Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information
Igartua Arregui, Ernesto
Mansour Elsayed, Elsayed
Cantalapiedra, Carlos P.
Gracia Gimeno, Ma. Pilar
Molina Cano, José Luis
Ciudad, F. J.
Thomas, William T. B.
Casas Cendoya, Ana Maria
MetadataShow full item record
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.
Is part ofMolecular Breeding, 2015, vol. 35, núm. 11
European research projects
Showing items related by title, author, creator and subject.
Candidate genes underlying QTL for flowering time and their interactions in a wide spring barley (Hordeum vulgare L.) cross Casas Cendoya, Ana Maria; Gazulla, Carlota R.; Monteagudo Gálvez, Arantxa; Cantalapiedra, Carlos P.; Moralejo Vidal, Mª Angeles; Gracia Gimeno, Ma. Pilar; Ciudad, F. J.; Thomas, William T. B.; Molina Cano, José Luis; Boden, Scott; Contreras‐Moreira, Bruno; Igartua Arregui, Ernesto (Crop Science Society of China and Institute of Crop Science, CAASElsevier, 2020-11-18)Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant's response to these environmental signals are ...
Resequencing the Vrs1 gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike Casas Cendoya, Ana Maria; Contreras‐Moreira, Bruno; Cantalapiedra, Carlos P.; Sakuma, Shun; Gracia Gimeno, Ma. Pilar; Moralejo Vidal, Mª Angeles; Molina Cano, José Luis; Komatsuda, Takao; Igartua Arregui, Ernesto (Springer Science+Business Media B.V., part of Springer Nature, 2018-04-12)Six-rowed spike 1 (Vrs1) is a gene of major importance for barley breeding and germplasm management as it is the main gene determining spike row-type (2-rowed vs. 6-rowed). This is a widely used DUS trait, and has been ...
Quantitative trait loci for agronomic traits in an elite barley population for Mediterranean conditions Mansour Elsayed, Elsayed; Casas Cendoya, Ana Maria; Gracia Gimeno, Ma. Pilar; Molina Cano, José Luis; Moralejo Vidal, Mª Angeles; Cattivelli, Luigi; Thomas, William T. B.; Igartua Arregui, Ernesto (Springer, 2013-09-15)Advances in plant breeding through marker-assisted selection (MAS) are only possible when genes or quantitative trait loci (QTLs) can contribute to the improvement of elite germplasm. A population of recombinant inbred ...