Assessment of genetic diversity of global sugar beet germplasm through silico dart and SNP markers covering whole genome

Despite the relatively brief domestication history of Beta vulgaris ssp. vulgaris, our knowledge of its genomic diversity is still limited, hindering advancements in breeding efforts. To tackle this challenge, the genetic diversity of 94 genotypes originating from 16 countries was analyzed using 4609 SNP markers and 6950 SilicoDArT markers. The investigated germplasm shows a high degree of genetic diversity. However, the SNP markers data set had higher diversity values than the SilicoDArT marker system. However, the SNP markers data set had higher diversity values than the SilicoDArT marker system. Obtained data from SNP markers revealed three main clusters: S-I, S-II, and S-III. Cluster S-I was the smallest group, with 35 accessions and 51% of them having USA origin. European accessions shared 14% of the cluster. Furthermore, accession from the USA was grouped in Cluster S-III-B, with over 80% from Middle East countries. Results obtained from using SilicoDArT markers revealed that the most distinct accessions were NSL 176303 (Serbia) and PI 140355 (Montenegro). The germplasm was divided into D-I and D-II. First cluster containing 90% of accessions originated from the USA. The D-II cluster was diverse, with accessions from the UK, Türkiye, Iran, and Iraq. The SNP-based clustering supported the D-I cluster, and the SilicoDArT markers-based PCA clustering results agreed with the UPGMA and STRUCTURE results. The AMOVA results confirmed that genetic variation in the germplasm was largely due to differences among accessions or within the clusters (rather than among countries), accounting for 74.5-77.6% of the total variation. Finally, the study identified Ames 2644 and Ames 8297 as the most genetically distinct genotypes, which are ideal for breeding sugar beet.