Single nucleotide polymorphism discovery in elite north american potato germplasm

Abstract

BackgroundCurrent breeding approaches in potato rely almost entirely on phenotypic evaluations; molecular markers, with the exception of a few linked to disease resistance traits, are not widely used. Large-scale sequence datasets generated primarily through Sanger Expressed Sequence Tag projects are available from a limited number of potato cultivars and access to next generation sequencing technologies permits rapid generation of sequence data for additional cultivars. When coupled with the advent of high throughput genotyping methods, an opportunity now exists for potato breeders to incorporate considerably more genotypic data into their decision-making.ResultsTo identify a large number of Single Nucleotide Polymorphisms (SNPs) in elite potato germplasm, we sequenced normalized cDNA prepared from three commercial potato cultivars: 'Atlantic', 'Premier Russet' and 'Snowden'. For each cultivar, we generated 2 Gb of sequence which was assembled into a representative transcriptome of ~28-29 Mb for each cultivar. Using the Maq SNP filter that filters read depth, density, and quality, 575,340 SNPs were identified within these three cultivars. In parallel, 2,358 SNPs were identified within existing Sanger sequences for three additional cultivars, 'Bintje', 'Kennebec', and 'Shepody'. Using a stringent set of filters in conjunction with the potato reference genome, we identified 69,011 high confidence SNPs from these six cultivars for use in genotyping with the Infinium platform. Ninety-six of these SNPs were used with a BeadXpress assay to assess allelic diversity in a germplasm panel of 248 lines; 82 of the SNPs proved sufficiently informative for subsequent analyses. Within diverse North American germplasm, the chip processing market class was most distinct, clearly separated from all other market classes. The round white and russet market classes both include fresh market and processing cultivars. Nevertheless, the russet and round white market classes are more distant from each other than processing are from fresh market types within these two groups.ConclusionsThe genotype data generated in this study, albeit limited in number, has revealed distinct relationships among the market classes of potato. The SNPs identified in this study will enable high-throughput genotyping of germplasm and populations, which in turn will enable more efficient marker-assisted breeding efforts in potato.

Genetic Variance Partitioning and Genome-Wide Prediction with Allele Dosage Information in Autotetraploid Potato

“…TP samples were genotyped with either version 1 or version 2 of the SolCAP potato SNP array, which have in common a set of 8303 markers used for this study (Hamilton et al 2011;Felcher et al 2012). Tetraploid genotype calls (coded 0-4) were made using version founders (clones with no parent) and 1138 total clones in the pedigree (File S3).…”

Design of efficient simplified genomic DNA and bisulfite sequencing in large plant populations

“…Thus, amount of short-read data required and associated cost can be dramatically reduced. In the past five years, RNA-sequencing has been implemented to identify tens to thousands of genetic variants in human, cottonwood and potato genomes [16][17][18]. Because expression of genes in different samples can vary widely and change dynamically, the RNA-seq based approach bears several key inherent weaknesses.…”

Genetic mapping in polyploids

“…In polyploids, SNP arrays have been developed in numerous species, which include both autopolyploid (or predominantly polysomic polyploids) and allopolyploid species. Examples of the former include alfalfa (Li et al, 2014b), chrysanthemum (van Geest et al, 2017c, potato (Hamilton et al, 2011;Felcher et al, 2012;Vos et al, 2015), rose and sour cherry (Peace et al, 2012). Examples of allopolyploid SNP arrays include cotton (Hulse-Kemp et al, 2015), oat (Tinker et al, 2014), oilseed rape (Dalton- Morgan et al, 2014;Clarke et al, 2016), peanut (Pandey et al, 2017), strawberry (Bassil et al, 2015) and wheat (Akhunov et al, 2009;Cavanagh et al, 2013;Wang et al, 2014b;Winfield et al, 2016).…”