QTL detection of production traits for the Kuruma prawn Penaeus japonicus (Bate) using AFLP markers

The objective of this study was to use Amplified Fragment Length Polymorphism (AFLP) markers to determine the genetic location and effects of genomic regions controlling weight (WT), total length (TL) and carapace length (CL) in one full-sib Penaeus japonicus family. One hundred and two extreme progeny from an intermediate F2 cross of high (HH) and low (LL) growth parents were used to identify these regions. Two analytical methods were applied in this study. They were interval mapping (IM) and composite interval mapping (CIM). There was no significant marker-trait association in the female map. One region controlling part of the variation for CL and TL was identified in linkage group 1 of the male map by IM, and the same region and one other suggestive QTL marker in linkage group 25 of the male map were detected by CIM. Both regions were located on the end of linkage groups. In order to derive additional markers, the Bulk Segregant Analysis (BSA) technique was applied to these regions to generate further AFLP markers. From 45 markers scored using 11 AFLP primer combinations, one AFLP marker was mapped to the QTL region in linkage group 1 and one in the middle of group 25. The new results supported the findings from the early analyses prior to using BSA. The magnitude of phenotypic variation explained by the joint action of the QTL markers indicated that genetic factors of large effect were involved in the control of the studied characters. This study is the first to identify QTLs for growth traits in a penaeid species

Detection of Synergistes jonesii and genetic variants in ruminants from different geographical locations

Leucaena leucocephala is a nutritionally rich forage tree legume that contains a toxic non-protein amino acid, mimosine, from which other toxic compounds 3,4-dihydroxypyridone (3,4-DHP) and 2,3-DHP are formed in the rumen. The rumen bacterium Synergistes jonesii is able to degrade these DHP isomers into non-toxic end products. In this study we developed new PCR-based assays to improve the specificity and sensitivity of detection of S. jonesii in the rumen. Using these new assays in a survey of ruminants from different countries, S. jonesii appeared to be ubiquitous rather than isolated geographically. The bacterium was present as a minor population

Development of two microsatellite multiplex systems for black tiger shrimp Penaeus monodon and its application in genetic diversity study for two populations

Despite large numbers of putative microsatellites currently listed in databases for Penaeus monodon, there are no publications on assessing these markers for multiplexed high throughput systems either for fingerprinting or population genetics study purposes in P. monodon. Accordingly, we started our investigation on the development of high throughput systems for P. monodon. Ninety publicly-available P. monodon microsatellite sequences were initially screened for suitability. They were assessed for the presence of tri- or tetra-nucleotide repeats, repeat number and type, suitability of flanking sequences for primer design and estimated size of product (100 to 350\ua0bp). Nineteen sequences were chosen for preliminary assessment on a panel of 15 animals. Of the 19 tested, only 12 were suitable for further investigation. Therefore a 2-step enrichment library approach was adopted to develop additional microsatellites. Of 42 new unique microsatellite sequences obtained, eight sequences were assessed and seven showed polymorphism. Together, these 19 markers were examined further for their ease of amplification and reliability of allele calling for inclusion in high throughput systems. Thirteen polymorphic markers were incorporated into two multiplex systems (six and seven markers, respectively). These multiplexed systems were then used to evaluate the genetic diversity between two populations of P. monodon, one from the East Coast of Australia and a single pond containing farmed animals from Thailand. There were significant differences between the two populations. Three markers in system 1 showed Hardy-Weinberg disequilibrium in both populations, indicating their unsuitability as high throughput system markers. Using two systems and the UPGMA clustering methods revealed the existence of sub-populations within the Australian wild population. The results indicate the usefulness of the two multiplexed microsatellite systems in genetic diversity studies. Crown Copyrigh

Evidence for positive selection of taurine genes within a QTL region on chromosome X associated with testicular size in Australian Brahman cattle

