QTL discovery for agronomic and quality traits in diploid potato clones using PotatoMASH amplicon sequencing.

ABSTRACT: We genotyped a population of 618 diploid potato clones derived from six independent potato-breeding programmes from NW-Europe. The diploids were phenotyped for 23 traits, using standardized protocols and common check varieties, enabling us to derive whole population estimators for most traits. We subsequently performed a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) for all traits with SNPs and short-read haplotypes derived from read-backed phasing. In this study, we used a marker platform called PotatoMASH (Potato Multi-Allele Scanning Haplotags); a pooled multiplex amplicon sequencing based approach. Through this method, neighboring SNPs within an amplicon can be combined to generate multiallelic short-read haplotypes (haplotags) that capture recombinatio

SUBMITTER: Vexler L 

PROVIDER: S-EPMC11457057 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature