Wheat is the world’s third largest food crop, and is relied upon as a food source by millions of people. Securing the supply of wheat is a problem because it is susceptible to many biotic and abiotic factors that limit production. One such factor, sprouting of the grain in the head, because of untimely rainfall prior to harvest, is a substantial problem worldwide. Pre-harvest sprouting has a significant impact on wheat growers, who suffer considerable economic hardship as a result of yield loss during harvesting and subsequent downgrading of their sprouted crops. Wheat processors are also affected by this problem, because sprouted grain has significantly altered chemical properties, making it unsuitable for its intended purpose, and often rendering it suitable for animal consumption only. This study investigated mechanisms of dormancy, in the diploid wheat Triticum tauschii (Coss.) Schmalh., to assess their suitability for use in hexaploid (bread) wheat to prevent pre-harvest sprouting. A soluble germination inhibitor was found in the bracts (palea, lemma and glumes) surrounding the grain of T. tauschii. Fractionation of an aqueous extract from the bracts, by HPLC, identified vanillic acid as being likely to be involved in this inhibition. Further analysis of the extract also identified a strong anti-oxidant capacity, indicating that part of the inhibition of germination may arise from the prevention of oxygen reaching the embryo.

Cattle are naturally colonized by enterohemorrhagic Escherichia coli within the gastrointestinal tract. The most notorious of the enterohemorrhagic E. coli is E. coli O157:H7, which can cause serious illness to humans if ingested. To ensure that the United States has a safe food supply, research is ongoing in pre-harvest food safety and pathogen intervention strategies. While advances in pre-harvest intervention strategies are encouraging, no method has proven to completely eliminate and/or control O157:H7. A key limitation to successful pathogen intervention strategies is the inability to track and monitor pathogens in a real-time fashion. Through the use of bioluminescent plasmids harboring the luxCDABE cassette, pathogen tracking could be a viable solution. Bioluminescent plasmids are capable of facilitating the tracking, pathogenesis and physical locations of pathogens, thus enabling researchers to have a better understanding of the pathogenic process.

Pre-harvest sprouting (PHS) in bread wheat (<i>Triticum aestivum</i> L.) is one of the major abiotic constraints influencing the production of high quality grain. The flour milled from sprouted wheat grains has increased Ñ-amylase activity as compared to non-sprouted grain. PHS negatively affects the properties of flour with deleterious effects on bread and noodle quality. White-grained wheat is generally more susceptible to PHS damage than red-grained wheat. The objectives of this study were to identify a suitable method for phenotyping PHS resistance and to identify PHS resistance genomic regions and markers that could be used for marker-assisted selection in wheat improvement programs. A doubled haploid (DH) mapping population from a cross between two white-grained spring wheat genotypes, Argent (non-dormant) and W98616 (dormant) was used in this study. Forty DH lines (20 dormant and 20 non-dormant) were evaluated for germination frequency, Falling Number, and Ñ-amylase activity in dry and water-imbibed seeds and spikes. The germination test was the most reliable method for measurement of PHS resistance, whereas the Falling Number and Ñ-amylase activity in dry harvested seeds could not be correlated to dormancy levels. However, a positive association (r = 0.60***) was detected between germination frequency and Ñ-amylase activity in imbibed seeds. To identify the genomic regions associated with PHS resistance, a genetic linkage map with a total genome coverage of 2,577 cM was developed. The map was constructed from 913 scored markers (356 SSR, 290 AFLP, 258 DArT and 9 EST) with an average marker density of 3.7 cM/marker. Five genomic regions on chromosomes 1A, 3A, 4A, 7A and 7D were associated with PHS resistance by interval mapping and all regions were contributed by the dormant parent W98616. A total of 60 Canadian wheat cultivars and experimental lines were screened with three SSR markers, DuPw004, barc170 and wmc650, located under the major quantitative trait locus (QTL) on chromosome 4A. The SSR markers explained 60-75% of the total variation in germination frequency among different wheat genotypes. By using the DuPw004 marker in marker-assisted back crossing, the population size in the BC1F1 and BC2F1 generations were reduced by 41% and 59%, respectively. Thus, the 4A QTL markers have been proven useful for marker-assisted selection of PHS resistance for wheat improvement.

