Vineland Research and Innovation Center

Ontario, United States

Vineland Research and Innovation Center

Ontario, United States
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The present invention provides methods for isolation of a member of a population which has one or more mutation(s) in one or more target sequence(s) in a population. The method may comprise the steps of: (a) pooling genomic DNA isolated from each member of the population in one or more dimensions; (b) amplifying the one or more target sequence(s) in the pooled genomic DNA, wherein optionally the amplification products are pooled; (c) sequencing the amplified products or obtaining the sequence reads for the amplified products, wherein, optionally, sequencing is by pair-end sequencing and further comprises merging the paired-end reads into composite read(s); (d) identifying the mutation(s) based on alignment-free sequence analysis of sequencing data, optionally by k-mer analysis and (e) identifying individual member(s) of the population comprising the one or more identified mutations in the target sequences, optionally by high-resolution DNA melting (HRM).

El-Sharkawy I.,Vineland Research and Innovation Center | Mila I.,French National Institute for Agricultural Research | Bouzayen M.,French National Institute for Agricultural Research | Jayasankar S.,University of Guelph
Journal of Experimental Botany | Year: 2010

Germin-like proteins (GLPs) have several proposed roles in plant development and defence. Two novel genes (Ps-GLP1 and 2) encoding germin-like protein were isolated from plum (Prunus salicina). Their regulation was studied throughout fruit development and during ripening of early and late cultivars. These two genes exhibited similar expression patterns throughout the various stages of fruit development excluding two important stages, pit hardening (S2) and fruit ripening (S4). During fruit development until the ripening phase, the accumulation of both Ps-GLPs is related to the evolution of auxin. However, during the S2 stage only Ps-GLP1 is induced and this could putatively be in a H2O2-dependent manner. On the other hand, the diversity in the Ps-GLPs accumulation profile during the ripening process seems to be putatively due to the variability of endogenous auxin levels among the two plum cultivars, which consequently change the levels of autocatalytic ethylene available for the fruit to co-ordinate ripening. The effect of auxin on stimulating ethylene production and in regulating Ps-GLPs transcripts was also investigated. These data, supported by their localization in the extracellular matrix, suggest that auxin is somehow involved in the regulation of both transcripts throughout fruit development and ripening. © 2010 The Author(s).

Gunnaiah R.,McGill University | Kushalappa A.C.,McGill University | Duggavathi R.,McGill University | Fox S.,Agriculture and Agri Food Canada | Somers D.J.,Vineland Research and Innovation Center
PLoS ONE | Year: 2012

Background: Resistance in plants to pathogen attack can be qualitative or quantitative. For the latter, hundreds of quantitative trait loci (QTLs) have been identified, but the mechanisms of resistance are largely unknown. Integrated non-target metabolomics and proteomics, using high resolution hybrid mass spectrometry, were applied to identify the mechanisms of resistance governed by the fusarium head blight resistance locus, Fhb1, in the near isogenic lines derived from wheat genotype Nyubai. Findings: The metabolomic and proteomic profiles were compared between the near isogenic lines (NIL) with resistant and susceptible alleles of Fhb1 upon F. graminearum or mock-inoculation. The resistance-related metabolites and proteins identified were mapped to metabolic pathways. Metabolites of the shunt phenylpropanoid pathway such as hydroxycinnamic acid amides, phenolic glucosides and flavonoids were induced only in the resistant NIL, or induced at higher abundances in resistant than in susceptible NIL, following pathogen inoculation. The identities of these metabolites were confirmed, with fragmentation patterns, using the high resolution LC-LTQ-Orbitrap. Concurrently, the enzymes of phenylpropanoid biosynthesis such as cinnamyl alcohol dehydrogenase, caffeoyl-CoA O-methyltransferase, caffeic acid O-methyltransferase, flavonoid O-methyltransferase, agmatine coumaroyltransferase and peroxidase were also up-regulated. Increased cell wall thickening due to deposition of hydroxycinnamic acid amides and flavonoids was confirmed by histo-chemical localization of the metabolites using confocal microscopy. Conclusion: The present study demonstrates that the resistance in Fhb1 derived from the wheat genotype Nyubai is mainly associated with cell wall thickening due to deposition of hydroxycinnamic acid amides, phenolic glucosides and flavonoids, but not with the conversion of deoxynivalenol to less toxic deoxynivalenol 3-O-glucoside. © 2012 Gunnaiah et al.

