Polymorphisms Detected in the Tyrosinase and MATP (SLC45A2) Genes Did Not Explain Coat Colour Dilution in a Sample of Alpaca (Vicugna pacos)

The molecular basis of inheritance of alpaca fibre colour is poorly understood. However, colour dilution genes are anticipated to be causing a major effect on alpaca fibre colour. Candidate genes for dilutions included tyrosinase (tyr) and membrane associated transport protein (matp), both of which have been associated with coat colour dilution in other species. The coding regions of the tyr and matp genes were sequenced in 24 animals with various colour phenotypes. No polymorphism found in the coding region of tyr and matp exons 1, 3, 4, 5 and 7 could account for the dilutions in fibre colour observed

Identification of a Potential Marker for Absence of Dark Fibre in Vicugna pacos (alpaca)

The Melanocortin-1 receptor gene was sequenced in a group of 41 Australian alpacas and seven single nucleotide polymorphisms (SNPs) were identified within the coding region (D42D, N118N, L206L, E311E, T28A, G126S and R301C). Three of these SNP (T28A, G126S and R301C) showed an association with phenotypic colour variants when both skin and fibre colour were used to segregate animals into groups. We propose the identification of a haplotype (T28A/G126S), which appears to be a marker for the absence of dark pigment in alpaca fleeces. Animals with the G82/C126 combination did not have any dark pigment. Both A82G & C901T are potentially capable of altering MC1R function. It?s therefore possible that we have identified wild type (dominant) and loss-of-function (recessive) alleles of the alpaca MC1R gene

Characterization of the sheep Complement Factor B gene (CFB)

The Complement Factor B gene (CFB) of the alternative complement pathway has been identified in the sheep Major Histocompatibility Complex (MHC) and its genomic sequence determined. CFB is located approximately 600bp upstream of the complement C2 gene, contains 18 exons, and manifests the domain signature characteristic of CFB protein. Thirteen single nucleotide polymorphisms were identified in merino sheep and interbreed variation was identified by comparison with International Sheep Genomics Consortium data. Two predicted non synonymous substitutions were observed and in-silico analysis indicates that these are likely to have a destabilising effect on the protein structure. Sheep and cattle CFB were compared and shown to contain a common nine nucleotide deletion in exon 18 relative to human CFB. Predicted CFB amino acid sequences for these two species contain 761 aa relative to 764 aa in the human orthologue. Sequencing of the cosmid and BAC clones used in this study permitted the relative positions of three adjacent loci to be determined and showed that the previously described microsatellite locus (BfMs) is located within SKIV2L

New species and new records of sponge-inhabiting barnacles (Cirripedia, balanidae, acastinae) from Australia

The subfamily Acastinae contains a diverse group of barnacles that are obligate symbionts of sponges and alcyonacean and antipatharian corals. Integrating morphological and genetic (COI) data to compare against known species, this paper reports on nine species of sponge-inhabiting barnacles of the subfamily Acastinae, including three undescribed species (Acasta caveata sp. nov., Euacasta acutaflava sp. nov., and E. excoriatrix sp. nov.) and three species previously not recorded in Australian waters (A. sandwichi, Pectinoacasta cancellorum, and P. sculpturata). The new species are distinguished from similar species by a suite of morphological characters as well as genetic distances. A lectotype for Pectinoacasta cancellorum is designated. Sponge hosts were identified for all specimens where possible and are represented by 19 species from eight families and five orders

A rapid non-destructive DNA extraction method for insects and other arthropods

Preparation of arthropods for morphological identification often damages or destroys DNA within the specimen. Conversely, DNA extraction methods often destroy the external physical characteristics essential for morphological identification. We have developed a rapid, simple and non-destructive DNA extraction technique for arthropod specimens. This technique was tested on four arthropod orders, using specimens that were fresh, preserved by air drying, stored in ethanol, or collected with sticky or propylene glycol traps. The technique could be completed in twenty minutes for Coleoptera, Diptera and Hemiptera, and two minutes for the subclass Acarina, without significant distortion, discolouration, or other damage to the specimens

Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]

