Potatoes were first brought to Europe in the sixteenth century^1,2. Two hundred years later, one of the species had become one of the most important food sources across the entire continent and, later, even the entire world³. However, its highly heterozygous, autotetraploid genome has complicated its improvement since then^4–7. Here we present the pan-genome of European potatoes generated from phased genome assemblies of ten historical potato cultivars, which includes approximately 85% of all haplotypes segregating in Europe. Sequence diversity between the haplotypes was extremely high (for example, 20× higher than in humans), owing to numerous introgressions from wild potato species. By contrast, haplotype diversity was very low, in agreement with the population bottlenecks caused by domestication and transition to Europe. To illustrate a practical application of the pan-genome, we converted it into a haplotype graph and used it to generate phased, megabase-scale pseudo-genome assemblies of commercial potatoes (including the famous French fries potato ‘Russet Burbank’) using cost-efficient short reads only. In summary, we present a nearly complete pan-genome of autotetraploid European potato, we describe extraordinarily high sequence diversity in a domesticated crop, and we outline how this resource might be used to accelerate genomics-assisted breeding and research.

Legumes have a high demand for phosphorus (P) due to energetically costly biological nitrogen fixation, but they also have effective physiological and morphological strategies for P mobilization. To evaluate the inter- and intraspecific P efficiency of small-grain legumes supplied with different P recycling fertilisers, eight accessions each of alfalfa (Medicago sativa L.) and red clover (Trifolium pratense L.) were cultivated in two pot experiments under greenhouse conditions until the flowering stage. To substantiate the results, some accessions were used in both experiments. Five treatments (no P, triple-superphosphate (TSP), sewage sludge ash (SSA), biowaste compost (compost), and struvite) were considered P sources. In addition to plant P uptake, the soil P pools were analysed in detail. Red clover showed higher yields and nutrient uptakes compared to alfalfa, but intraspecific effects were marginal. The addition of P resulted only partly in an increase in yield, despite the low P content in the soil. While struvite application clearly enhanced the P uptake of the plants in both experiments, SSA application had no effect compared to the control. The same treatment effect occurs with the bio-available soil P contents, which were on average 72.6 mg kg⁻¹ after struvite and 44.3 mg kg⁻¹ after SSA addition. Struvite as a P source was especially effective when applied to red clover. Our study aligns with previous field results and underscores the high potential of P mobilization of small-grain legumes without pronounced inter- or intraspecific differences. While struvite is suitable as a P fertiliser, the application of SSA to legumes is not recommended.

Lolium perenne L. is the most important forage grass species in temperate regions. It is also considered as a sustainable source of biomass for energy production. However, improvement in biomass yield has been limited by comparison with other major crops. More efficient utilisation of genetic resources and improved breeding schemes are required to advance L. perenne breeding. In an attempt to elucidate the extent of genetic diversity in L. perenne, 1384 DArT, 182 SNP and 48 SSR markers were applied to 297 accessions (Set I) contributed by three German breeding companies and the IPK Genebank. Due to the heterogeneous nature of Lolium accessions, bulk samples were used. Apart from germplasm set I, additional set II and set III was used to determine the reproducibility of marker system and judge the feasibility of bulk strategy in this study. By assessing different bulk sizes, 24 individuals per sample were shown to be a representative number of plants to discriminate different accessions. Among the 297 accessions, all marker types revealed a high polymorphism rate; 1.99, 2.00 and 8.19 alleles, were obtained per locus on average using DArTs, SNPs and SSRs, respectively. The Jaccard distance for DArT markers ranged from 0.00 to 0.73, the Modified Roger’s distance (MRD) for SNP markers ranged from 0.03 to 0.52, and for SSR markers from 0.26 to 0.76. Gene diversity for dominant DArT and co-dominant SNP and SSR markers was found to be 0.26, 0.32 and 0.45, respectively. DArT markers showed the highest consistency and reproducibility. The resulting data were evaluated using a number of different classification methods, but none of the methods showed a clear differentiation into distinct genetic pools. With regard to hybrid breeding, this will possibly impede substantial progress towards increased biomass yields of L. perenne by utilising heterosis.