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.

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Rae, S. J., Macaulay, M., Ramsay, M., Leigh, F., Matthews, D., O'Sullivan, D., Donini, P., Morris, P. C., Powell, W., Waugh, R., Thomas, W. T. B. (2006). Molecular barley breeding. Euphytica 158, (3), 295-303 Sponsorship: SEERAD; BBSRCBreeding progress in barley yield in the UK is being sustained at a rate in the order of 1% per annum against a background of declining seed sales. Commercial barley breeders are largely concentrating upon the elite local gene pool but with genotypic evidence suggesting that there is still considerable variation between current recommended cultivars, even those produced as half-sibs by the same breeder. Marker Assisted Selection (MAS) protocols could be substituted for conventional selection for a number of major-gene targets but, in the majority of cases, conventional selection is more resource efficient. Results from current QTL mapping studies have not yet identified sufficiently robust and validated targets for UK barley breeders to adopt MAS to assist in the selection of complex traits such as yield and malting quality. Results from multiple population mapping amongst the elite gene pool being utilised by breeders and from association studies of elite germplasm tested as part of the UK recommended list trial process do, however, show some promise.Peer reviewe

Background Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus. An F2 mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type. Results Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC. Conclusions These findings demonstrate the effectiveness of the ddRAD approach to sample the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F2 populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.

In autumn-sown greenfeed trials on a Templeton silt loam following cereal1 cropping, the herbage yield from 'Grasslands Tama' Westerwolds ryegrass at first grazing in July and the subsequent regrowth to late August was 27% higher than from 'Grasslands Paroa' Italian ryegrass. The margin in yield was less where both grasses were spelled until late August. Subsequent regrowth in spring was similar for both grasses where there was one prior grazing in late winter, but growth of. Paroa was less than Tama ryegrass where there were two prior grazings in mid- and late winter. Grazing twice in July and August gave a 27% higher total yield from Tama ryegrass than a single grazing in late August. Yields of both grasses were higher with 67 kg/ha than with 22 kg/ha of nitrogen at drilling. Both grasses responded to further nitrogen Bpplied in mid-winter, Paroas more so than Tama ryegrass. Up to late winter, Amuri oats outyielded Tama ryegrass and C.R.D. ryecorn. Yields from an oats-Tama ryegrass mixture were 25% higher than from Tama ryegrass alone. They gave higher yields than Tama ryegrass alone to mid-winter when the cereal dominated, and provided as good recovery growth as Tama ryegrass alone in late winter and spring. when ryegrass dominated.