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

Abstract

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 Electronic supplementary material The online version of this article (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.

Identification of quantitative trait loci for agronomic traits contributed by a barley (Hordeum vulgare) Mediterranean landrace

“…Orria [(((Api x Kristina) x M66.85) x Sigfrido's) x 79W40762] is a semidwarf cultivar selected in Spain from a CIMMYT nursery, which is highly productive across most Spanish regions. This cultivar is an outstanding parent of the Spanish national barley breeding program (Igartua et al 2015).…”

Molecular Genetic Diversity and Combining Ability for Some Physiological and Agronomic Traits in Rice under Well-Watered and Water-Deficit Conditions

“…Conversely, DNA-based markers are more reliable, stable, and repeatable. Accordingly, DNA-based markers have been widely applied to investigate genetic divergence among genotypes [ 28 , 29 ]. Microsatellites or simple sequence repeats (SSR) are valuable markers due to their co-dominant transmission, multi-allelic nature, relative abundance, genome coverage, informativeness, and low DNA requirement [ 30 ].…”

Response of High-Yielding Peanut Cultivars to Various Seed Treatments Under Marginal Fertility Sandy Soil Conditions

“…The evaluated peanut cultivars exhibited highly significant differences in yield and quality traits. These findings indicated the existence of genetic variability in the assessed cultivars, which need exploiting for developing high-yielding genotypes (Igartua et al, 2015;Salem et al, 2020;Kamara et al, 2021b;ElShamey et al, 2022a). Similarly, Puangbut et al (2009), Dang et al (2013), El-Far et al 2017) depicted that inoculation fixes atmospheric nitrogen, solubilizes phosphate, synthesizes growth-promoting substances, and boosts the decomposition of plant residues Accordingly, Rhizobium inoculation improves soil fertility, which aids plant growth and productivity, particularly in low-fertility soils in arid regions.…”