Changes to the Bacterial Microbiome in the Rhizosphere and Root Endosphere of Persea americana (Avocado) Treated With Organic Mulch and a Silicate-Based Mulch or Phosphite, and Infested With Phytophthora cinnamomi.

Plant growth and responses of the microbial profile of the rhizosphere soil and root endosphere were investigated for avocado plants infested or not infested with Phytophthora cinnamomi and the changes were compared in plants grown with various soil additives or by spraying plants with phosphite. Soil treatments were organic mulches or silica-based mineral mulch. Reduction of root growth and visible root damage was least in the infested plants treated with phosphite or mineral mulch applied to the soil. Rhizosphere soils and root endospheres were analyzed for bacterial communities using metabarcoding. Bacterial abundance and diversity were reduced in infested rhizospheres and root endospheres. The presence or absence of mineral mulch resulted in greater diversity and larger differences in rhizosphere community composition between infested and non-infested pots than any other treatment. Some rhizosphere bacterial groups, especially Actinobacteria and Proteobacteria, had significantly higher relative abundance in the presence of Phytophthora. The bacterial communities of root endospheres were lower in abundance than rhizosphere communities and not affected by soil treatments or phosphite but increased in abundance after infection with P. cinnamomi. These findings suggested that the addition of silicate-based mineral mulch protects against Phytophthora root rot, which may be partly mediated through changes in rhizosphere bacterial community composition. However, the changes to the microbiome induced by spraying plants with phosphite are different from those resulting from the application of mineral mulch to the soil.

Estimating heritability using family-pooled phenotypic and genotypic data: a simulation study applied to aquaculture.

Estimating heritability based on individual phenotypic and genotypic measurements can be expensive and labour-intensive in commercial aquaculture breeding. Here, the feasibility of estimating heritability using within-family means of phenotypes and allelic frequencies was investigated. Different numbers of full-sib families and family sizes across ten generations with phenotypic and genotypic information on 10 K SNPs were analysed in ten replicates. Three scenarios, representing differing numbers of pools per family (one, two and five) were considered. The results showed that using one pool per family did not reliably estimate the heritability of family means. Using simulation parameters appropriate for aquaculture, at least 200 families of 60 progeny per family divided equally in two pools per family was required to estimate the heritability of family means effectively. Although application of five pools generated more within- and between- family relationships, it reduced the number of individuals per pool and increased within-family residual variation, hence, decreased the heritability of family means. Moreover, increasing the size of pools resulted in increasing the heritability of family means towards one. In addition, heritability of family mean estimates were higher than family heritabilities obtained from Falconer's formula due to lower intraclass correlation estimate compared to the coefficient of relationship.

Hens That Exhibit Poorer Feed Efficiency Produce Eggs with Lower Albumen Quality and Are Prone to Being Overweight.

Feed efficiency (FE) is an important measure of productivity in the layer industry; however, little is known about how FE differs between individual hens during the egg-laying cycle and the implications for egg quality parameters. Individual 25-week-old ISA Brown hens were observed for 42 days, ranked into three FE groups (n = 48 per High (HFE), Medium (MFE) and Low (LFE) FE groups and then monitored later in the laying cycle from 35-40 weeks. The groups exhibited different feed to egg conversion ratios (p < 0.001) from 35-40 weeks. Average daily feed intake and body weight were highest (p < 0.001) in the LFE group compared to the MFE and HFE groups, while albumen height, Haugh unit and amino acid concentrations of the albumen were significantly higher in the HFE groups compared to the LFE cohort (p < 0.001). This study concludes that FE status established in early lay is a stable variable until at least 40 weeks of age, and overweight, mid-laying hens that had poor FE produced inferior egg albumen quality measurements and composition. The distinct traits of the highly efficient hens and the poor feed efficient hens may provide important information to improving productivity in egg production.

Are infectious reproductive pathogens of large ruminants a threat to improving food security? An investigation from Cambodia.

