Genetic Linkage Mapping of Economically Important Traits in Cultivated Tetraploid Potato (Solanum tuberosum L.)

Abstract

The objective of this study was to construct a single nucleotide polymorphism (SNP)-based genetic map at the cultivated tetraploid level to locate quantitative trait loci (QTL) contributing to economically important traits in potato (Solanum tuberosum L.). The 156 F1 progeny and parents of a cross (MSL603) between “Jacqueline Lee” and “MSG227-2” were genotyped using the Infinium 8303 Potato Array. Furthermore, the progeny and parents were evaluated for foliar late blight reaction to isolates of the US-8 genotype of Phytophthora infestans (Mont.) de Bary and vine maturity. Linkage analyses and QTL mapping were performed using a novel approach that incorporates allele dosage information. The resulting genetic maps contained 1972 SNP markers with an average density of 1.36 marker per cM. QTL mapping identified the major source of late blight resistance in “Jacqueline Lee.” The best SNP marker mapped ∼0.54 Mb from a resistance hotspot on the long arm of chromosome 9. For vine maturity, the major-effect QTL was located on chromosome 5 with allelic effects from both parents. A candidate SNP marker for this trait mapped ∼0.25 Mb from the StCDF1 gene, which is a candidate gene for the maturity trait. The identification of markers for P. infestans resistance will enable the introgression of multiple sources of resistance through marker-assisted selection. Moreover, the discovery of a QTL for late blight resistance not linked to the QTL for vine maturity provides the opportunity to use marker-assisted selection for resistance independent of the selection for vine maturity classifications.

Genetic mapping in polyploids

“…We mapped 2706 of these SolCAP markers, allowing a direct comparison of our genetic maps with previously-published tetraploid maps which use these markers (Hackett et al, 2013;Massa et al, 2015). Only a single marker from this set was found to have been assigned to a different linkage group between the three studies (solcap_snp_c1_15085), which was mapped on chromosome 6 by Hackett et al and which both we and Massa et al mapped on chromosome 4.…”

“…The SolCAP 8303 Infinium array (Felcher et al, 2012) has been used to genotype at least two other published tetraploid potato mapping populations (Hackett et al, 2013;Massa et al, 2015). We compared the genetic map positions of the common markers as a further check on the validity of our maps.…”

“…Comparison between previously-published tetraploid potato linkage maps (Hackett et al, 2013;Massa et al, 2015) and the integrated map described here. Published as Bourke, P.M., Arens, P., Voorrips, R.E., Esselink, G.D., KoningBoucoiran, C.F.S., Van 'T Westende, W.P.C., et al It has long been recognised that polyploid species do not always neatly fall into the categories of auto-or allopolyploid, leading to the term "segmental allopolyploid" to describe everything in between.…”

“…Recently, methods to incorporate all marker segregation types from a tetraploid cross have been developed (Hackett et al, 2013). However, these methods do not automatically generate homologue maps, as these must be derived using chromosomal maps and phase information (Hackett et al, 2013;Massa et al, 2015).…”

PERGOLA: fast and deterministic linkage mapping of polyploids

“…3,101 of the 40,851 genotypes are missing. The autotetraploid data set consists of 156 samples of the MSL603 potato population [10]. For our linkage map we used a subset of markers where both parents were heterozygous (AABB).…”