Pre-harvest sprouting (PHS) in bread wheat (<i>Triticum aestivum</i> L.) is one of the major abiotic constraints influencing the production of high quality grain. The flour milled from sprouted wheat grains has increased Ñ-amylase activity as compared to non-sprouted grain. PHS negatively affects the properties of flour with deleterious effects on bread and noodle quality. White-grained wheat is generally more susceptible to PHS damage than red-grained wheat. The objectives of this study were to identify a suitable method for phenotyping PHS resistance and to identify PHS resistance genomic regions and markers that could be used for marker-assisted selection in wheat improvement programs. A doubled haploid (DH) mapping population from a cross between two white-grained spring wheat genotypes, Argent (non-dormant) and W98616 (dormant) was used in this study. Forty DH lines (20 dormant and 20 non-dormant) were evaluated for germination frequency, Falling Number, and Ñ-amylase activity in dry and water-imbibed seeds and spikes. The germination test was the most reliable method for measurement of PHS resistance, whereas the Falling Number and Ñ-amylase activity in dry harvested seeds could not be correlated to dormancy levels. However, a positive association (r = 0.60***) was detected between germination frequency and Ñ-amylase activity in imbibed seeds. To identify the genomic regions associated with PHS resistance, a genetic linkage map with a total genome coverage of 2,577 cM was developed. The map was constructed from 913 scored markers (356 SSR, 290 AFLP, 258 DArT and 9 EST) with an average marker density of 3.7 cM/marker. Five genomic regions on chromosomes 1A, 3A, 4A, 7A and 7D were associated with PHS resistance by interval mapping and all regions were contributed by the dormant parent W98616. A total of 60 Canadian wheat cultivars and experimental lines were screened with three SSR markers, DuPw004, barc170 and wmc650, located under the major quantitative trait locus (QTL) on chromosome 4A. The SSR markers explained 60-75% of the total variation in germination frequency among different wheat genotypes. By using the DuPw004 marker in marker-assisted back crossing, the population size in the BC1F1 and BC2F1 generations were reduced by 41% and 59%, respectively. Thus, the 4A QTL markers have been proven useful for marker-assisted selection of PHS resistance for wheat improvement.

Master of Science / Food Science Institute / Sara E. Gragg / Leafy greens have been recognized as vehicles for transmission of foodborne pathogens and an effective pre-harvest intervention to control them is currently lacking. After harvest, lettuce is often subjected to chlorinated water to reduce the microbial load in the water and on the lettuce tissue. While moderately effective, there is also a need for improved postharvest interventions. The purpose of Objective I was to 1) determine potassium bisulfate efficacy at reducing populations of Escherichia coli (E. coli) and Listeria innocua (L. innocua) when applied pre-harvest to lettuce, and 2) assess the impact on product quality at harvest. Potassium bisulfate reduced E. coli populations on inoculated lettuce by 1.32 log₁₀ CFU/g (P=0.0002) and L. innocua by 1.18 log₁₀ CFU/g (P=0.0017). No detectable differences were observed in color (P>0.05); however, brown spots were observed on various leaves sprayed with potassium bisulfate. The purpose of Objective II was to employ a blend of benzalkonium chloride, acetic acid, and methyl paraben (BAM) as a postharvest wash on romaine and iceberg lettuce and to 1) determine efficacy at reducing populations of Listeria monocytogenes (L. monocytogenes), E. coli O157:H7 and Salmonella, 2) measure changes in aerobic bacteria throughout the shelf life, and 3) quantify benzalkonium chloride and methyl paraben residues post-washing. To quantify efficacy of BAM reducing pathogenic bacterial populations, fresh-cut romaine and iceberg lettuce were inoculated with L. monocytogenes, E. coli O157:H7, or Salmonella and washed in BAM at concentrations of 0%, 1%, 2% or 3% for one or five minutes. When plated on recovery media, contact time and wash concentration was not significant (P>0.05) for Salmonella on either product. Concentration was significant (P=0.0189) for L. monocytogenes on romaine; however, the greatest reduction observed was <1.0 log₁₀ CFU/g. The 3% wash significantly reduced E. coli O157:H7 on romaine by 1.75 log₁₀ CFU/g, which is 0.66 log₁₀ CFU/g better than the 0% wash. Following washing, wash water was analyzed and data demonstrate that all wash concentrations significantly (P≤0.05) reduced each foodborne pathogen by >2.0 log₁₀ CFU/g in the wash water. To quantify benzalkonium chloride and methyl paraben residues, as well as changes in aerobic bacteria and product quality, fresh-cut romaine and iceberg lettuce were subjected to a 1 minute wash in BAM at concentrations of 0%, 1%, 2%, or 3% and immediately sampled to determine aerobic populations and product quality. Concentrations 0% and 2% were also packaged into retail storage bags and sampled on days 0, 3, 5, and 7. Residues were quantified on these days as well. On day 0, aerobic populations did not vary according to wash concentration (P>0.05). With regards to shelf-life data, the 2% wash significantly reduced (P=0.0203) aerobic bacteria on romaine lettuce; however, no significant difference was observed on iceberg lettuce (P=0.0819). With regards to overall visual appearance of romaine or iceberg lettuce, no significant difference was detected between 0% and 2% BAM washes for each day throughout the shelf-life study (P>0.05). Methyl paraben and benzalkonium chloride residues were <5.0 and <10.0 ppm, respectively, on both products on each sampling day.

In malting barley, rapid germination is desirable and linked to end use quality. Modern malting varieties have been bred for low seed dormancy leading to issues with pre-harvest sprouting in wetter growing regions. To maintain malting capacity while minimizing germination on the maternal plant requires in-depth understanding of the genetic regulation of dormancy in malting barley. Currently, the major effect QTLs SD1 and SD2 have been shown to influence dormancy across multiple populations of barley, though the physiological mechanisms involved remain unclear. To search for novel genetic regions that influence primary dormancy, three mapping populations were assessed including two Canadian biparental populations (Synch and Legci) as well as a diversity panel sourced from multiple locations worldwide (ICARDA AM-14). The SD2 locus had a major effect in the Synch population while the SD1 locus had a major effect in the Legci population and neither SD1 nor SD2 were linked to dormancy in the diversity panel. Instead, 14 additional marker trait associations were identified in AM-14 suggesting that investigating a broader range of genetic regulation of dormancy outside of North American varieties may provide solutions to regulate this trait. Additional testing on SD1 revealed that variation at this locus did not affect ABA sensitivity during germination or GA or ABA-regulated gene expression during grain fill. Indeed, lines containing the non-dormant SD1 allele germinate at a similar rate as the dormant SD1 seeds when the glumella was removed from the embryo. This indicated that the effect of the alanine aminotransferase gene underlying the SD1 allele is dependent on physical restriction on the embryo or the hypoxic effects produced by the glumella. Imposing a hypoxic (5% oxygen) environment on exposed embryos revealed an association between non-dormancy at SD1 and reduced sensitivity to the suppressive effects of hypoxia on germination. This suggests that alanine aminotransferase regulates dormancy release during barley germination at least in part through regulation of the seed’s response to hypoxia.

