PotatoMASH—A Low Cost, Genome-Scanning Marker System for Use in Potato Genomics and Genetics Applications

Abstract

We have developed PotatoMASH (Potato Multi-Allele Scanning Haplotags), a novel low-cost, genome-scanning marker platform. We designed a panel of 339 multi-allelic regions placed at 1 Mb intervals throughout the euchromatic portion of the genome. These regions were assayed using a multiplex amplicon sequencing approach, which allows for genotyping hundreds of plants at a cost of 5 EUR/sample. We applied PotatoMASH to a population of over 700 potato lines. We obtained tetraploid dosage calls for 2012 short multi-allelic haplotypes in 334 loci, which ranged from 2 to 14 different haplotypes per locus. The system was able to diagnose the presence of targeted pest-resistance markers, to detect quantitative trait loci (QTLs) by genome-wide association studies (GWAS) in a tetraploid population, and to track variation in a diploid segregating population. PotatoMASH efficiently surveys genetic variation throughout the potato genome, and can be implemented as a single low-cost genotyping platform that will allow the routine and simultaneous application of marker-assisted selection (MAS) and other genotyping applications in commercial potato breeding programmes.

High-density linkage map constructed from a skim sequenced diploid potato population reveals transmission distortion and QTLs for tuber and pollen production

“…With the low cost of next-generation sequencing, genotyping-by-sequencing (GBS) strategies are an interesting option. GBS strategies can include a step of genome complexity reduction using restriction enzymes (Elshire et al, 2011), capture baits (Uitdewilligen et al, 2013), or amplicon sequencing like potatoMASH (Leyva-Pérez et al, 2022).…”

Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato

“…Although the pattern (Fig. 3 ) and proportion (data not shown) of GBS SNPs in euchromatic and heterochromatic regions, as described by Sharma et al ( 2013 ) and Leyva-Perez et al ( 2022 ), for chromosome 8 did not significantly differ from rest of the chromosomes, the pronounced shift in LD decay rate for this chromosome using GBS SNPs is somewhat intriguing.…”

“…Numerous studies have successfully reported application of GWAS in potato (Berdugo-Cely et al 2017 ; Carley et al 2017 ; D’hoop et al 2008 , 2014 ; Fischer et al 2013 ; Kloosterman et al 2013 ; Lindqvist-Kreuze et al 2014 ; Rosyara et al 2016 ; Schönhals et al 2016 ; Sharma et al 2018 ; van Eck et al 2017 ; Vos et al 2017 ). Reports involving other SBG approaches in potato, especially for low cost genome scanning, are also emerging (Leyva-Perez et al 2022 ).…”

Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato

“…We generated marker data for all three populations using the amplicon sequencing strategy potatoMASH (Leyva-Pérez et al 2022 ). DNA extraction, library preparation, and bioinformatic processing of sequencing reads to obtain marker dosages were performed according to Leyva-Pérez et al ( 2022 ), with the exception that we aligned short-reads to DM v6.1 (Pham et al 2020 ) instead of DM v4.03. Unique amplicon alleles, referred to as haplotags, were used as genetic markers.…”