Background: Previous genome-wide association studies have identified significant regions of the X chromosome associated with reproductive traits in two Bos indicus-influenced breeds: Brahman cattle and Tropical Composites. Two QTL regions on this chromosome were identified in both breeds as strongly associated with scrotal circumference measurements, a reproductive trait previously shown to be useful for selection of young bulls. Scrotal circumference is genetically correlated with early age at puberty in both male and female offspring. These QTL were located at positions 69-77 and 81-92 Mb respectively, large areas each to which a significant number of potential candidate genes were mapped.Results: To further characterise these regions, a bioinformatic approach was undertaken to identify novel non-synonymous SNP within the QTL regions of interest in Brahman cattle. After SNP discovery, we used conventional molecular assay technologies to perform studies of two candidate genes in both breeds. Non-synonymous SNP mapped to Testis-expressed gene 11 (Tex11) were associated (P < 0.001) with scrotal circumference in both breeds, and associations with percentage of normal sperm cells were also observed (P < 0.05). Evidence for recent selection was found as Tex11 SNP form a haplotype segment of Bos taurus origin that is retained within Brahman and Tropical Composite cattle with greatest reproductive potential.Conclusions: Association of non-synonymous SNP presented here are a first step to functional genetic studies. Bovine species may serve as a model for studying the role of Tex11 in male fertility, warranting further in-depth molecular characterisation

First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community

Infection with SARS-CoV-2, the etiologic agent of the ongoing COVID-19 pandemic, is accompanied by the shedding of the virus in stool. Therefore, the quantification of SARS-CoV-2 in wastewater affords the ability to monitor the prevalence of infections among the population via wastewater-based epidemiology (WBE). In the current work, SARS-CoV-2 RNA was concentrated from wastewater in a catchment in Australia and viral RNA copies were enumerated using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) resulting in two positive detections within a six day period from the same wastewater treatment plant (WWTP). The estimated viral RNA copy numbers observed in the wastewater were then used to estimate the number of infected individuals in the catchment via Monte Carlo simulation. Given the uncertainty and variation in the input parameters, the model estimated a median range of 171 to 1,090 infected persons in the catchment, which is in reasonable agreement with clinical observations. This work highlights the viability of WBE for monitoring infectious diseases, such as COVID-19, in communities. The work also draws attention to the need for further methodological and molecular assay validation for enveloped viruses in wastewater

Detection of SARS-CoV-2 RNA in Commercial Passenger Aircraft and Cruise Ship Wastewater: A Surveillance Tool for Assessing the Presence of COVID-19 Infected Travellers

Background: Wastewater-based epidemiology (WBE) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be an important source of information for coronavirus disease 2019 (COVID-19) management during and after the pandemic. Currently, governments and transportation industries around the world are developing strategies to minimize SARS-CoV-2 transmission associated with resuming activity. This study investigated the possible use of SARS-CoV-2 RNA wastewater surveillance from airline and cruise ship sanitation systems and its potential use as a COVID-19 public health management tool. Methods: Aircraft and cruise ship wastewater samples (n = 21) were tested for SARS-CoV-2 using two virus concentration methods, adsorption-extraction by electronegative membrane (n = 13) and ultrafiltration by Amicon (n = 8), and five assays using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and RT-droplet digital PCR (RT-ddPCR). Representative qPCR amplicons from positive samples were sequenced to confirm assay specificity. Results: SARS-CoV-2 RNA was detected in samples from both aircraft and cruise ship wastewater; however concentrations were near the assay limit of detection. The analysis of multiple replicate samples and use of multiple RT-qPCR and/or RT-ddPCR assays increased detection sensitivity and minimized false-negative results. Representative qPCR amplicons were confirmed for the correct PCR product by sequencing. However, differences in sensitivity were observed among molecular assays and concentration methods. Conclusions: The study indicates that surveillance of wastewater from large transport vessels with their own sanitation systems has potential as a complementary data source to prioritize clinical testing and contact tracing among disembarking passengers. Importantly, sampling methods and molecular assays must be further optimized to maximize detection sensitivity. The potential for false negatives by both wastewater testing and clinical swab testing suggests that the two strategies could be employed together to maximize the probability of detecting SARS-CoV-2 infections amongst passengers