Goyette B.,Vineland Research and Innovation Center | Vigneault C.,Agriculture and Agri Food Canada | Raghavan V.,McGill University | Charles M.-T.,Agriculture and Agri Food Canada
Food and Bioprocess Technology | Year: 2012

An experimental hyperbaric system was designed and built to explore the effect of hyperbaric treatment on the respiration rate (RR) and respiratory quotient (RQ) of tomato. It consists of five containers that can be individually pressurized from 1 to 9 atm abs. The respirometer was equipped with a flow meter, control valve, pressure transducer, CO 2 and O 2 gas analyzer, and type T thermocouples that are all connected to a data acquisition and control card. A software interface was programmed to allow control of the air flow rate through the proportional valve of the flow meter based on a proportional-integral-derivative algorithm system. Hyperbaric treatments have been performed on tomato fruit, and it was observed that RR was inversely proportional to pressure. © 2011 Springer Science+Business Media, LLC.

Saito T.,Vineland Research and Innovation Center | Bjornson S.,Saint Mary's University, Halifax
Journal of Invertebrate Pathology | Year: 2013

Convergent lady beetles, Hippodamia convergens Guérin-Méneville are host to the braconid endoparasitoid, Dinocampus coccinellae (Schrank) and the microsporidian pathogen, Tubulinosema hippodamiae. The interrelationship between the endoparasitoid and the pathogen in H. convergens adults under laboratory conditions was examined by quantifying the effect of microsporidiosis on D. coccinellae development and host preference. Uninfected wasps were provided either uninfected or T. hippodamiae-infected beetles as hosts and the development of their progeny was observed over 30. days. The duration of endoparasitoid development from egg deposition in the host until adult eclosion for D. coccinellae did not differ significantly, regardless of the infection status of the host beetle. All wasp progeny that developed within, and emerged from, T. hippodamiae-infected beetles were infected with the microsporidian pathogen (n=48; 100% transmission). Infected D. coccinellae adults were also provided either uninfected or T. hippodamiae infected host beetles so that the development of their progeny could be assessed over 30. days. Endoparasitoid development did not differ significantly; however, a significantly greater proportion of beetles stung by microsporidia-infected wasps did not contain an endoparasitoid larva when dissected at the end of the 30-day trial when compared to those stung by uninfected wasps. This suggests that the pathogen may reduce wasp fecundity or egg viability. Examination of paraffin-embedded D. coccinellae adult tissues revealed an extensive microsporidian infection throughout all major organs and tissues with exception of the ovary. During host choice trials, uninfected and microsporidia-infected D. coccinellae adults pursued, took an ovipositional stance, and attacked uninfected beetles more often than microsporidia-infected hosts but these observations did not differ significantly (P> 0.05). © 2013 Elsevier Inc.

Fu Y.-B.,Agriculture and Agri Food Canada | Somers D.J.,Vineland Research and Innovation Center
Euphytica | Year: 2011

Genetic impacts under selective breeding of agricultural crops have been frequently investigated with molecular tools, but inadequate attention has been paid to assess genetic changes under long-term genetic improvement of plant traits. Here we analyzed allelic changes with respect to wheat trait improvement in 78 Canadian hard red spring wheat cultivars released from 1845 to 2004 and screened with 370 mapped SSR markers. The improvements in quality, maturity, yield, disease, stem rust, leaf rust, sawfly resistance, and agronomy were considered. A total of 154 (out of 370) loci with significant allelic changes across 21 chromosomes were detected in the 78 wheat cultivars separated into improved versus non-improved groups for eight traits. The number of significant loci for improving a trait ranged from four for quality to 68 for yield and averaged 35. Many more loci with significant allelic reduction for improving a trait were detected than those with significant allelic increase. Selection for early maturity introduced more alleles, but improving the other traits purged more alleles. Significantly lower numbers of unique alleles were found in the cultivars with improved traits. The distributions of unique allele counts also varied greatly across the 21 chromosomes with respect to trait improvement. Significant SSR variation between two cultivar groups was observed for improvement in seven traits, but not in stem rust. The proportional SSR variation residing between two groups ranged from 0. 014 to 0. 118. The proportional SSR variations within the improved cultivar groups consistently were much lower than those within the non-improved groups. These findings clearly demonstrate the association between allelic changes and wheat trait improvements and are useful for understanding the genetic modification of the wheat genome by long-term wheat breeding. © 2010 Her Majesty the Queen in Right of Canada.

Grygorczyk A.,University of Guelph | Lesschaeve I.,Vineland Research and Innovation Center | Corredig M.,University of Guelph | Duizer L.,University of Guelph
Food Quality and Preference | Year: 2013

During development of a new product, it is important to understand the key attributes of importance to consumers. From a sensory perspective, it is not possible to determine this via conventional profiling where consumer information is not sought. The method examined in this study, which we will refer to as preferred attribute elicitation (PAE), attempts to derive this information from an untrained panel of consumers by asking the group of panelists to agree on a set of attributes which they consider important. This approach also aids in reducing the amount of ambiguity in interpreting terms selected by consumers as all panelists must agree to the terms and feel capable of rating them. The employment of the PAE method in the food industry has so far been limited, therefore, there exists a need to study the strengths and weaknesses of the PAE method in comparison to descriptive analysis to better understand its place among sensory analysis methodologies. The method was effective for extracting key sensory properties of yogurts and panelists were capable of characterizing yogurts in a meaningful way. There is a need to continue assessment of the technique, particularly with more complex food systems. © 2012 Elsevier Ltd.

McGrath D.,Vineland Research and Innovation Center | Henry J.,Vineland Research and Innovation Center
Urban Forestry and Urban Greening | Year: 2016

Soil compaction significantly impacts urban tree survival and herbaceous vegetation recruitment along roadsides. Soil samples were collected at two highway tree planting sites in Ontario, Canada. The average soil bulk density in the 0–10 and 20–30 cm range was 1.45 g cm−3 and 1.55 g cm−3, respectively, at Site 1. At site 2, the average soil bulk density in the 0–10 and 20–30 cm range was 1.49 g cm−3 and 1.67 g cm−3, respectively. Six treatments were established on each site to determine the amount of organic amendment required to decrease bulk density and increase tree growth as a measurement of successful tree establishment. Compost was incorporated into the soil at 0%, 10%, 25% and 50% on a volume-to-volume basis at both sites. In 2014 Acer x freemanii Autumn Blaze® ‘Jeffersred’ whips were planted into each treatment bed (Site 1, n = 36 and Site 2 n = 42). Bulk density, porosity, soil pH, EC, tree survival, height, shoot extension and chlorophyll content were measured for the 2014 and 2015 growing seasons. Incorporation of 25% v/v compost consistently decreased bulk density to below-root restricting thresholds, resulting in improved tree growth. Significant differences were observed in chlorophyll content between organic-amended remediated treatment beds compared to the control; chlorophyll content was significantly higher (p < 0.05) for the 25% and 50% treatments throughout the 2015 growing season at both sites. Incorporation of compost at 10% and 25% v/v effectively reduced soil bulk density, leading to increased growth and reduced tree stress at both sites. This study demonstrates the importance of understanding the baseline of soil physical structure in prescribing remediation strategies, including organic amendments, in urban tree planting © 2016 Elsevier GmbH

Bowen A.J.,Brock University | Bowen A.J.,Vineland Research and Innovation Center | Reynolds A.G.,Brock University
Journal of Agricultural and Food Chemistry | Year: 2012

This study aimed to elucidate the odor potency of aroma compounds in Riesling and Vidal blanc (syn. Vidal) table wines and icewines from the Niagara Peninsula using stir bar sorptive extraction-gas chromatography-olfactometry- mass spectrometry. Dilution analysis determined the most odor-potent compounds in Vidal and Riesling icewines (n = 2) and table wines (n = 2) from a commercial producer. The top 15 odor-potent compounds in each wine were identified and quantified, resulting in 23 and 24 compounds for Riesling and Vidal, respectively. The most odor-potent compounds were β-damascenone, decanal, 1-hexanol, 1-octen-3-ol, 4-vinylguaiacol, ethyl hexanoate, and ethyl 3-methylbutyrate. In general, icewines had higher concentrations of most aroma compounds compared to table wines. Through computation of odor activity values, the compounds with the highest odor activity for the icewines were β-damascenone, 1-octen-3-ol, ethyl octanoate, cis-rose oxide, and ethyl hexanoate. In table wines the highest odor activity values were found for ethyl octanoate, β-damascenone, ethyl hexanoate, cis-rose oxide, ethyl 3-methylbutyrate, and 4-vinylguaiacol. These findings provide a foundation to determine impact odorants in icewines and the effects of viticultural and enological practices on wine aroma volatile composition. © 2012 American Chemical Society.

The present invention provides high-throughput methods of screening for members of a population comprising mutation(s) in one or more target sequence(s). The methods may comprise the steps of: pooling genomic DNA isolated from each member of said population; amplifying the one or more target sequence(s) in the pooled genomic DNA; pooling the amplification products of step (b) to create a library of amplification products; sequencing the amplified products by pair-end sequencing to produce paired-end reads for each sequencing reaction or obtaining paired-end sequence reads for the amplified products; merging the paired-end reads into composite read(s); mapping the composite read(s) to reference sequence(s) to identify mutation(s) in the one or more target sequence(s); and identifying member(s) of the population comprising one or more of the identified mutations in the target sequence(s). The invention further provides kits for use with the methods.

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