Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L.) germplasm

A genotyping database for 312 tobacco accessions was profiled with 49 SSR markers. Principal Coordinate Analysis (PCoA) and Bayesian cluster analysis revealed structuring of the tobacco population with regard to commercial classes and six main clades were identified, which correspond to "Oriental", Flue-Cured", "Burley", "Dark", "Primitive", and "Other" classes. Pairwise kinship was calculated between accessions, and an overall low level of co-ancestry was observed. A set of 89 genotypes was identified that captured the whole genetic diversity detected at the 49 loci. LD was evaluated on these genotypes, using 422 SSR markers mapping on seven linkage groups. LD was estimated as squared correlation of allele frequencies (r2). The pattern of intrachromosomal LD revealed that in tobacco LD extended up to distances as great as 75 cM with r2 > 0.05 or up to 1 cM with r2 > 0.2. The pattern of LD was clearly dependent on the population structure.A global population of tobacco is highly structured. Clustering highlights the accessions with the same market class. LD in tobacco extends up to 75 cM and is strongly dependent on the population structure.Nicotiana tabacum is a non-obligatory, selfing amphidiploid species derived from a hybridization event between Nicotiana sylvestris and Nicotiana tomentosiformis (summarized in [1]). As with other crops, breeding history and yield management have contributed to its genetic erosion [2].Most of the existing variability is maintained at the ex-situ U.S. Nicotiana Germplasm Collection [3], which contains around 1,900 accessions of N. tabacum, including 656 cultivars and 1,244 tobacco introductions (TIs). The TIs probably capture most of the genetic variability that existed before modern agricultural intensification [2]. Before modern breeding [4], main tobacco classes were distinguished, based on method of curing and biochemical characteristics, into Flue-cured, Burley, Oriental, Cigar, Dark (air/fire cured), and Primitive. Burley to