. Overall, 15 genomic regions in the F8 lines had allele frequencies beyond chosen thresholds, indicating selection, 8 towards parent Orria and 7 towards Plaisant. These selection footprints partially validated QTLs detected though 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 genomic selection.