Meta-assembly of genomic associations to identify cattle fat depot candidate genes and pleiotropic effects.

Background: Fat traits in cattle are considered important due to their contribution to beef eating quality and carcass economic value. Discovering the genes controlling fat traits in cattle will enable better selection of these traits, but identifying these genes in individual experiments has proven difficult. Compared to individual experiments, meta-analyses allow greater statistical power for detecting quantitative trait loci and identifying genes that influence single and multiple economically important fat traits.

A Splice Site Variant in Is the Likely Causal Variant for Pulmonary Hypoplasia with Anasarca in Persian/Persian-Cross Sheep.

Pulmonary hypoplasia with anasarca, or hydrops fetalis, is characterized by stillbirth, diffuse oedema, and generalized lymph node hypoplasia. The enlarged fetus frequently causes dystocia. The disease has been reported in cattle and sheep as an inherited condition with a recessive mode of inheritance.

A Review and Meta-Analysis of Genotype by Environment Interaction in Commercial Shrimp Breeding.

(1) Background: Genotype-by-environment interaction (G×E) can adversely impact genetic improvement programs. The presence of G×E is mainly measured as the genetic correlation between the same trait measured in different environments where departure from unity can be taken as presence of G×E. (2) Methods: To understand the extent of G×E in shrimp production, a review and meta-analysis was conducted using the results from 32 peer-reviewed studies.

Evaluating the Efficacy of Target Capture Sequencing for Genotyping in Cattle.

(1) Background: Target capture sequencing (TCS) is potentially a cost-effective way to detect single-nucleotide polymorphisms (SNPs) and an alternative to SNP array-based genotyping. (2) Methods: We evaluated the effectiveness and reliability of TCS in cattle breeding scenarios using 48 female and 8 male samples. DNA was extracted from blood samples, targeted for 71,746 SNPs with TWIST probes, and sequenced on an MGI platform.

Genomic Analysis of Lymphoma Risk in Bullmastiff Dogs.

Lymphoma is the most common haematological malignancy affecting dogs and has a high incidence in the Bullmastiff breed. The aim of this study was to identify risk loci predisposing this breed to the disease. The average age of lymphoma diagnosis in 55 cases was less than 6 years, similar to the median age of 64 cases from our clinical and pathology databases.

Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis.

There has been considerable interest in studying cancer in dogs and its potential as a model system for humans. One area of research has been the search for genetic risk variants in canine lymphoma, which is amongst the most common canine cancers. Previous studies have focused on a limited number of breeds, but none have included Border Collies.

Identification of Genomic Signatures in Bullmastiff Dogs Using Composite Selection Signals Analysis of 23 Purebred Clades.

Dog breeds represent canine sub-populations with distinctive phenotypic features and limited genetic diversity. We have established a resource to study breed-specific genetic diversity. Utilising genetic resources within our laboratory biobank, public domain genotype data and the phylogenetic framework of 23 breed clades, the primary objective for this study was to identify genomic regions that differentiate the Bullmastiff breed.

Analysis of dog breed diversity using a composite selection index.

During breed development, domestic dogs have undergone genetic bottlenecks and sustained selective pressures, as a result distinctive genomic diversity occurs to varying degrees within and between breed groups. This diversity can be identified using standard methods or combinations of these methods. This study explored the application of a combined selection index, composite selection signals (CSS), derived from multiple methods to an existing genotype dataset from three breed groups developed in distinct regions of Asia: Qinghai-Tibet plateau dogs (adapted to living at altitude), Xi dogs (with superior running ability) and Mountain hounds (used for hunting ability).

Genome wide association study for growth in Pakistani dromedary camels using genotyping-by-sequencing.

Objective: Growth performance and growth-related traits have a crucial role in livestock due to their influence on productivity. This genome-wide association study (GWAS) in Pakistani dromedary camels was conducted to identify single nucleotide polymorphisms (SNPs) associated with growth at specific camel ages, and for selected SNPs, to investigate in detail how their effects change with increasing camel age. This is the first GWAS conducted on dromedary camels in this region.

Genetic analysis of digital image derived morphometric traits of black tiger shrimp () by incorporating G × E investigations.

