Identification of genomic regions that exhibit sexual dimorphism for size and muscularity in cattle

Sexual dimorphism, the phenomenon whereby males and females of the same species are distinctive in some aspect of appearance or size, has previously been documented in cattle for traits such as growth rate and carcass merit using a quantitative genetics approach. No previous study in cattle has attempted to document sexual dimorphism at a genome level; therefore, the objective of the present study was to determine whether genomic regions associated with size and muscularity in cattle exhibited signs of sexual dimorphism. Analyses were undertaken on 10 linear-type traits that describe the muscular and skeletal characteristics of both males and females of five beef cattle breeds: 1,444 Angus (AA), 6,433 Charolais (CH), 1,129 Hereford, 8,745 Limousin (LM), and 1,698 Simmental. Genome-wide association analyses were undertaken using imputed whole-genome sequence data for each sex separately by breed. For each single-nucleotide polymorphism (SNP) that was segregating in both sexes, the difference between the allele substitution effect sizes for each sex, in each breed separately, was calculated. Suggestively (P ≤ 1 × 10⁻⁵) sexually dimorphic SNPs that were segregating in both males and females were detected for all traits in all breeds, although the location of these SNPs differed by both trait and breed. Significantly (P ≤ 1 × 10⁻⁸) dimorphic SNPs were detected in just three traits in the AA, seven traits in the CH, and three traits in the LM. The vast majority of all segregating autosomal SNPs (86% in AA to 94% in LM) had the same minor allele in both males and females. Differences (P ≤ 0.05) in allele frequencies between the sexes were observed for between 36% (LM) and 66% (AA) of the total autosomal SNPs that were segregating in both sexes. Dimorphic SNPs were located within a number of genes related to muscularity and/or size including the NAB1, COL5A2, and IWS1 genes on BTA2 that are located close to, and thought to be co-inherited with, the MSTN gene. Overall, sexual dimorphism exists in cattle at the genome level, but it is not consistent by either trait or breed.     

Factors affecting the field performance of an attracticide against the codling moth Cydia pomonella

Factors affecting the efficacy of an attracticide strategy for the control of the codling moth Cydia pomonella L (Lepidoptera: Tortricidae) were investigated using laboratory and field experiments. The sex-pheromone-based insect-control strategy utilises 100-microliters droplets of a sticky, paste-like formulation containing 1 mg g-1 (E,E)-8,10-dodecadien-1-ol (codlemone) as an attractant for male moths and 40 mg g-1 cyfluthrin, a contact insecticide, applied to branches in the upper parts of the tree crown. The longevity of the treatment under field conditions was assessed in the laboratory by biological testing of variously aged samples of the attracticide formulation which had been applied to the bark of apple trees growing in commercial orchards. Electroantennogram responses of male moth antennae were used to compare codlemone release from the attracticide after different lengths of environmental exposure. Changes in insecticidal efficacy of the same samples were assessed with reference to the speed of knockdown (KT50) and the mortalities after 48 h among populations of male moths confined in cages containing samples of fresh and field-aged formulations. Gradual declines in both the amount of pheromone released and insecticidal activity were observed over the 10-week period of the experiments. Various factors associated with the behaviour of codling moths in the field which might influence the attracticide strategy were also investigated. Although the vertical position of attracticide sources within apple trees had a strong influence on their attractiveness, their horizontal position had none. Results of field trials showed that efficacy of the attracticide depends on the population density of the pest. Under the conditions of the current study a density of three or more sources per tree (= 4500 sources per ha) was required to attain satisfactory levels of codling moth control.     

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.     

Structural Characterization of Maitotoxins Produced by Toxic Gambierdiscus Species

Identifying compounds responsible for the observed toxicity of the Gambierdiscus species is a critical step to ascertaining whether they contribute to ciguatera poisoning. Macroalgae samples were collected during research expeditions to Rarotonga (Cook Islands) and North Meyer Island (Kermadec Islands), from which two new Gambierdiscus species were characterized, G. cheloniae CAWD232 and G. honu CAWD242. Previous chemical and toxicological investigations of these species demonstrated that they did not produce the routinely monitored Pacific ciguatoxins nor maitotoxin-1 (MTX-1), yet were highly toxic to mice via intraperitoneal (i.p.) injection. Bioassay-guided fractionation of methanolic extracts, incorporating wet chemistry and chromatographic techniques, was used to isolate two new MTX analogs; MTX-6 from G. cheloniae CAWD232 and MTX-7 from G. honu CAWD242. Structural characterization of the new MTX analogs used a combination of analytical chemistry techniques, including LC–MS, LC–MS/MS, HR–MS, oxidative cleavage and reduction, and NMR spectroscopy. A substantial portion of the MTX-7 structure was elucidated, and (to a lesser extent) that of MTX-6. Key differences from MTX-1 included monosulfation, additional hydroxyl groups, an extra double bond, and in the case of MTX-7, an additional methyl group. To date, this is the most extensive structural characterization performed on an MTX analog since the complete structure of MTX-1 was published in 1993. MTX-7 was extremely toxic to mice via i.p. injection (LD₅₀ of 0.235 µg/kg), although no toxicity was observed at the highest dose rate via oral administration (155.8 µg/kg). Future research is required to investigate the bioaccumulation and likely biotransformation of the MTX analogs in the marine food web.     

Can phyllosphere yeasts explain the effect of scab fungicides on russeting of Elstar apples?

In 1999 and 2000, the effects of scab fungicides on yeast composition and russeting of Elstar apples were assessed. Yeast composition of fungicide-treated and untreated young apple fruit with or without russet symptoms was investigated and enzyme activity of the yeasts was studied. Cryptococcus albidus, C.laurentii,Rhodotorula glutinis, Sporobolomyces roseus andMetschnikowia pulcherrima dominated the apple fruit surface. Russeted apple fruitlets had a higher red yeast density than non-russeted fruitlets. Invitro fungicide susceptibility of the dominant yeast species varied. Dithianon and dodine were active against all tested species, captan and tolylfluanid showed specificity for certain species, whereas pyrimethanil and bupirimate were largely ineffective. Fungicide treatment in the field had a clear effect on the yeast composition. Metschnikowia etschnikowia pulcherrima was eliminated from the phyllosphere and cryptococco$ï species diminished by both captan and dithianon. The red yeast population was not significantly changed by either fungicide. Captan, dithianon, tolylfluanid and pyrimethanil reduced russet in the field in both years, dodine and kresoxim-methyl only in 2000. All yeast species had cutinolytic activity, all but M.pulcherrimaand Debaryomyces hansenii were lipolytic, and some of the isolates showed proteolytic activity.     

Evaluating the upper thermal limits of glochidia for selected freshwater mussel species (Bivalvia: Unionidae) in central and east Texas,and the implications for their conservation

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