Analisis de genotipificación por secuencia (gbs) en una población de Solanum tuberosum grupo phureja (variedad criolla colombiana)

Abstract

The present research was performed a genotyping analysis by sequence of 6 accessions of Solanum tuberosum gurpo phureja in order to identify single nucleotide polymorphisms (SNP) of nucleotide near coding regions and near regions of interest, for which a protocol was performed for a GWAS study using GBS data, which consisted of an alignment of the sequences with the updated reference genome DM_1 3_516_R44_potato_genome_assembly. v6.1, variant calling, genotyping and functional variant annotation with NGSEPcore, to generate the matrix it was planned to use vcftools and PLINK to finally perform the genetic association analysis with the Rstudio GAPIT tool using the linear mixed model to avoid false positives. The results show a limitation in the functional variant annotation process, a limitation mainly attributed to the annotation file with the genetic models for Solanum tuberosum phureja group and to the nature of the data and its quality prior to sequencing.