Hazelnut is consumed worldwide and is of critical economic importance to the rural communities of Turkey's northern coast. A new disease outbreak has drastically decreased yields across Turkey and climate change is emerging as a new threat to cultivation. Our study is the first to provide a genomic perspective on diversity in this vulnerable crop, which will prove valuable for future breeding efforts. Such research into perennial crops like hazelnut can help to improve farmer livelihoods and ensure the sustainability of crop production in a changing world. Summary• Assessing and describing genetic diversity in crop plants is a crucial first step toward their improvement. The European hazelnut, Corylus avellana L., is one of the most economically important tree nut crops worldwide. It is primarily produced in Turkey where rural communities depend on it for their livelihoods. Despite this, we know little about its domestication history and the genetic diversity it holds.• We use double digest restriction-site associated DNA (ddRAD) sequencing to produce a genome-wide dataset containing wild and domesticated hazelnut. We uncover patterns of population structure and diversity, determine levels of crop-wild gene flow, and estimate the relationships among different genetic clusters.• We use a dataset of over 60k single nucleotide polymorphisms to find that genetic clusters of cultivars do not reflect their given names and that there is limited evidence for a reduction in genetic diversity in domesticated individuals. We find evidence that hazelnut may have been domesticated more than once and that admixture has likely occurred multiple times between wild and domesticated hazelnut.• We provide the first genomic assessment of Turkish hazelnut diversity and suggest that there has not been an extreme bottleneck during the domestication of this crop, leading to cultivars at different stages of domestication. Our study provides a platform for further research that will protect hazelnut from the threats of climate change and an emerging fungal disease. | 327 HELMSTETTER ET aL.

Assessing and describing genetic diversity in crop plants is a crucial first step towards 28 their improvement. The European hazelnut, Corylus avellana, is one of the most 29 economically important tree nut crops worldwide. It is primarily produced in Turkey 30 where rural communities depend on it for their livelihoods. Despite this we know little 31 about hazelnut's domestication history and the genetic diversity it holds. 32• We use double digest Restriction-site Associated DNA (ddRAD) sequencing to 33 produce genome-wide dataset containing wild and domesticated hazelnut. We 34 uncover patterns of population structure and diversity, determine levels of crop-wild 35 gene flow and estimate the timing of key divergence events. 36• We find that genetic clusters of cultivars do not reflect their given names and that 37 there is limited evidence for a reduction in genetic diversity in domesticated 38 individuals. Admixture has likely occurred multiple times between wild and 39 domesticated hazelnut. Domesticates appear to have first diverged from their wild 40 relatives during the Mesolithic. 41• We provide the first genomic assessment of Turkish hazelnut diversity and suggest 42 that it is currently in a partial stage of domestication. Our study provides a platform 43 for further research that will protect this crop from the threats of climate change and 44 an emerging fungal disease. 45 46 47

European hazelnut (Corylus avellana) is a diploid (2n = 22), monecious and wind-pollinated species, extensively cultivated for its nuts. Turkey is the world-leading producer of hazelnut, supplying 70–80% of the world’s export capacity. Hazelnut is mostly grown in the Black Sea Region, and maintained largely through clonal propagation. Understanding the genetic variation between hazelnut varieties, and defining variety-specific and disease resistance-associated alleles, would facilitate hazelnut breeding in Turkey. Widely grown varieties ‘Karafındık’ (2), ‘Sarıfındık’ (5), and ‘Yomra’ (2) were collected from Akçakoca in the west, while ‘Tombul’ (8), ‘Çakıldak’ (3), ‘Mincane’ (2), ‘Allahverdi’ (2), ‘Sivri’ (4), and ‘Palaz’ (5) were collected from Ordu and Giresun provinces in the east (numbers in parentheses indicate sample sizes for each variety). Powdery mildew resistant and susceptible hazelnut genotypes were collected from the field gene bank and heavily infected orchards in Giresun. Every individual was subjected to double digest restriction enzyme-associated DNA sequencing (ddRAD-seq) and a RADtag library was created. RADtags were aligned to the ‘Tombul’ reference genome, and Stacks software used to identify polymorphisms. 101 private and six common alleles from nine hazelnut varieties, four private from resistants and only one from susceptible were identified for diagnosis of either a certain hazelnut variety or powdery mildew resistance. Phylogenetic analysis and population structure calculations indicated that ‘Mincane’, ‘Sarıfındık’, ‘Tombul’, ‘Çakıldak’, and ‘Palaz’ were genetically close to each other; however, individuals within every varietal group were found in different sub-populations. Our findings indicated that years of clonal propagation of some preferred varieties across the Black Sea Region has resulted in admixed sub-populations and great genetic diversity within each variety. This impedes the development of a true breeding variety. For example, ‘Tombul’ is the most favored Turkish variety because of its high quality nuts, but an elite ‘Tombul’ line does not yet exist. This situation continues due to the lack of a breed protection program for commercially valuable hazelnut varieties. This study provides molecular markers suitable for establishing such a program.