Functional annotation of livestock genomes is a critical and obvious next step to derive maximum benefit for agriculture, animal science, animal welfare and human health. The aim of the Fr-AgENCODE project is to generate multi-species functional genome annotations by applying high-throughput molecular assays on three target tissues/cells relevant to the study of immune and metabolic traits. An extensive collection of stored samples from other tissues is available for further use (FAANG Biosamples ‘FR-AGENCODE’). From each of two males and two females per species (pig, cattle, goat, chicken), strand-oriented RNA-seq and chromatin accessibility ATAC-seq assays were performed on liver tissue and on two T-cell types (CD3+CD4+&CD3+CD8+) sorted from blood (mammals) or spleen (chicken). Chromosome Conformation Capture (in situ Hi-C) was also carried out on liver. Sequencing reads from the 3 assays were processed using standard processing pipelines. While most (50–70%) RNA-seq reads mapped to annotated exons, thousands of novel transcripts and genes were found, including extensions of annotated protein-coding genes and new lncRNAs (see abstract #69857). Consistency of ATAC-seq results was confirmed by the significant proportion of called peaks in promoter regions (36–66%) and by the specific accumulation pattern of peaks around gene starts (TSS) v. gene ends (TTS). Principal Component Analyses for RNA-seq (based on quantified gene expression) and ATAC-seq (based on quantified chromatin accessibility) highlighted clusters characterised by cell type and sex in all species. From Hi-C data, we generated 40kb-resolution interaction maps, profiled a genome-wide Directionality Index and identified from 4,100 (chicken) to 12,100 (pig) topologically-associating do- mains (TADs). Correlations were reported between RNA-seq and ATAC-seq results (see abstract #71581). In summary, we present here an overview of the first multi-species and -tissue annotations of chromatin accessibility and genome architecture related to gene expression for farm animals

Inheritance of white colour in Alpacas: Identifying the genes involved

This RIRDC report describes the research conducted as part of the alpaca colour genetics project to identify the genes involved in the inheritance of white colour in alpacas. Three approaches were used (Mendelian, physical and genetic) in an attempt to unravel the mystery surrounding colour inheritance in alpacas. This project has successfully identified key mutations in genes that lead to differences in fibre colour in alpacas. Other genes, which play a role in colour variation in other species, were cleared of involvement in colour variation in alpacas. Through extensive observational analysis a model for Mendelian inheritance of the major colours was developed. In combination, these findings provide breeders with information that allows them to make informed colour breeding choices

Quantitative genetic analysis of micron blowout in Alpacas

Some alpacas maintain fine fibre throughout life, while others suffer from significant coarsening of fibre as they age, a trait known as micron blowout. Micron blowout results in reduced productivity, through reduced yield of high quality fibre over the life of an animal. Data from a well-established alpaca herd in Peru was used in a complex quantitative genetics analysis to determine if genetics plus environment, or environment alone was responsible for micron blowout in alpacas. This project has shown that micron blowout has a moderate heritability in alpacas, and that selection against micron blowout would be successful in reducing the extent of the problem. This report is targeted at Australian alpaca breeders

Characterisation of the Melanocortin 1 Receptor gene in Alpaca and identification of possible markers associated with phenotypic variations

The aim of this study was to determine if any correlation exists between MC1R polymorphisms, and skin and fibre colour in alpacas. Primers capable of amplifying the entire alpaca MC1R were designed from a comparative alignment of Bos taurus and Mus musculus MC1R gene sequences. The complete MC1R of 36 alpacas exhibiting a range of fibre colours, and which were sourced from farms across Australia, was sequenced from PCR products. Twenty one single nucleotide polymorphisms were identified within MC1R. Two of these polymorphisms (A82G and C901T) have the potential to reduce eumelanin production by disrupting the activity of MC1R. No agreement was observed between fibre colour alone, and MC1R genotype in the 36 animals in this study. However, when the animals were assigned to groups based on the presence or absence of eumelanin in their fibre and skin; only animals that had at least one allele with the A82/ C901 combination expressed eumelanin. We propose that A82/ C901 is the wildtype dominant 'E' MC1R allele, while alpacas with either G82/ T901 or G82/ Y901 are homozygous for the recessive 'e' MC1R allele and are therefore unable to produce eumelanin