Key messageTheBrassica napusIllumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploidB. napusand its progenitor diploid genomes.AbstractA high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid Brassica napus. A stringent selection process employing the short probe sequence for each SNP assay was used to limit the majority of the selected markers to those represented a minimum number of times across the highly replicated genome. As a result approximately 60 % of the SNP assays display genome-specificity, resolving as three clearly separated clusters (AA, AB, and BB) when tested with a diverse range of B. napus material. This genome specificity was supported by the analysis of the diploid ancestors of B. napus, whereby 26,504 and 29,720 markers were scorable in B. oleracea and B. rapa, respectively. Forty-four percent of the assayed loci on the array were genetically mapped in a single doubled-haploid B. napus population allowing alignment of their physical and genetic coordinates. Although strong conservation of the two positions was shown, at least 3 % of the loci were genetically mapped to a homoeologous position compared to their presumed physical position in the respective genome, underlying the importance of genetic corroboration of locus identity. In addition, the alignments identified multiple rearrangements between the diploid and tetraploid Brassica genomes. Although mostly attributed to genome assembly errors, some are likely evidence of rearrangements that occurred since the hybridisation of the progenitor genomes in the B. napus nucleus. Based on estimates for linkage disequilibrium decay, the array is a valuable tool for genetic fine mapping and genome-wide association studies in B. napus and its progenitor genomes.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2746-7) contains supplementary material, which is available to authorized users.

Brassica napus (oilseed rape, canola) is one of the world’s most important sources of vegetable oil for human nutrition and biofuel, and also a model species for studies investigating the evolutionary consequences of polyploidisation. Strong bottlenecks during its recent origin from interspecific hybridisation, and subsequently through intensive artificial selection, have severely depleted the genetic diversity available for breeding. On the other hand, high-throughput genome profiling technologies today provide unprecedented scope to identify, characterise and utilise genetic diversity in primary and secondary crop gene pools. Such methods also enable implementation of genomic selection strategies to accelerate breeding progress. The key prerequisite is availability of high-quality sequence data and identification of high-quality, genome-wide sequence polymorphisms representing relevant gene pools. We present comprehensive genome resequencing data from a panel of 52 highly diverse natural and synthetic B. napus accessions, along with a stringently selected panel of 4.3 million high-confidence, genome-wide SNPs. The data is of great interest for genomics-assisted breeding and for evolutionary studies on the origins and consequences in allopolyploidisation in plants.

This study explores the potential of Spanish germplasm for the development of hybrids adapted to southern Europe, a new region for hybrid barley (Hordeum vulgare). A set of 140 locally adapted, advanced breeding lines, developed in a Spanish public breeding program, were evaluated for their potential to widen the germplasm available for hybrid barley development. A subset of 24 lines was introduced into three-way hybrid combinations and tested in a field trial network of four locations and 2 yr. The hybrid performance of the rest of the lines was estimated based on genomic prediction models. No three-way hybrid exceeded the best check. We succeeded in identifying lines with high general combining ability, which could produce promising two-way hybrids. Some were among those tested in the field, whereas others resulted from genomic predictions, validating the strategy followed of mining locally adapted breeding lines. Rachis brittleness detected in field trials revealed a low but detrimental effect of the presence of alternative brittle mutations in the hybrid combination. The success of hybrid breeding in southern Europe requires further investigation of the underlying heterotic patterns, and appropriate management