ANOVA of <i>Pm-0</i> in interspecific F₂ population

<p>ANOVA of <i>Pm-0</i> in interspecific F₂ population</p

Petiole rating using a 1–5 scale.

<p>1—No pathogen colonies visible on petioles. 2—A small number of colonies limited to the base of some petioles. 3—Colonies on nearly all petioles near the base, and extending halfway up the petiole. 4—Colonies on all petioles, extending the full length of the petiole to the leaf blade, but lacking colony density of fully susceptible cultivars, especially near the leaf blade. 5—All petioles covered with pathogen colonies from petiole base to the leaf blade at high density; most individual colonies have coalesced into larger colonies.</p

<i>Cucurbita okeechobeensis</i> subsp. <i>martinezii</i>.

<p>The wild inedible gourd, native to the Gulf Coast of Mexico [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167715#pone.0167715.ref035" target="_blank">35</a>], is depicted growing in Ithaca, NY. <i>C</i>. <i>okeechobeensis</i> subsp. <i>martinezii</i> is central in the <i>Cucurbita</i> clade and interfertile with other <i>Cucurbita [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167715#pone.0167715.ref036" target="_blank">36</a>]</i>. <i>C</i>. <i>okeechobeensis</i> subsp. <i>martinezii</i> is the original source of powdery mildew resistance now found in <i>C</i>. <i>pepo</i>.</p

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived <i>Pm-0</i>, the Major Powdery Mildew Resistance Locus in Squash

<div><p>Powdery mildew is a major fungal disease on squash and pumpkin (<i>Cucurbita</i> spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within <i>Cucurbita pepo</i> and only infrequently in <i>Cucurbita moschata</i>, but has been achieved in both species through the introgression of a major resistance gene from the wild species <i>Cucurbita okeechobeensis</i> subsp. <i>martinezii</i>. At present, this gene, <i>Pm-0</i>, is used extensively in breeding, and is found in nearly all powdery mildew-resistant <i>C</i>. <i>pepo</i> and <i>C</i>. <i>moschata</i> commercial cultivars. In this study, we mapped <i>C</i>. <i>okeechobeensis</i> subsp. <i>martinezii</i>-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant <i>C</i>. <i>pepo</i> and <i>C</i>. <i>moschata</i> cultivars bred at Cornell University that, by common possession of <i>Pm-0</i>, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 <i>de novo</i> SNP markers in each of the three <i>Cucurbita</i> species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the <i>Pm-0</i> introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a <i>C</i>. <i>pepo</i> cultivar panel that included the Cornell lines, heirlooms, and 68 additional <i>C</i>. <i>pepo</i> cultivars and with an independent F₂ population derived from <i>C</i>. <i>okeechobeensis</i> subsp. <i>martinezii</i> x <i>C</i>. <i>moschata</i>. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection.</p></div

GBS sequencing read and marker statistics for genotyped <i>Cucurbita</i>.

<p>GBS sequencing read and marker statistics for genotyped <i>Cucurbita</i>.</p

CAPS markers with complete co-segregation with <i>Pm-0</i> in a panel of susceptible and resistant cultivars.

<p>R = Homozygous for the <i>C</i>. <i>okeechobeensis</i> subsp. <i>martinezii-</i>derived resistance allele. S = Homozygous for the <i>C</i>. <i>pepo</i>/<i>C</i>. <i>moschata</i> susceptibility allele. H = Heterozygous. ‘Amber Delight’ is a hybrid of ‘Bugle’ and ‘Honeynut’. Left. NBS_S9_1495924 in a putative NBS-LRR gene with an <i>A</i>. <i>thaliana</i> powdery mildew resistance domain. Right. S9_1539675 in an unknown putative gene.</p

Germplasm used for introgression and association mapping of <i>Pm-0</i>.

<p>Germplasm used for introgression and association mapping of <i>Pm-0</i>.</p

Introgression maps of Cornell-bred and heirloom <i>Cucurbita</i> inbreds.

<p>Genomic regions homozygous for the <i>C</i>. <i>pepo</i> alleles, as defined by the heirlooms, are shaded gray; genomic regions homozygous for the <i>C</i>. <i>okeechobeensis</i> subsp. <i>martinezii</i> alleles are shaded dark blue, and heterozygotes are shaded light blue. Cultivars are ordered based on petiole rating, from most resistant to least resistant, and secondly by the size of the largest and most prevalent <i>C</i>. <i>okeechobeensis</i> subsp. <i>martinezii</i> introgression on LG 10. (A) Whole Genome Map. LG 10 contains the <i>Pm-0</i>-containing introgression. (B) LG 10 Map. A dotted box appears around the 516.4 kb region of the introgression that all resistant cultivars share in common, indicating the putative interval for <i>Pm-0</i>. The region spans two scaffolds from the v.3.2 draft genome.</p

Mapping the <i>Pm-0</i> gene in the cultivar panel.

<p>Manhattan plot of negative log p-values for each marker across all 20 LGs. The threshold for significance was set at bonferonni-adjusted α = 0.05 of 1.96e-6. 145 markers on LG 10 are significant and the most highly significant markers fall within the <i>Pm-0</i> candidate interval identified through introgression mapping.</p

Genotype table for entire chile pepper collection

Genotype table for entire chile pepper collection, in variant call format. Includes one individual per each accession, and only SNPs of sufficient quality, for comparison between the chile pepper collection from Mexico and the global collection