Significance testing and genomic inflation factor using high‐density genotypes or whole‐genome sequence data

Significance testing for genome‐wide association study (GWAS) with increasing SNP density up to whole‐genome sequence data (WGS) is not straightforward, because of strong LD between SNP and population stratification. Therefore, the objective of this study was to investigate genomic control and different significance testing procedures using data from a commercial pig breeding scheme. A GWAS was performed in GCTA with data of 4,964 Large White pigs using medium density, high density or imputed whole‐genome sequence data, fitting a genomic relationship matrix based on a leave‐one–chromosome‐out approach to account for population structure. Subsequently, genomic inflation factors were assessed on whole‐genome level and the chromosome level. To establish a significance threshold, permutation testing, Bonferroni corrections using either the total number of SNPs or the number of independent chromosome fragments, and false discovery rates (FDR) using either the Benjamini–Hochberg procedure or the Benjamini and Yekutieli procedure were evaluated. We found that genomic inflation factors did not differ between different density genotypes but do differ between chromosomes. Also, the leave‐one‐chromosome‐out approach for GWAS or using the pedigree relationships did not account appropriately for population stratification and gave strong genomic inflation. Regarding different procedures for significance testing, when the aim is to find QTL regions that are associated with a trait of interest, we recommend applying the FDR following the Benjamini and Yekutieli approach to establish a significance threshold that is adjusted for multiple testing. When the aim is to pinpoint a specific mutation, the more conservative Bonferroni correction based on the total number of SNPs is more appropriate, till an appropriate method is established to adjust for the number of independent tests.     

Breeding Strategies for Adaptation of Pearl Millet and Sorghum to Climate Variability and Change in West Africa

Semi‐arid and subhumid West Africa is characterized by high inter‐annual rainfall variability, with variable onset of the rainy season, somewhat more predictable endings, and drought or excess water occurrence at any time during the growing season. Climate change is predicted to increase this variability. This article summarizes options for plant breeders to enhance the adaptation of pearl millet (Pennisetum glaucum [L.] R. Br.) and sorghum (Sorghum bicolor [L.] Moench) to climate variability in West Africa. Developing variety types with high degrees of heterozygosity and genetic heterogeneity for adaptation traits helps achieving better individual and population buffering capacity. Traits that potentially enhance adaptive phenotypic plasticity or yield stability in variable climates include photoperiod‐sensitive flowering, plastic tillering, flooding tolerance, seedling heat tolerance and phosphorus efficiency. Farmer‐participatory dynamic gene pool management using broad‐based populations and diverse selection environments is useful to develop new diverse germplasm adapted to specific production constraints including climate variability. For sustainable productivity increase, improved cultivars should respond to farmer‐adoptable soil fertility management and water harvesting techniques. Larger‐scale, on‐farm participatory testing will enable assessments of varietal performance under evolving climatic variability, provide perspective on needs and opportunities and enhance adoption. Strengthening seed systems will be required to achieve sustainable impacts.     

Effects of mass inoculation on induced oleoresin response in intensively managed loblolly pine

Oleoresin flow is an important factor in the resistance of pines to attack by southern pine beetle, Dendroctonus frontalis Zimm., and its associated fungi. Abiotic factors, such as nutrient supply and water relations, have the potential to modify this plant-insect-fungus interaction; however, little is known of the effects of inoculation with beetle-associated fungi on oleoresin flow. We observed that constitutive and induced resin yield in loblolly pine, Pinus taeda L., were affected by either fungal inoculation (with the southern pine beetle-associated fungus Ophiostoma minus (Hedgcock) H. & P. Sydow) or silvicultural treatment. The effects of mass wounding (400 wounds m(-2)) and mass wounding and inoculation with O. minus were assessed by comparison with untreated (control) trees. The treatments were applied to trees in a 2 x 2 factorial combination of fertilizer and irrigation treatments. Fertilization did not significantly affect constitutive resin yield. Even as long as 105 days post-treatment, however, mass-inoculated trees produced higher induced resin yields than control or wounded-only trees, indicating a localized induced response to fungal inoculation. We noted no systemic induction of host defenses against fungal colonization. Although beetles attacking previously attacked trees face a greater resinous response from their host than beetles attacking trees that had not been previously attacked, the effect of an earlier attack may not last more than one flight season. Despite mass inoculations, O. minus did not kill the host trees, suggesting that this fungus is not a virulent plant pathogen.     

Multiple phosphorylation sites confer reproducibility of the rod's single-photon responses

Although signals controlled by single molecules are expected to be inherently variable, rod photoreceptors generate reproducible responses to single absorbed photons. We show that this unexpected reproducibility-the consistency of amplitude and duration of rhodopsin activity-varies in a graded and systematic manner with the number but not the identity of phosphorylation sites on rhodopsin's C terminus. These results indicate that each phosphorylation site provides an independent step in rhodopsin deactivation and that collectively these steps tightly control rhodopsin's active lifetime. Other G protein cascades may exploit a similar mechanism to encode accurately the timing and number of receptor activation.     

Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons

For characterization of sequence and posttranslational modifications, molecular and fragment ion mass data from ionizing and dissociating a protein in the mass spectrometer are far more specific than are masses of peptides from the protein's digestion. We extend the approximately 500-residue, approximately 50-kilodalton (kD) dissociation limitation of this top-down methodology by using electrospray additives, heated vaporization, and separate noncovalent and covalent bond dissociation. This process can cleave 287 interresidue bonds in the termini of a 1314-residue (144-kD) protein, specify previously unidentified disulfide bonds between 8 of 27 cysteines in a 1714-residue (200-kD) protein, and correct sequence predictions in two proteins, one with 2153 residues (229 kD).     

Effects of selenium source on measures of selenium status and immune function in horses

The effects of selenium (Se) supplementation and source on equine immune function have not been extensively studied. This study examined the effects of oral Se supplementation and Se source on aspects of innate and adaptive immunity in horses. Fifteen horses were assigned to 1 of 3 groups (5 horses/group): control, inorganic Se (sodium selenite), organic Se (Se yeast). Immune function tests performed included: lymphocyte proliferation in response to mitogen concanavalin A, neutrophil phagocytosis, antibody production after rabies vaccination, relative cytokine gene expression in stimulated lymphocytes [interferon gamma (IFNγ), interleukin (IL)-2, IL-5, IL-10, tumor necrosis factor alpha (TNFα)], and neutrophils (IL-1, IL-6, IL-8, IL-12, TNFα). Plasma, red blood cell Se, and blood glutathione peroxidase activity were measured. Plasma and red blood cell Se were highest in horses in the organic Se group, compared with that of inorganic Se or control groups. Organic Se supplementation increased the relative lymphocyte expression of IL-5, compared with inorganic Se or no Se. Selenium supplementation increased relative neutrophil expression of IL-1 and IL-8. Other measures of immune function were unaffected. Dietary Se content and source appear to influence immune function in horses, including alterations in lymphocyte expression of IL-5, and neutrophil expression of IL-1 and IL-8.     

Gallbladder mucocele in dogs: 30 cases (2000-2002)

OBJECTIVE: To determine long-term outcome of dogs with gallbladder mucocele. DESIGN: Retrospective study. ANIMALS: 30 dogs with gallbladder mucocele, including 23 that underwent cholecystectomy. PROCEDURE: Medical records were reviewed for signalment, history, and clinical, ultrasonographic, and surgical findings. Follow-up information was obtained for all dogs that survived the perioperative hospitalization period. RESULTS: 23 dogs had signs of systemic illness; 7 had no clinical signs. Median values for serum activities of alanine aminotransferase and alkaline phosphatase, serum total bilirubin concentration, and total WBC count were significantly higher among dogs with gallbladder rupture than among dogs without rupture. Sensitivity of sonography for detection of rupture was 85.7%. Overall perioperative mortality rate for dogs that underwent cholecystectomy was 21.7%; mortality rate was not significantly greater for dogs with rupture. Aerobic bacteria were isolated from the bile or gallbladder wall in 8.7% of dogs. All 18 dogs discharged from the hospital had complete resolution of clinical signs. In dogs that underwent in-hospital reexamination, serum liver enzyme activities were significantly decreased, compared with preoperative activities. Persistent increases in serum activities of 1 or more liver enzymes were detected in 9 of 12 dogs; 6 of 12 dogs had persistent abnormalities in hepatic echogenicity. Mean follow-up period was 13.9 months. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that cholecystectomy is an effective treatment for gallbladder mucocele. Although perioperative mortality rate is high, prognosis after discharge from the hospital is excellent. Rupture of the gallbladder warrants emergency surgical intervention but does not preclude a positive outcome.