Foodborne outbreaks have continued to be associated with produce contamination originating from on-farm sources, such as soil or agricultural water. Additionally, the heterogeneity of the pre-harvest environment complicates the development of universal strategies for managing produce safety risks. Understanding the ecology and epidemiology of foodborne pathogens and fecal indicator bacteria (FIB) by growing regions, sample types, scale of analysis, and detection method is essential for developing targeted mitigation strategies. This dissertation utilized quantitative research methods and statistical modeling to examine the impact of sampling method, spatial, temporal, meteorological, and physicochemical factors on pathogen prevalence and FIB levels. Key findings highlight that the drivers of prevalence differ between pathogens and were influenced by sample type, scale, and region.. The variations in associations emphasize that risk varies by space and time. Therefore, results support regional and scale-dependent food safety standards and guidance documents for controlling hazards to minimize risk. Additionally, the method used for pathogen detection influences prevalence highlighting the need for standard methods since methodological differences confound comparisons across studies. Furthermore, since agricultural water quality is an important food safety priority, this dissertation aimed to determine the efficacy of chemical antimicrobial sanitizers against Salmonella in pre-harvest agricultural water. Results demonstrated that certain sanitizer treatments and conditions can significantly reduce Salmonella populations in preharvest agricultural water sources and thus may serve as a risk reduction option when used correctly. / Doctor of Philosophy / Fresh fruits and vegetables are continually implicated in foodborne outbreaks. Additionally, the source of the pathogen that causes illness in these outbreaks is often due to contact with contaminated soil or water on the farm. Since the environment is extremely diverse, the risk of foodborne pathogens is not uniform across a farm and between farms. Therefore, the development of a one-size-fits-all plan to reduce the risk of foodborne pathogens from contaminating produce on a farm is difficult. Understanding the incidence and distribution of foodborne pathogens and fecal bacteria and how these microorganisms interact with the environment is important to develop strategies to manage risk. Additionally, understanding how the prevalence of bacteria varies by state, medium (water vs soil), and farm is needed to develop targeted mitigation plans. This dissertation utilized laboratory and field-based experiments to understand how space, time, weather, and physical properties impact the occurrence of foodborne pathogens and fecal bacteria. The primary results show factors that impact prevalence are different between pathogens (Salmonella vs Listeria vs E. coli). Furthermore, the occurrence differed by sampling method (molecular vs culture), sample type (water vs soil), scale (within a farm vs between multiple farms), and region emphasizing that the risk from foodborne pathogens varies over space and time. Overall, this dissertation's results suggest that both regional and scale-specific guidelines are needed to reduce foodborne pathogen risks in the farm environment. Lastly, since the quality of the water used in growing fresh produce is an important food safety priority, the effectiveness of chemical antimicrobial sanitizers against Salmonella in agricultural water was evaluated. Results demonstrated that certain sanitizer treatments and conditions (sanitizer concentrations, water temperatures) can significantly reduce Salmonella populations in pre-harvest water sources and may serve as a risk reduction option when sanitizers are used correctly.

Doctor of Philosophy / Department of Agronomy / Guihua Bai / Allan K. Fritz / Wheat pre-harvest sprouting (PHS), germination of physiologically matured grains in a wheat spike before harvesting, can cause significant reduction in grain yield and end-use quality. Many quantitative trait loci (QTL) for PHS resistance have been reported in different sources. To determine the genetic architecture of PHS resistance and its relationship with grain color (GC) in US hard winter wheat, a genome-wide association study (GWAS) on both PHS resistance and GC was conducted using in a panel of 185 U.S. elite breeding lines and cultivars and 90K wheat SNP arrrays. PHS resistance was assessed by evaluating sprouting rates in wheat spikes harvested from both greenhouse and field experiments. Thirteen QTLs for PHS resistance were identified on 11 chromosomes in at least two experiments, and the effects of these QTLs varied among different environments. The common QTLs for PHS resistance and GC were identified on the long arms of the chromosome 3A and 3D, indicating pleiotropic effect of the two