Simultaneous fine mapping of closely linked epistatic quantitative trait loci using combined linkage disequilibrium and linkage with a general pedigree

Causal mutations and their intra- and inter-locus interactions play a critical role in complex trait variation. It is often not easy to detect epistatic quantitative trait loci (QTL) due to complicated population structure requirements for detecting epistatic effects in linkage analysis studies and due to main effects often being hidden by interaction effects. Mapping their positions is even harder when they are closely linked. The data structure requirement may be overcome when information on linkage disequilibrium is used. We present an approach using a mixed linear model nested in an empirical Bayesian approach, which simultaneously takes into account additive, dominance and epistatic effects due to multiple QTL. The covariance structure used in the mixed linear model is based on combined linkage disequilibrium and linkage information. In a simulation study where there are complex epistatic interactions between QTL, it is possible to simultaneously map interacting QTL into a small region using the proposed approach. The estimated variance components are accurate and less biased with the proposed approach compared with traditional models.     

Exposure Time to Lethal Temperatures for Meloidogyne incognita Suppression and Its Implication for Soil Solarization

Meloidogyne incognita eggs or J2 were incubated in test tubes containing sand:peat mix and immersed in a water bath heated to 38, 39, 40, 41, 42, 43, 44 and 45°C for a series of time intervals. Controls were maintained at 22°C. Nematodes surviving or hatching were collected from Baermann trays after three weeks of incubation. Regression analyses between percent survival or egg hatch and hours of heat treatment were performed for each temperature. Complete suppression of egg hatch required 389.8, 164.5, 32.9, 19.7 and 13.1 hours at 38, 39, 40, 41 and 42°C, respectively. Complete killing of J2 required 47.9, 46.2, 17.5 and 13.8 hours at 39, 40, 41 and 42°C, respectively. J2 were not completely killed at 38°C within 40 hours of treatment, but were killed within one hour at 44 and 45°C. Effect of temperature on nematode killing is not determined by heat units. Oscillating temperature between cool and warm did not interfere with the nematode suppressive effect by the heat treatment. Six-week solarization in the field during the summers of 2003 and 2004 in Florida accumulated heat exposure times in the top 15 cm of soil that surpassed levels required to kill M. incognita as determined in the water bath experiments. Although near zero M. incognita were detected right after solarization, the nematode population densities increased after a cycle of a susceptible pepper crop. Therefore, future research should address failure of solarization to kill nematodes in the deeper soil layers.     

Damage Potential and Reproduction of Belonolaimus longicaudatus and Hoplolaimus galeatus on Alyceclover

Alyceclover (Alysicarpus spp.) is an annual, high-quality leguminous forage, suitable for production under tropical and subtropical climates where the husbandry of conventional leguminous forages, Trifolium spp., is uneconomical. The damage potential and reproduction of Belonolairaus longicaudatus and Hoplolaimus galeatus on alyceclover were studied under greenhouse conditions, using sand and sandy clay loam soil materials, respectively. Both nematode species reproduced on alyceclover, but only B. longicaudatus was pathogenic. Symptoms of B. longicaudatus damage were suppression of shoot yield, limited root system, stunting, incipient wilting, and occasional seedling mortality. In one experiment, the threshold-damage density was three nematodes/100 cm³ sand, whereas in the other experiment it was zero nematodes.     

Characterising the Mucosal and Systemic Immune Responses to Experimental Human Hookworm Infection

The mucosal cytokine response of healthy humans to parasitic helminths has never been reported. We investigated the systemic and mucosal cytokine responses to hookworm infection in experimentally infected, previously hookworm naive individuals from non-endemic areas. We collected both peripheral blood and duodenal biopsies to assess the systemic immune response, as well as the response at the site of adult worm establishment. Our results show that experimental hookworm infection leads to a strong systemic and mucosal Th2 (IL-4, IL-5, IL-9 and IL-13) and regulatory (IL-10 and TGF-β) response, with some evidence of a Th1 (IFN-γ and IL-2) response. Despite upregulation after patency of both IL-15 and ALDH1A2, a known Th17-inducing combination in inflammatory diseases, we saw no evidence of a Th17 (IL-17) response. Moreover, we observed strong suppression of mucosal IL-23 and upregulation of IL-22 during established hookworm infection, suggesting a potential mechanism by which Th17 responses are suppressed, and highlighting the potential that hookworms and their secreted proteins offer as therapeutics for human inflammatory diseases.     

Leaching Soluble Salts Increases Population Densities of Tylenchulus semipenetrans

The effect of salinity on population densities of Tylenchulus semipenetrans was measured on 3-month-old salt-tolerant Rangpur lime growing on either loamy sand, sand, or organic mix and on 4-month-old salt-sensitive Sweet lime in organic mix. Salinity treatments were initiated by watering daily with 25 mol/m³ NaCl + 3.3 mol/m³ CaCl₂ for 3 days and every other day with 50 mol/m³ NaC1 + 6.6 mol/m³ CaC1₂ for one week, with no salt (NS) treatments as controls. Salinity was discontinued in one treatment (DS) by leaching with tap water prior to inoculation with nematodes, whereas the continuous salinity (CS) treatment remained unchanged. Overall, in Rangpur lime organic soil supported the highest population densities of T. semipenetrans, followed by loamy sand and sand. The DS treatment resulted in the highest (P ≤ 0.05) mean population densities of T. semipenetrans in the three soil types. Similarly, the DS treatment in Sweet lime resulted in the highest (P ≤ 0.05) nematode populations. The DS treatment predisposed citrus to nematode infection through accumulated salt stress, whereas leaching soluble salt in soil solution offered nematodes a suitable nonosmotic habitat. Nematode females under the DS treatment also had the highest (P ≤ 0.05) fecundity.