In Cambodia, information on common pathogens causing reproductive losses in cattle and buffalo are lacking, despite there being a need to address livestock health to enhance food security. We analysed stored buffalo (n = 29) and cattle (n = 471) serum samples collected in 2016 using commercially available enzyme-linked immunosorbent assay kits. Antibodies to Neospora caninum, bovine viral diarrhoea virus (BVDV), Leptospira interrogans serovar Hardjo and Brucella abortus were detected in buffalo samples at 79.3% (95% CI 64.6-94.0), 3.4% (95% CI 0-10.0), 0% and 0%, respectively, and in cattle at 4.2% (95% CI 2.4-6.0), 6.4% (95% CI 4.2-8.6), 8.1% (95% CI 5.6-10.6) and 0%, respectively. The high N. caninum seroprevalence in buffalo was associated with increasing age, with buffalo having a 13.1% chance of being seropositive at birth, increasing to 99.4% by age 7 (p = 0.045). This suggests a predominance of horizontal transmission, possibly from exposure to faeces from free-roaming village dogs. Cattle L. interrogans serovar Hardjo seroprevalence was highest in Tbong Khmum province (20.4%) compared to other provinces (p < 0.001), and may be compromising bovine fertility and creating a zoonotic risk for smallholders who may contract leptospirosis from farm work. These high infection rates prompt further research to determine: to what extent these pathogens are linked to the low reproductive efficiency observed in large ruminants in Cambodia, the risk factors to pathogen exposure and appropriate strategies to reduce these risks. Low BVDV and B. abortus exposure is an important observation. Increasing large ruminant livestock trade into the country will require improved biosecurity and disease surveillance to prevent their emergence. An enhanced understanding of the status of infectious reproductive livestock pathogens in Cambodia can assist development projects to make evidence-based strategies to enhance cattle and buffalo health and improve food security.

Reaction norm analysis of pig growth using environmental descriptors based on alternative traits.

Contemporary group (CG) estimates of different phenotypes have not been widely explored for pigs. The objective of this study was to extend the traits used to derive environmental descriptors of the growing pig, to include CG estimates of early growth between birth and start of feed intake test (EADG), growth during feed intake test (TADG), lifetime growth (ADG), daily feed intake (DFI), backfat (BF) and muscle depth (MD). Pedigree and performance records (n = 7,746) from a commercial Australian piggery were used to derive environmental descriptors based on CG estimates of these six traits. The CG estimates of growth traits described different aspects of the environment from the CG estimates of carcass traits (r < 0.10). These definitions of the environment then were used in reaction norm analysis of growth, to evaluate sire-by-environment interaction (Sire × E) for growth. The most appropriate reaction norm model to evaluate Sire × E for growth was dependent on the environmental descriptor used. If the trait used to derive an environmental descriptor was distinctly different from growth (e.g., BF and MD), CG as an additional random effect was required in the model. If not included, inflated common litter effect and sire intercept variance suggest there was unaccounted environmental variability. There was no significant Sire × E using any of the definitions of the environment, with estimated variance in sire slopes largest when environments were defined by BF ( σ ^ bi 2  = 97 ± 83 (g/day)2 ), followed by environments defined by DFI ( σ ^ bi 2  = 39 ± 101 (g/day)2 ). While there appears to be differences in ability to detect Sire × E, improved data structure is required to better assess these environmental descriptors based on alternative traits. The ideal trait, or combination of traits, used to derive environmental descriptors may be unique for individual herds. Therefore, multiple phenotypes should be further explored for the evaluation of Sire × E for growth in the pig.

Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep.

