ddRAD-seq para el análisis de asociación genómico de los principales caracteres agronómicos y calidad organoléptica en melocotonero

Abstract

Double-digest RAD sequencing (ddRAD-Seq) is a powerful method for SNP discovery at a genome-wide scale. It relies on breaking the genome into a certain size of DNA fragments using two restriction enzymes: i) one common cutter with a short recognition site and ii) a low frequency cutter having a large recognition motif . Amplification step in library preparation can introduce PCR artefacts. Those are expected to skew allele frequency by increasing homozygosity leading to false genotype calls. In this context, we carried out a comparison study between DNA-variants generated with duplicates and those generated after removing with either "'SAMtools:rmdup" or "Stacks clone filter". On the other hand, the accuracy of genetic variants identification is a crucial step towards understanding phenotypical traits and monitoring breeding programs. Thereby, a good combination of computational tools for alignment and variant calling is crucial to tackle the possible artifacts. In response to this challenge, three variant callers (BCFtools, Freebayes and GATK-HaplotypeCaller) were combined on top of the BWA-mem read mapper. SNPs derived from the intersection of these callers were used for a genome wide association study to genetic variants associated with agronomic and organoleptic traits (In this poster, we illustrate only one study case trait). A diverse set of 90 peach accessions were sampled from the Experimental Station of Aula Dei (CSIC) located at Zaragoza (northern of Spain). This germplasm collection includes landraces and modem breeding lines from different origins.