Data_Sheet_1_Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids.DOCX

<p>Haploid potato populations derived from a single tetraploid donor constitute an efficient strategy to analyze markers segregating from a single donor genotype. Analysis of marker segregation in populations derived from crosses between polysomic tetraploids is complicated by a maximum of eight segregating alleles, multiple dosages of the markers and problems related to linkage analysis of marker segregation in repulsion. Here, we present data on two monoparental haploid populations generated by prickle pollination of two tetraploid cultivars with Solanum phureja and genotyped with the 12.8 k SolCAP single nucleotide polymorphism (SNP) array. We show that in a population of monoparental haploids, the number of biallelic SNP markers segregating in linkage to loci from the tetraploid donor genotype is much larger than in putative crosses of this genotype to a diverse selection of 125 tetraploid cultivars. Although this strategy is more laborious than conventional breeding, the generation of haploid progeny for efficient marker analysis is straightforward if morphological markers and flow cytometry are utilized to select true haploid progeny. The level of introgressed fragments from S. phureja, the haploid inducer, is very low, supporting its suitability for genetic analysis. Mapping with single-dose markers allowed the analysis of quantitative trait loci (QTL) for four phenotypic traits.</p

Boxplots of the rAUDPC values of eight quantitative resistant (R8) and susceptible (S8) tetraploid potato genotypes used to construct the samples for RNA-Seq analysis.

<p>Boxplots of the rAUDPC values of eight quantitative resistant (R8) and susceptible (S8) tetraploid potato genotypes used to construct the samples for RNA-Seq analysis.</p

SNPs in candidate genes showing association with rAUDPC, MCR and/or PM in three or four association models with -Log10(P) > 2.

<p>Full data are available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.s004" target="_blank">S4</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.s006" target="_blank">S6</a> Files.</p

Number of SolCAP SNPs and corresponding loci showing putative associations with MCR, rAUDPC and PM based on different ranking criteria.

<p>Number of SolCAP SNPs and corresponding loci showing putative associations with MCR, rAUDPC and PM based on different ranking criteria.</p

Genes with functions in the jasmonate pathway that were tested for association with MCR, rAUDPC and PM.

<p>Genes with functions in the jasmonate pathway that were tested for association with MCR, rAUDPC and PM.</p

Number of genes containing from 1 to 60 SNPs with different allele frequency in the R8 and S8 genotype pools.

<p>Number of genes containing from 1 to 60 SNPs with different allele frequency in the R8 and S8 genotype pools.</p

Genomic segments harboring QTL for MCR, rAUDPC and PM based on GWAS.

<p>Genomic segments harboring QTL for MCR, rAUDPC and PM based on GWAS.</p

Frequency distribution of the <i>tbr</i> (<i>S</i>. <i>tuberosum</i>) SNP alleles with different allele frequencies (q < 0.01) in the R8 and S8 genotype pools (significant SNPs) and without significant differences (q > 0.01, non-significant SNPs).

<p>Frequency distribution of the <i>tbr</i> (<i>S</i>. <i>tuberosum</i>) SNP alleles with different allele frequencies (q < 0.01) in the R8 and S8 genotype pools (significant SNPs) and without significant differences (q > 0.01, non-significant SNPs).</p

SolCAP SNPs associated with MCR, rAUDPC and/or PM in three or four association models (-Log10(P) > 4).

<p>Full data are available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.s009" target="_blank">S9</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.s011" target="_blank">S11</a> Files.</p

Physical maps of the potato chromosomes I to VI (pseudomolecules v4.03).

<p>Maps ‘a’ show to the left of the central bar (representing the chromosome) the positions of markers that were previously shown to be linked with <i>P</i>. <i>infestans</i> QRL in potato and the highly syntenic tomato (<i>Solanum lycopersicum</i>). Markers linked to <i>P</i>. <i>infestans</i> QRL in tomato are underlined (for physical positions and references see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.s008" target="_blank">S8 File</a>). The candidate loci tested for association with MCR, rAUDPC and PM in the PIN184 population previously [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.ref005" target="_blank">5</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.ref011" target="_blank">11</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.ref024" target="_blank">24</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.ref034" target="_blank">34</a>] and in this paper (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.s003" target="_blank">S3 File</a>) are shown to the right of maps ‘a’. Nine major genes for resistance to <i>P</i>. <i>infestans</i> (<i>R1</i>, <i>R2</i>, <i>R3</i>, <i>Rpi-blb1/RB</i>, <i>Rpi-blb2</i>, <i>Rpi-blb3</i>, <i>Rpi-vnt1</i>, <i>Rpi-abpt</i>, <i>Ph-3</i>) and the <i>StCDF1</i> locus controlling day length dependent tuberization are also included in maps ‘a’ (physical positions and references in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.s008" target="_blank">S8 File</a>). Loci harboring DNA variants associated with MCR, rAUDPC and/or PM are labelled with green, blue and red stars, respectively. Maps ‘b’ show the positions of the SolCAP SNPs that were associated with MCR (green bars), rAUDPC (blue bars) and PM (red bars) in the PIN184 population, on the left according to the association model without correction for population structure (model S) and on the right according to the association models correcting for population structure with different methods (K₁, K₂ and K₂Q, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#sec012" target="_blank">Materials and Methods</a>). SolCAP SNPs associated with at least one trait with p < 10⁻⁴ were included. The length of the horizontal bars is proportional to the p-value. The dotted vertical lines indicate–Log10(P) = 4. Maps ‘c’ show on the right (blue dots) the positions of candidate genes that (i) harbor SNPs with different allele frequencies in the R8 and S8 genotype pools with high (R) and low (S) resistance to late blight (Materials and Methods), and (ii) had differential transcript levels between three genotype pools with different MCR levels in SuperSAGE analysis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.ref023" target="_blank">23</a>]. The green dots on the left of maps ‘c’ show the positions of candidate genes that (i) harbor SNPs with different allele frequencies in the R8 and S8 genotype pools, (ii) had differential transcript levels between the three genotype pools with different MCR levels in SuperSAGE, and (iii) were up or down regulated upon infection with <i>P</i>. <i>infestans</i> in SuperSAGE (for details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156254#pone.0156254.s007" target="_blank">S7 File</a>). Maps ‘d’ show the distribution of 42,688 SNPs with different allele frequencies in the R8 and S8 genotype pools (q < 0.01) on the potato pseudomolecules. The scale [number of SNPs per Mbp] is shown horizontally on top of each chromosome. SNP density peaks which overlapped with genomic segments harboring QTL for MCR or PM based on GWAS are indicated by numbers 1 to 8.</p