Population structure and linkage disequilibrium in an Andean potato population from the Northwestern region of Argentina

CARBONI, MARTÍN FEDERICO; SOFIA SUCAR; MONTE, MARCELO NICOLÁS; CASTELLOTE, MARTÍN ALFREDO; FLORENCIA REY BURUSCO; MASSA GABRIELA ALEJANDRA; FEINGOLD SERGIO ENRIQUE

Congreso; 11 th International plant molecular biology congress; 2015

A genotyping-by-sequencing approach was used to characterize a collection of Solanumtuberosum group Andigena. Previous studies have reported a high variability within thistaxonomic group, which contrasts with the narrow genetic diversity shown bycommercial varieties (mainly from Tuberosum group). The present study evaluates acollection of 109 genotypes from 65 varieties from the Northwestern region of Argentina,4 commercial varieties and the reference sequenced genotype (DM).DArTseqTM is a technology that reduces genome complexity using restriction enzymesfollowed by Illumina short-read sequencing. It provides information of SNPs and dominantmarkers called SilicoDArTs.A total of 56,169 SNPs were generated, from which 42,165 were localized in the potatoreference genome, resulting in an extensive coverage of 115 markers/Mb or 87markers/cM.Population analyses were carried out with a Bayesian approach. Accessions wereassigned to three groups. One of them includes commercial genotypes, DM and 18Andean accessions. A smaller group of 14 genotypes includes most of the stronglypigmented accessions and a bigger one of 77 genotypes comprises the rest of them. Adistance-based hierarchical clustering approach confirmed the occurrence of three groupswith minor mislocated genotypes.Genome wide linkage disequilibrium in the collection was calculated using 25,362 highlyreproducible SNPs resulting in r2=0.23 on average for 200kb mean distances betweenmarkers. This value enables future association mapping studies with the required markerdensity.This study constitutes the first massive genotyping and the first report of structure in anAndigena potato collection from Argentina.