QTLs. Significant QTLs were also detected on chromosome arms 3AS and 4AL, which were not related to GC, suggesting that it is possible to improve PHS resistance in white wheat. To identify markers closely linked to the 4AL QTL, genotyping-by-sequencing (GBS) technology was used to analyze a population of recombinant inbred lines (RILs) developed from a cross between two parents, “Tutoumai A” and “Siyang 936”, contrasting in 4AL QTL. Several closely linked GBS SNP markers to the 4AL QTL were identified and some of them were coverted to KASP for marker-assisted breeding. To investigate effects of the two non-GC related QTLs on 3AS and 4AL, both QTLs were transferered from “Tutoumai A” and “AUS1408” into a susceptible US hard winter wheat breeding line, NW97S186, through marker-assisted backcrossing using the gene marker TaPHS1 for 3AS QTL and a tightly linked KASP marker we developed for 4AL QTL. The 3AS QTL (TaPHS1) significantly interacted with environments and genetic backgrounds, whereas 4AL QTL (TaMKK3-A) interacted with environments only. The two QTLs showed additive effects on PHS resistance, indicating pyramiding these two QTLs can increase PHS resistance. To improve breeding selection efficiency, genomic prediction using genome-wide markers and marker-based prediction (MBP) using selected trait-linked markers were conducted in the association panel. Among the four genomic prediction methods evaluated, the ridge regression best linear unbiased prediction (rrBLUP) provides the best prediction among the tested methods (rrBLUP, BayesB, BayesC and BayesC0). However, MBP using 11 significant SNPs identified in the association study provides a better prediction than genomic prediction. Therefore, for traits that are controlled by a few major QTLs, MBP may be more effective than genomic selection.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / T. G. Nagaraja / Escherichia coli O157:H7 and over 380 non-O157 serotypes of Shiga toxin producing E. coli (STEC) are human food-borne pathogens that inhabit the hindgut of ruminants and are shed in the feces, which subsequently contaminate food products. Recent epidemiological data have shown that six non-O157 STEC (O26, O103, O111, O121, O45 and O145) account for majority of human STEC infections. Fecal shedding of STEC is influenced by a number of factors, including diets, supplements, and feed additives, because of their potential to alter hindgut ecosystem. Not much is known about the fecal shedding of non-O157 STEC in cattle because of lack of standardized detection methods. Fecal shedding of E. coli O157:H7 was studied to determine the effects of supplemental urea, monensin, an ionophore, and ractopamine, a beta-agonist. Cattle fed monensin at 44 mg/kg of feed had lower (P = 0.05) fecal O157:H7 prevalence than cattle fed 33 mg/kg. Supplemental urea (0.35 or 0.70% of the diet) and inclusion of ractopamine at 200 mg/animal/day had no effect on fecal shedding of E. coli O157:H7. In an experimental inoculation study, inclusion of corn starch to a distiller’s grains (DG)-supplemented diet had no effect on fecal shedding of E. coli O157 suggesting that either the decreased starch content in the DG-supplemented diet is not a factor in the increased shedding of E. coli O157:H7 or inclusion of pure starch in the diet may not have achieved our intended goal to have starch flow into the hindgut similar to that of corn grain. A multiplex PCR to detect O26, O45, O103, O111, O121, O145, and O157 was designed and applicability to detect the seven serogroups in cattle feces was evaluated. A multiplex PCR, designed to detect E. coli O104, feces showed presence of O104 in cattle feces (20.6%), but the isolated strains did not carry genes characteristic of the virulent strain responsible for the 2011 food-borne outbreak in Germany. Two preharvest interventions, a siderophore receptor and porin proteins-based vaccine and a Lactobacillus acidophilus-based direct-fed microbial, intended to control E. coli O157, had no effect on fecal shedding of O26 assessed by culture-based or PCR-based method.

At the Swedish forest owner association Mellanskog pre-harvest planning prior to thinning is traditionally performed by company foresters. In the past three years, Mellanskog has in one business area, instead outsourced pre-harvest planning to thinning contractors. The purpose of this study was to investigate how the outsourcing of pre-harvest planning is perceived by the company foresters and contractors and how it affects the working environment and costs. The study showed positive experiences from foresters and contractors, though there were some responsibility issues and economic concerns. Outsourcing improves the contractor’s working environment, but deteriorates that of the foresters. Having foresters performing the pre-harvest planning is more expensive than having contractors performing it, especially on small harvesting worksites.