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

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

Fos de Iguazu

Congreso; 1th International Congress of Plant Molecular Biology IPMB2015; 2015

A genotyping-by-sequencing approach was used to characterize a collection of Solanum tuberosum group Andigena. Previous studies have reported a high variability within this taxonomic group, which contrasts with the narrow genetic diversity shown by commercial varieties (mainly from Tuberosum group). The present study evaluates a collection of 109 genotypes from 65 varieties from the Northwestern region of Argentina, 4 commercial varieties and the reference sequenced genotype (DM).DArTseq TM is a technology that reduces genome complexity using restriction enzymes followed by Illumina short-read sequencing. It provides information of SNPs and dominant markers called SilicoDArTs.A total of 56,169 SNPs were generated, from which 42,165 were localized in the potato reference genome, resulting in an extensive coverage of 115 markers/Mb or 87 markers/cM.Population analyses were carried out with a Bayesian approach. Accessions were assigned to three groups. One of them includes commercial genotypes, DM and 18 Andean accessions. A smaller group of 14 genotypes includes most of the strongly pigmented accessions and a bigger one of 77 genotypes comprises the rest of them. A distance-based hierarchical clustering approach confirmed the occurrence of three groups with minor mislocated genotypes.Genome wide linkage disequilibrium in the collection was calculated using 25,362 highly reproducible SNPs resulting in r 2 =0.23 on average for 200kb mean distances between markers. This value enables future association mapping studies with the required marker density.This study constitutes the first massive genotyping and the first report of structure in an Andigena potato collection from Argentina.