1. Representation of the DAPC clusters on the map
Genetic diversity analysis among cultivated and wild species accessions of sugar beet (Beta vulgaris L.) based on SNP and DArT markers
HENRY-BOUNAN, KARINE1, BRIGITTE MANGIN2, FLORIAN SANDRON2, DEVAUX, BRIGITTE1, LAURENT, VALERIE1, and DEVAUX, PIERRE1.
1Florimond Desprez Veuve & Fils SAS, BP41, 3, Rue Florimond Desprez, F Cappelle-en-Pévèle, France;
2Institut National de la Recherche Agronomique, BIA Unit, 24, BP52627, Chemin de Borde Rouge, F Castanet-Tolosan Cedex, France.
Introduction
This study aims at characterizing and comparing the genetic variability between wild populations of Beta macrocarpa, vulgaris maritima, adanensis, patula and cultivated beets using SNP and DArTs markers. The genetic information derived from this study will be useful for future studies on beet genetic diversity and population structure of genus Beta (genepool I) and the identification of genetic diversity useful for breeding program.
Material and Methods
A. Sample collection
A total of 2600 accessions were collected from GRIN-ARS, Eurisco and own collection after a preselection made on passport datas and species information.
B. Genotyping
All accessions were sampled and DNA was extracted for SNP analyses through private marker dataset (378 SNPs) and for constitution of a DArTs array (Australia). This array was then used to genotype the 2600 accessions (4497 polymorphic markers in the study).
C. Statistical analysis
The structure of the population was represented by clusters of individuals and computed according to different methods including: PCA using K-means algorythm, DAPC, STRUCTURE. Ordination methods using DArwin (Unweighted Neighbor Joining) were added. Linkage map building was made through Mapmaker. Ecogeographical analysis have been made with DIVA-GIS.
Map of collected accessions per country
Results and Discussions
A. Population structuration
Analysis was based on SNPs and DArTs markers separately. They are both drawing the same pictures with accurate precision for DArTs results. The different analysis give the same representation of the global diversity with a very nice structuration according first to species contribution (macrocarpa, adanensis, cultivated group) and geographic distribution (mainly in Beta vulg. maritima and Leaf beet). Beta vulg. adanensis and Beta macrocarpa are the most distant population from cultivated groups. There are clearly 2 groups of Beta vulg. maritima linked to geographical origins.
Ordination of accessions with unweighted Neighbor Joining method using DArTs results
Beta macrocarpa Beta vulg. maritima
Beta vulg. adanensis Beta vulg. sugar beet
Beta vulg. leaf beet Beta vulg. garden beet
Beta vulg. fodder beet Beta vulg. elite
B. Spatial analysis
Spatial analysis can contribute significantly to the call for the improved understanding of Beta species biodiversity. Reporting grouping obtained from DAPC analysis on the geographic map, show clearly the geographical differenciation. Results obtained from spatial analysis allow the formulation and implementation of more targeted and hence more effective core collection strategies. Outputs from spatial studies can provide critical information on the diversity present in specific geographic areas and can be used for various purposes.
DAPC using Adegenet with DArTs results
C. Linkage map
In order to check for distribution of DArTs markers along genome, a mapping population of 152 DH was analysed with the generated DArTs array. A consensus map of 850 polymorphic DArTs and 378 SNPs markers was constructed.
Representation of the DAPC clusters on the map
(macrocarpa and adanensis were discarded because of their strong distance from other groups)
Conclusion
The improvement needed to preserve and enhance the competitiveness of the French sugar beet industry cannot be achieved with the limited genetic variability that is available in current breeding lines. Genetic improvement is considered to be the key issue. The strong morphological (species specificity) and genetic diversity of genus Beta highlights the potential for introduction of desired traits into breeding material and should allow the constitution of exotic libraries (marker-defined genomic regions taken from wild species and introgressed into the background of elite sugar beet lines).
Aknowledgements : this Research programme has been selected and granted by the French Government and funding are under the management of the Research National Agency (ANR : Agence Nationale de la Recherche)
AKER is included in the « Investissements d’avenir » as refered as ANR-11-BTBR-0007 
74th IIRB congress
Dresden, 1-3 July 2014