Applying genetic markers for self-compatibility in the WSU sweet cherry breeding program

Sweet cherry (Prunus avium) is a member of the Rosaceae family, with a gametophytic self-incompatibility system that strongly affects pollination and fruit set. Alleles at the S-locus control this system, and fertilization does not occur if the Sallele of a haploid pollen gamete matches either S-allele of the diploid maternal pistil. To produce fruit, self-incompatible cherry trees require nearby crosscompatible trees with synchronous flowering. In cherry orchards, two or more cross-compatible pollinizer cultivars are therefore usually inter-planted with the main cultivar. Fortunately, self-compatibility exists, the result of a mutation of one of the alleles at the S-locus, permitting the breeding of self-compatible cultivars that do not require pollinizer trees. The Washington State University (WSU) sweet cherry breeding program seeks to produce self-compatible cultivars (in addition to superior fruit quality and other trait improvements) and desires an early detection system for self-compatible seedlings. PCR-based S-genotyping that included primers for detecting self-compatibility was conducted for 243 seedlings from crosses made in 2004 that initiated this modern breeding program. While self-compatible seedlings were identified, a large proportion of seedlings resulted from unintended parentage, with implications for future breeding strategies

Genetic diversity and virulence profiles of Listeria monocytogenes recovered from bulk tank milk, milk filters, and milking equipment from dairies in the United States (2002 to 2014).

Unpasteurized dairy products are known to occasionally harbor Listeria monocytogenes and have been implicated in recent listeriosis outbreaks and numerous sporadic cases of listeriosis. However, the diversity and virulence profiles of L. monocytogenes isolates recovered from these products have not been fully described. Here we report a genomic analysis of 121 L. monocytogenes isolates recovered from milk, milk filters, and milking equipment collected from bovine dairy farms in 19 states over a 12-year period. In a multi-virulence-locus sequence typing (MVLST) analysis, 59 Virulence Types (VT) were identified, of which 25% were Epidemic Clones I, II, V, VI, VII, VIII, IX, or X, and 31 were novel VT. In a multi-locus sequence typing (MLST) analysis, 60 Sequence Types (ST) of 56 Clonal Complexes (CC) were identified. Within lineage I, CC5 and CC1 were among the most abundant, and within lineage II, CC7 and CC37 were the most abundant. Multiple CCs previously associated with central nervous system and maternal-neonatal infections were identified. A genomic analysis identified variable distribution of virulence markers, Listeria pathogenicity islands (LIPI) -1, -3, and -4, and stress survival island-1 (SSI-1). Of these, 14 virulence markers, including LIPI-3 and -4 were more frequently detected in one lineage (I or II) than the other. LIPI-3 and LIPI-4 were identified in 68% and 28% of lineage I CCs, respectively. Results of this analysis indicate that there is a high level of genetic diversity among the L. monocytogenes present in bulk tank milk in the United States with some strains being more frequently detected than others, and some being similar to those that have been isolated from previous non-dairy related outbreaks. Results of this study also demonstrate significant number of strains isolated from dairy farms encode virulence markers associated with severe human disease

Frequency of detection for all lineage I clonal complexes.

<p>Frequency of detection for all lineage I clonal complexes.</p

Maximum likelihood phylogenetic tree of 121 <i>L</i>. <i>monocytogenes</i> isolates collected from US dairies.

<p>The displayed phylogeentic tree is based on 166,603 core-genome SNPs identified among the study isolates. The phylogenetic tree was inferred using the General Time Reversible model of nucleotide substitution in RAxML with 100 bootstrap replicates. Bar length represents number of substitutions per site.</p

Presence/absence of genes associated with virulence among the study isolates.

<p>Blue = detected. Light blue = shorter than the reference gene used in the analysis. Red = not detected. Columns 1 to 62 (at the bottom of the figure) were based on the analysis described by Kuenne et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197053#pone.0197053.ref047" target="_blank">47</a>] and columns 63 to 76 were based on the analysis described by Maury et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197053#pone.0197053.ref009" target="_blank">9</a>].</p

Presence/absence of genomic island and pathogenicity islands identified among the study CCs.

<p>Blue = detected. Red = not detected.</p

Frequency of detection for all lineage II clonal complexes.

<p>Frequency of detection for all lineage II clonal complexes.</p

Virulence factors that were more frequently detected in one lineage than the other (lineages I and II).

<p>Virulence factors that were more frequently detected in one lineage than the other (lineages I and II).</p

Numbers of isolates, states from which these isolates were recovered, sequence types, clonal complexes (including singletons), virulence types, and epidemic clones (VT epidemic clones) for each lineage represented in this study.

<p>Numbers of isolates, states from which these isolates were recovered, sequence types, clonal complexes (including singletons), virulence types, and epidemic clones (VT epidemic clones) for each lineage represented in this study.</p