Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species.

Comprehending the genetic architecture of complex traits has many applications in evolution, ecology, conservation biology and plant and animal production systems. Underlying research questions in these fields are diverse species that often have limited genetic information available. In aquaculture, for example, genetic progress has been slow in many species due to a lack in such genetic information. In this study, zebrafish (as a well-studied model species) was used in cross-species transfer to develop genomic resources and identify candidate genes underling growth differentials in dusky kob. Dusky kob is a Sciaenid finfish and an emerging aquaculture species. The zebrafish All Exon Predesigned Probe-set capture protocol was used to enrich fractionated DNA samples from kob, classified as either large or small, before massive parallel sequencing on the Ion Torrent platform. Although vast quantities of sequence data were generated, only about 30% of contigs could be identified as zebrafish homologues. There were numerous species-specific sequences and inconsistent coverage of sequencing products across samples, likely due to non-specific binding of the probe-set as a result of the evolutionary divergence between zebrafish and kob. Nonetheless, more than 55,000 SNPs could be reliably identified and genotyped to the individual level. Using SNP genotypic divergence estimates, between large and small cohorts, a number of candidate genes associated with growth was also identified for future investigation. These findings contribute to the growing body of evidence demonstrating the utility of a cross-species capture approach in the development of important genomic resources for understanding traits of interest in species without reference genomes.

Genetic parameter estimates for milkability traits and their relationship with somatic cell score in South African Holstein cattle.

Milkability is an important functional trait, which is directly related to milking costs and udder health. There are no milkability traits incorporated in the South African dairy cattle breeding objectives and genetic parameter estimates for these traits are not available in this population. The main objective of the study was, therefore, to estimate the genetic parameters for milkability traits and its correlation with somatic cell scores in South African Holstein cattle. Data consisted of production and milkability records of 2719 Holstein cows, from ten herds, collected from 2016 to 2018. Genetic parameters were estimated by a multi-trait animal model using the restricted maximum likelihood (REML) procedure. Means for milking time (MT), average milk flow (AMF), maximum milk flow (MMF), and somatic cell score (SCS) were 5.20 min, 1.91 kg/min, 2.99 kg/min, and 2.06, respectively. The heritability estimates were low to moderate from 0.19 ± 0.07, 0.24 ± 0.06, 0.36 ± 0.11, and 0.41 ± 0.12, respectively, for SCS, AMF, MT, and MMF. The genetic correlations were significant (P < 0.05) among the three milkability traits ranged from - 0.31 ± 0.05 between AMF and MT to 0.85 ± 0.02 between AMF and MMF. Positive genetic correlations were observed between AMF and MMF, while the correlations for MT with the remaining milkability traits were negative. Genetic correlations of SCS with AMF, MMF, and MT were - 0.13 ± 0.04, 0.13 ± 0.04, and - 0.25 ± 0.12, respectively. The mean estimated breeding value (EBV) was estimated using cattle birth dates, and there was an increase in AMF of 0.0001 kg/min EBV per year on cattle born during the period 2002 to 2014. Maximum milk flow also showed an increasing genetic trend of 0.0003 kg/min per year over the same period. On the other hand, the genetic trend for MT was undesirable, as it increased by 0.0003 kg/min per year. The moderate to high heritability estimates for milkability traits showed that selection for improvement was possible in South African Holstein cattle. High genetic correlation between AMF and MMF implied that these two may be regarded as the same trait. Milking time can contribute towards improving the accuracy of estimating EBVs for SCS in a multi-trait analysis, and vice versa, due to the moderate correlation between the two traits. The marginal genetic trend in milkability traits may be an interrelated response to selection of other traits already under selection in the population such as SCS. Results of the current study provided a basis for including milkability traits of South African Holstein cattle in the breeding objectives.

Genetic and phenotypic consequences of early domestication in black soldier flies (Hermetia illucens).

The black soldier fly, Hermetia illucens, is an emerging biotechnological agent with its larvae being effective converters of organic waste into usable bio-products including protein and lipids. To date, most operations use unimproved commercial populations produced by mass rearing, without cognisance of specific breeding strategies. The genetic and phenotypic consequences of these commercial practices remain unknown and could have a significant impact on long-term population viability and productivity. The aim of this study was thus to assess the genetic and phenotypic changes during the early phases of colony establishment and domestication in the black soldier fly. An experimental colony was established from wild founder flies and a new microsatellite marker panel was developed to assess population genetic parameters along with the phenotypic characteristics of each generational cohort under captive breeding. The experimental colony was characterised by a small effective population size, subsequent loss of genetic diversity and rapid genetic and phenotypic differentiation between the generational cohorts. Ultimately, the population collapsed by the fifth generation, most likely owing to the adverse effect of inbreeding depression following the fixation of deleterious alleles. Species with r-selected life history characteristics (e.g. short life-span, high fecundity and low larval survival) are known to pose particular challenges for genetic management. The current study suggests that sufficient genetic and phenotypic variations exist in the wild population and that domestication and strain development could be achieved with careful population augmentation and selection during the early stages of colony establishment.

Metagenomic assessment of body surface bacterial communities of the sea urchin, Tripneustes gratilla.

Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface bacterial communities associated with T. gratilla, using a 16S rDNA gene metagenomics approach, to provide insight into the bacterial agents associated with this aquaculture species, as well as with this balding disease. Bacterial samples were collected from non-lesioned healthy animals obtained from natural locations along the eastern coast of South Africa, as well as from different cultured cohorts: non-lesioned healthy-, lesioned diseased- and non-lesioned stressed animals. A total of 1,067,515 individual bacterial operational taxonomic units (OTUs) were identified, belonging to 133 family-, 123 genus- and 113 species level OTU groups. Alpha diversity analyses, based on Chao1, Shannon and Simpson indices, showed that there were no statistically significant differences (ANOVA; P > 0.05) between the respective cohorts, as all cohorts displayed a high degree of bacterial diversity. Similarly, beta diversity analyses (Non-metric multidimensional scaling) showed a large degree of overlapping OTUs across the four cohorts. Within each cohort, various OTUs commonly associated with marine environments were found, predominantly belonging to the families Vibrionaceae, Saprospiraceae, Flavobacteriaceae and Sphingomonadaceae. Differential abundance analysis (DESeq2) revealed that OTUs that are differentially abundant across cohorts were likely not responsible for this balding disease, suggesting that complex bacterial agents, rather than a specific pathogenic agent, are likely causing this disease. Furthermore, the putative metabolic functions assigned to the bacterial communities showed that heterotrophic bacteria appear to be responsible for tissue lysis of degrading animal matter. The results from this study, obtained through univariate and multivariate-based approaches, contributes to future management strategies of this emerging aquaculture species by providing insight into the bacterial communities associated with both natural and cultured environments.

New microsatellite markers for the abalone Haliotis midae developed by 454 pyrosequencing and in silico analyses.

Farming of Haliotis midae is the most lucrative aquaculture venture in South Africa. The genome of this species needs to be studied to assist in selective breeding programs aimed at increasing overall yield, and molecular markers will be required to attain this goal. We identified and characterized 82 polymorphic microsatellite loci by using repeat-enriched genomic libraries and high-throughput pyrosequencing technology. The observed number of alleles ranged from 2 to 21, expected heterozygosity from 0.063 to 0.968, observed heterozygosity from 0.000 to 1.000, and polymorphic information content from 0.059 to 0.934. Three loci gave significant hits to other haliotid genes and/or microsatellite loci; hits to genes were always located in the 5'/3'-UTR or intron region. Many of these newly designed markers would be useful for parentage, population and linkage studies.

Therapy of bovine ocular squamous-cell carcinoma with local doses of interleukin-2: 67% complete regressions after 20 months of follow-up.

We have tested the therapeutic potency of peritumorally injected low doses of interleukin-2 (IL-2). Seventy tumours of the bovine ocular squamous-cell carcinoma (BOSCC), 1-3 cm in diameter, were treated with 5000, 20,000 or 200,000 U IL-2 from Eurocetus (Chiron) to find the optimal dose for treatment. Injections were given peritumorally on Monday to Friday on 2 consecutive weeks. The size of the tumours was measured before treatment and 1, 3, 4, 9 and 20 months after treatment. After 9 months complete regression was observed in 89% of the tumours treated with 5000 U IL-2, 80% treated with 20,000 U and 67% treated with 200,000 U. After 20 months, there was complete regression of 35%, 31% and 67% of the tumours respectively. The 9- and 20-month results of the 200,000-U treatment are significantly better than those of the 5000-U and 20,000-U treatments taken together. This protocol may be useful to treat advanced inoperable tumours (e.g. of the nasopharynx or skin) of human patients.

Dairy cows as reservoirs of Coxiella burnetii in Zimbabwe.

Sera obtained from 274 dairy cows in commercial dairies around Zimbabwe examined by indirect immunofluorescence for antibodies reactive with phase II Coxiella burnetii antigens. Overall, 41 pc of the cows were reactive at a titre of 1/40 or greater with the seroprevalence in dairies varying from 33-75 pc. The implications for human and animal health are discussed.

Transient infections of goats with a novel spotted fever group rickettsia from Zimbabwe.

A novel spotted fever group rickettsia has recently been isolated from Amblyomma hebraeum ticks in Zimbabwe. In a survey of 172 goat sera collected throughout Zimbabwe the highest prevalence of antibodies reactive with this rickettsia was in the south of the country, the area where A hebraeum is most commonly found. Nine goats were infected using male and female A hebraeum taken from a tick line shown to be infected with the novel rickettsia. By week 3 after infection, seroconversion occurred in all nine goats but no clinical signs of disease could be detected. A leucocytosis due to a mature neutrophilia one to two weeks after infection was the only abnormality. Rickettsaemia was detected only on day 3 after exposure to infected ticks. Immunosuppression failed to induce recrudescence of the rickettsaemia.

Pacinian corpuscle neuroma of digital nerves.

Symptoms and incapacitation due to abnormal aggregations of pacinian corpuscles are uncommon. Indeed, only three reports have been found in the scientific literature. A case is presented in which the patient's chief complaint was pain and localized tenderness in the hand which interfered with normal activity. Surgical exploration of the palm showed abnormalities of pacinian corpuscles attached to the median digital nerve in the form of a grape-like cluster and a single enlarged corpuscle beneath the epineurium; the abnormality attached to the ulnar digital nerve appeared as an offshoot of hyperplastic corpuscles lying in tandem. The abnormal corpuscles were excised. The symptoms have not recurred to date. These abnormalities in size, position, and number of pacinian corpuscles are compared to the findings of the few other reports in the literature. The neuroma formation found attached to this ulnar nerve has not been cited previously.