BACKGROUND: Discerning the traits evolving under neutral conditions from those traits evolving rapidly because of various selection pressures is a great challenge. We propose a new method, composite selection signals (CSS), which unifies the multiple pieces of selection evidence from the rank distribution of its diverse constituent tests. The extreme CSS scores capture highly differentiated loci and underlying common variants hauling excess haplotype homozygosity in the samples of a target population. RESULTS: The data on high-density genotypes were analyzed for evidence of an association with either polledness or double muscling in various cohorts of cattle and sheep. In cattle, extreme CSS scores were found in the candidate regions on autosome BTA-1 and BTA-2, flanking the POLL locus and MSTN gene, for polledness and double muscling, respectively. In sheep, the regions with extreme scores were localized on autosome OAR-2 harbouring the MSTN gene for double muscling and on OAR-10 harbouring the RXFP2 gene for polledness. In comparison to the constituent tests, there was a partial agreement between the signals at the four candidate loci; however, they consistently identified additional genomic regions harbouring no known genes. Persuasively, our list of all the additional significant CSS regions contains genes that have been successfully implicated to secondary phenotypic diversity among several subpopulations in our data. For example, the method identified a strong selection signature for stature in cattle capturing selective sweeps harbouring UQCC-GDF5 and PLAG1-CHCHD7 gene regions on BTA-13 and BTA-14, respectively. Both gene pairs have been previously associated with height in humans, while PLAG1-CHCHD7 has also been reported for stature in cattle. In the additional analysis, CSS identified significant regions harbouring multiple genes for various traits under selection in European cattle including polledness, adaptation, metabolism, growth rate, stature, immunity, reproduction traits and some other candidate genes for dairy and beef production. CONCLUSIONS: CSS successfully localized the candidate regions in validation datasets as well as identified previously known and novel regions for various traits experiencing selection pressure. Together, the results demonstrate the utility of CSS by its improved power, reduced false positives and high-resolution of selection signals as compared to individual constituent tests.

Acute involution in the tammar wallaby: identification of genes and putative novel milk proteins implicated in mammary gland function.

Marsupials provide a suitable alternative model to studying mammary gland involution. They have evolved a different reproductive strategy from eutherians, giving birth to an altricial young and secreting milk that changes in composition during lactation. In this study, we used a marsupial-specific EST microarray to identify 47 up-regulated genes during mammary gland involution in the tammar wallaby (Macropus eugenii). These include the pro-apoptotic tumour necrosis factor receptor superfamily 21 (TNFRSF21) gene, whose expression in the mammary gland has not previously been reported. Genes encoding putative novel milk proteins which may protect the mammary gland from infection were also found to be up-regulated, such as amiloride binding protein 1 (ABP1), complement component 1QB (C1QB), complement component 4A (C4A) and colony stimulating factor 2 receptor ß (CSF2Rß). Our results show that the marsupial reproductive strategy was successfully exploited to identify genes and putative novel milk proteins implicated in mammary gland involution.

Gadolinium-enhanced MR imaging and nephrogenic systemic fibrosis: retrospective study of a renal replacement therapy cohort.

PURPOSE: To retrospectively compare the frequency of administration and cumulative dose of gadolinium-based contrast agent in dialysis-dependent patients who did and those who did not develop nephrogenic systemic fibrosis. MATERIALS AND METHODS: The ethics committees granted exempt status for this study and also waived the need for informed consent. A retrospective analysis was performed of all adult patients undergoing dialysis in the west of Scotland between January 1, 2000, and July 1, 2006. Diagnoses of nephrogenic systemic fibrosis, episodes of gadolinium-enhanced magnetic resonance (MR) imaging, and cumulative doses of gadolinium-based contrast agent were recorded. Outcomes were analyzed by means of parametric and nonparametric testing. RESULTS: Fourteen of 1826 patients had a diagnosis of nephrogenic systemic fibrosis. Mortality was similar for affected and nonaffected patients. Thirteen (93%) of 14 patients with nephrogenic systemic fibrosis had undergone gadolinium-enhanced MR imaging compared with 408 (22.5%) of 1812 nonaffected patients (P<.001). Patients with nephrogenic systemic fibrosis received a higher median cumulative dose of gadodiamide (0.39 vs 0.23 mmol per kilogram of body weight, P=.008) and underwent more gadolinium-enhanced MR imaging than their nonaffected gadolinium-exposed counterparts. CONCLUSION: The data support a positive association between gadolinium-based contrast agent administration and development of nephrogenic systemic fibrosis in the established renal failure population; in addition, there is a positive association between cumulative dose of gadodiamide used and dosing events.