Retrospective View of North American Potato (Solanum tuberosumL.) Breeding in the 20th and 21st Centuries

Abstract

Cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid, has been bred for distinct market classes, including fresh market, pigmented, and processing varieties. Breeding efforts have relied on phenotypic selection of populations developed from intra- and intermarket class crosses and introgressions of wild and cultivated Solanum relatives. To retrospectively explore the effects of potato breeding at the genome level, we used 8303 single-nucleotide polymorphism markers to genotype a 250-line diversity panel composed of wild species, genetic stocks, and cultivated potato lines with release dates ranging from 1857 to 2011. Population structure analysis revealed four subpopulations within the panel, with cultivated potato lines grouping together and separate from wild species and genetic stocks. With pairwise kinship estimates clear separation between potato market classes was observed. Modern breeding efforts have scarcely changed the percentage of heterozygous loci or the frequency of homozygous, single-dose, and duplex loci on a genome level, despite concerted efforts by breeders. In contrast, clear selection in less than 50 years of breeding was observed for alleles in biosynthetic pathways important for market class-specific traits such as pigmentation and carbohydrate composition. Although improvement and diversification for distinct market classes was observed through whole-genome analysis of historic and current potato lines, an increased rate of gain from selection will be required to meet growing global food demands and challenges due to climate change. Understanding the genetic basis of diversification and trait improvement will allow for more rapid genome-guided improvement of potato in future breeding efforts.

Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers

“…In this study, the Infinium SolCAP 8K was used to genotype accessions of the CCC, providing informative data with 72% of polymorphic loci. Previous studies in potato germplasm of other collections reported similar level of polymorphism using the same array: 77% [9], 74% [22], 61% [23], 67% [25], and 76% [66]. A degree of ascertainment bias could be expected when the SolCAP 8K is used to analyze populations such as the Colombian potato germplasm because it was designed based on transcriptome data and EST databases of North American cultivars [19, 21].…”

Software for Genome‐Wide Association Studies in Autopolyploids and Its Application to Potato

“…The SolCAP potato diversity panel consists of both diploid and tetraploid wild species, genetic stocks, and cultivated potato lines with release dates ranging from 1857 to 2011 (Hirsch et al, 2013). The panel was genotyped with an Infinium SNP array of 8303 markers (Hamilton et al, 2011; Felcher et al, 2012), and tetraploid marker dosage was determined by Hirsch et al (2013), principally by visual inspection of the cluster boundaries. Our analysis of population structure was conducted using all 221 tetraploid lines in the panel (Supplemental Table S1), while GWAS results are based on the 187 tetraploid lines with both marker and phenotypic data.…”

Potato Variety Diversity, Determinants and Implications for Potato Breeding Strategy in Ethiopia

“…Ten to twenty five tubers were collected from each of the local varieties identified by growers, traders or marketers. Varieties were genotyped with 8303 SNPs, using the potato Illumina Infinium array developed by the SolCAP project (Hirsch et al 2013). Varieties that shared genotype calls at 99 % or more of the SNP loci were deemed identical.…”