Rapeseed (Brassica napus L.) is the leading European oilseed crop serving as source for edible oil and renewable energy. The objectives of our study were to (i) examine the population structure of a large and diverse set of B. napus inbred lines, (ii) investigate patterns of genetic diversity within and among different germplasm types, (iii) compare the two genomes of B. napus with regard to genetic diversity, and (iv) assess the extent of linkage disequilibrium (LD) between simple sequence repeat (SSR) markers. Our study was based on 509 B. napus inbred lines genotyped with 89 genome-specific SSR primer combinations. Both a principal coordinate analysis and software STRUCTURE revealed that winter types, spring types, and swedes were assigned to three major clusters. The genetic diversity of winter oilseed rape was lower than the diversity found in other germplasm types. Within winter oilseed rape types, a decay of genetic diversity with more recent release dates and reduced levels of erucic acid and glucosinolates was observed. The percentage of linked SSR loci pairs in significant (r (2) > Q (95 unlinked loci pairs)) LD was 6.29% for the entire germplasm set. Furthermore, LD decayed rapidly with distance, which will allow a relatively high mapping resolution in genome-wide association studies using our germplasm set, but, on the other hand, will require a high number of markers.

A set of 59 spring barley introgression lines (ILs) was developed from the advanced backcross population S42. The ILs were generated by three rounds of backcrossing, two to four subsequent selfings, and, in parallel, marker-assisted selection. Each line includes a single marker-defined chromosomal segment of the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is derived from the elite barley cultivar Scarlett (H. vulgare ssp. vulgare). Based on a map containing 98 SSR markers, the IL set covers so far 86.6% (1041.5 cM) of the donor genome. Each single line contains an average exotic introgression of 39.2 cM, representing 3.2% of the exotic genome. The utility of the developed IL set is illustrated by verification of QTLs controlling resistance to powdery mildew (Blumeria graminis f. sp. hordei L.) and leaf rust (Puccinia hordei L.) which were previously identified in the advanced backcross population S42. Altogether 57.1 and 75.0% of QTLs conferring resistance to powdery mildew and leaf rust, respectively, were verified by ILs. The strongest favorable effects were mapped to regions 1H, 0-85 cM and 4H, 125-170 cM, where susceptibility to powdery mildew and leaf rust was decreased by 66.1 and 34.7%, respectively, compared to the recurrent parent. In addition, three and one new QTLs were localized, respectively. A co-localization of two favorable QTLs was identified for line S42IL-138, which holds an introgressed segment in region 7H, 166-181. Here, a reduction effect was revealed for powdery mildew as well as for leaf rust severity. This line might be a valuable resource for transferring new resistance alleles into elite cultivars. In future, we aim to cover the complete exotic genome by selecting additional ILs. We intend to conduct further phenotype studies with the IL set in regard to the trait complexes agronomic performance, malting quality, biotic stress, and abiotic stress.

In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations.

Knowing the genetic basis of the plant ionome is essential for understanding the control of nutrient transport and accumulation. The aim of this research was to (i) study mineral nutrient concentrations in a large and diverse set of Brassica napus, (ii) describe the relationships between the shoot ionome and seedling development, and (iii) identify genetic regions associated with variation of the shoot ionome. The plant material under study was a germplasm set consisting of 509 inbred lines that was genotyped by a 6K single nucleotide polymorphism (SNP) array and phenotyped by analyzing the concentrations of eleven mineral nutrients in the shoots of 30 days old seedlings. Among mineral concentrations, positive correlations were found, whereas mineral concentrations were mainly negatively correlated with seedling development traits from earlier studies. In a genome-wide association mapping approach, altogether 29 significantly associated loci were identified across seven traits after correcting for multiple testing. The associations included a locus with effects on the concentrations of Cu, Mn, and Zn on chromosome C3, and a genetic region with multiple associations for Na concentration on chromosome A9. This region was situated within an association hotspot close to SOS1, a key gene for Na tolerance in plants.