SSR and ddRADseq genotyping to discriminate and protect an Italian white-type celery (Apium graveolens L.) landrace

• Genetic distinctiveness of an Italian celery collection was assessed by SSR and SNP/InDel. • SSR distinguished landraces from commercial varieties but not between them. • SNPs/InDels succeeded in genetically discriminating the celery landraces. • High genetic similarity was found for the white-type landrace Bianco di Sperlonga. • Two markers for Bianco di Sperlonga traceability were successfully validated. Celery is an important vegetable crop cultivated in Italy with different biotypes. This study investigated the genetic distinctiveness of the Italian white-type landrace “Bianco di Sperlonga” (BS). Nineteen celery accessions were genotyped by SSR and SNP/InDel markers. The collection included 17 white-type accessions, belonging to the landraces BS (n=12) and “Dorato d’Asti” (SA, n=1), and to commercial lines (n=4). Two black-type accessions, encompassing the “Nero di Trevi” (NT) landrace and a commercial variety were also included. Eight SSR markers provided 27 alleles that allowed to distinguish the commercial lines from the landraces and among the latter, the white- and black-type ones, but failed to differentiated BS and SA white-type landraces. By contrast, SNPs/InDels identified through ddRADseq analysis discriminated BS from SA populations. BS samples showed high genetic similarity (≥ 98.5%), also confirmed by clustering, population structure and PCoA analyses. This result was unexpected given the celery prevalent allogamous nature. Both the SSR and ddRAD datasets showed lower observed than expected heterozygosity, indicating inbreeding within the BS landrace. This resembles the genetic structure of prevalently autogamous species. This suggested a loss of genetic load in the BS landrace, possibly due to strict inbreeding in traditional seed multiplication practices. From the ddRAD dataset, BS private alleles were identified and two PCR-based markers potentially useful for assessing the BS authenticity and traceability were developed and successfully validated. Overall, the results supported the purposed derivation of BS from the SA landrace and provide valuable molecular tools for assessing BS genetic distinctiveness and ensuring traceability.