The black tiger shrimp, , is the second most economically important aquaculture shrimp species in the world, and in Australia it is one of the most commonly farmed shrimp species. Despite its economic significance, very few studies have reported the genetic evaluation of economically important morphological size and shape traits of shrimp grown in commercial grow-out environments. In this study we obtained genetic parameter estimates and evaluated genotype-by-environment interaction (GxE) for nine body morphological traits of shrimp derived from images.

Genetic parameters of color phenotypes of black tiger shrimp ().

Black tiger shrimp () is the second most important aquaculture species of shrimp in the world. In addition to growth traits, uncooked and cooked body color of shrimp are traits of significance for profitability and consumer acceptance. This study investigated for the first time, the phenotypic and genetic variances and relationships for body weight and body color traits, obtained from image analyses of 838 shrimp, representing the progeny from 55 sires and 52 dams.

Genetic parameters of milk and lactation curve traits of dairy cattle from research farms in Thailand.

Objective: This study was aimed to estimate the genetic parameters, including genetic and phenotypic correlations, of milk yield, lactation curve traits and milk composition of Thai dairy cattle from three government research farms.

Methods: The data of 25,789 test-day milk yield and milk composition records of 1,468 cattle from lactation 1 to 3 of Holstein Friesian (HF) and crossbred HF dairy cattle calved between 1990 and 2015 from three government research farms in Thailand were analysed. 305-day milk yield was estimated by the Wood model and a test interval method.

Rescued back from extinction in the wild: past, present and future of the genetics of the Arabian oryx in Oman.

The Arabian oryx was the first species to be rescued from extinction in the wild by the concerted efforts of captive programmes in zoos and private collections around the world. Reintroduction efforts have used two main sources: the 'World Herd', established at the Phoenix Zoo, and private collections in Saudi Arabia. The breeding programme at the Al-Wusta Wildlife Reserve (WWR) in Oman has played a central role in the rescue of the oryx.

Disability-adjusted life years (DALYs) due to the direct health impact of COVID-19 in India, 2020.

COVID-19 has affected all countries. Its containment represents a unique challenge for India due to a large population (> 1.38 billion) across a wide range of population densities.

Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence.

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited.

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.

Correction: Molecular basis for a new bovine model of Niemann-Pick type C disease.

[This corrects the article DOI: 10.1371/journal.pone.

Evaluation of genetic diversity and management of disease in Border Collie dogs.

Maintaining genetic diversity in dog breeds is an important consideration for the management of inherited diseases. We evaluated genetic diversity in Border Collies using molecular and genealogical methods, and examined changes to genetic diversity when carriers for Trapped Neutrophil Syndrome (TNS) and Neuronal Ceroid Lipofuscinosis (NCL) are removed from the genotyped population. Genotype data for 255 Border Collies and a pedigree database of 83,996 Border Collies were used for analysis.

The feasibility and acceptability of various bovine brucellosis control strategies in India.

Bovine brucellosis is a neglected zoonotic disease prevalent in several developing countries including India. It has been successfully controlled in many developed countries by using vaccination in conjunction with extensive surveillance and test-and-cull approaches, but some of these approaches do not suit Indian culture and norms. This study was conducted to investigate the feasibility and social acceptability of various bovine brucellosis control strategies in India.

Using Dairy Value Chains to Identify Production Constraints and Biosecurity Risks.

The dairy industry plays an important role in the economy and food security of India. A study of the dairy value chains was conducted in Punjab, India, to identify production constraints and biosecurity risks. Focus group discussions and key informant interviews were conducted during 2018-2019 with a total of 119 participants comprising veterinarians (41), paraveterinarians (15), veterinary academics (12), dairy farmers (46) and key informants (5).

Molecular basis for a new bovine model of Niemann-Pick type C disease.

Niemann-Pick type C disease is a lysosomal storage disease affecting primarily the nervous system that results in premature death. Here we present the first report and investigation of Niemann-Pick type C disease in Australian Angus/Angus-cross calves. After a preliminary diagnosis of Niemann-Pick type C, samples from two affected calves and two obligate carriers were analysed using single nucleotide polymorphism genotyping and homozygosity mapping, and NPC1 was considered as a positional candidate gene.

Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs.

Background: The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq).

Analysis of variation in growth and spline-based growth models for Marecha and Lassi dromedary camels.

Camel is an important domestic animal that is well adapted to extremely harsh environments. Due to its multi-purpose role, the camel is gaining importance, particularly as a meat producer. Body weights at different ages and growth curves have been extensively studied in several livestock species.