L-2 hydroxyglutaric aciduria in a South African Staffordshire Bull Terrier

L-2 hydroxyglutaric aciduria is an autosomal recessive error of metabolism that manifests as an encephalopathy. The most common presenting signs are seizures, tremors, ataxia and/ or dementia. Some affected dogs show only subtle behavioural changes. Amongst canines, the condition has been best described in Staffordshire Bull Terriers. Although this is the first reported case in South Africa, at least three other affected dogs have been indentified by polmerase chain reaction (PCR) in this country. Affected dogs have normal haematology, serum biochemistry and routine urine analysis. This report discusses the advantages and limitations of the three main diagnostic modalities, namely: magnetic resonance imaging, urine gas chromatography-mass spectrometry and genetic testing. The aim of this report is to increase awareness of the condition, assist diagnosis in encephalopathic dogs and improve detection of carriers amongst breeding stock

Genetic testing of canine degenerative myelopathy in the South African Boxer dog population

Canine degenerative myelopathy (DM) is a progressive disease process that is diagnosed late in life and mainly affects the pelvic limbs. Factors that make an ante-mortem definitive diagnosis of DM include: an insidious onset and clinical manifestation that mimics other disease processes of the pelvic limbs (hip dysplasia, cranial cruciate ligament rupture, etc.) or there may even be concurrent disease processes, old-age onset and lack of reliable diagnostic methods. Until recently, South African dog owners had to submit samples to laboratories overseas for genetic testing in order to confirm an affected dog (homozygous A/A) and to aid in the ante-mortem diagnosis of DM. Only affected dogs have been confirmed to manifest the clinical signs of DM. This study aimed to verify whether genetic testing by a local genetic laboratory was possible in order to detect a missense mutation of the superoxide dismutase gene (SOD1) that is implicated in causing the clinical signs of DM. The study also aimed to detect and map the inheritance of this disease process in a local Boxer dog population where the pedigree of the sampled population was known. Venous blood collected from Boxer dogs using a simple random sampling technique. The samples were genotyped for the SOD1:c.118G>A polymorphism. Carrier and affected Boxer dogs were detected. A pedigree that demonstrated the significance of inheriting a carrier or affected state in the population was mapped. The present study concludes that genotyping of the missense mutation in Boxer dogs is possible in South Africa. There are carrier and affected Boxer dogs in the local population, making DM a plausible diagnosis in aged dogs presenting with pelvic limb pathology

L-2 hydroxyglutaric aciduria in a South African Staffordshire Bull Terrier

L-2 hydroxyglutaric aciduria is an autosomal recessive error of metabolism that manifests as an encephalopathy. The most common presenting signs are seizures, tremors, ataxia and/ or dementia. Some affected dogs show only subtle behavioural changes. Amongst canines, the condition has been best described in Staffordshire Bull Terriers. Although this is the first reported case in South Africa, at least three other affected dogs have been indentified by polmerase chain reaction (PCR) in this country. Affected dogs have normal haematology, serum biochemistry and routine urine analysis. This report discusses the advantages and limitations of the three main diagnostic modalities, namely: magnetic resonance imaging, urine gas chromatography-mass spectrometry and genetic testing. The aim of this report is to increase awareness of the condition, assist diagnosis in encephalopathic dogs and improve detection of carriers amongst breeding stock

Canine multi-drug resistance-1 mutation prevalence : a South African perspective

The multi-drug resistance (mdr-1) gene mutation is a phenomenon well known to current veterinary practitioners. The mutation causes a predisposition for, amongst other phenomena, macrocyclic lactone-induced neurotoxicosis in affected canines, a condition that can be fatal. Various herding dog breeds can be heterozygous or homozygous for the mutation, and prevalence differs only slightly in dog populations between geographical regions. This report provides prevalence data of the canine mdr-1 mutation in 306 South African dogs.http://www.jsava.co.za/am201

Variations de couleur du plumage dans le genre Agapornis : une critique

The genus Agapornis consists of nine small African parrot species that are globally well known as pets, but are also found in their native habitat. Illegal trapping, poaching and habitat destruction are the main threats these birds face in the wild. In aviculture, Agapornis breeding is highly popular all across the globe. Birds are mainly selected based on their plumage colour variations but very little molecular research has been conducted on this topic. There are 30 known colour variations amongst the nine species and most of these are inherited as Mendelian traits. However, to date none of the genes or polymorphisms linked to these variations have been identified or verified. Due to unethical breeding practices, the need for the development of molecular tests such as identification verification tests or species identity tests is growing. Future research is paramount to ensure the conservation of wild populations as well as aiding breeders in improving breeding strategies.Le genre Agapornis se compose de neuf petites espèces de perroquets africains qui sont mondialement connus comme animaux de compagnie, mais qui se trouvent également dans leur habitat d’origine. Le piégeage illégal, le braconnage et la destruction de l’habitat sont les principales menaces auxquelles ces oiseaux sont confrontés dans la nature. En aviculture, l’élevage Agapornis est très populaire dans le monde entier. Les oiseaux sont principalement sélectionnés en fonction des variations des couleurs de leur plumage, mais très peu de recherches moléculaires ont été menées sur ce sujet. Il existe 30 variations de couleur connues parmi les neuf espèces et la plupart d’entre elles sont héritées des caractères Mendéliens. Cependant, à ce jour, aucun des gènes ou polymorphismes liés à ces variations n’a été identifié ou vérifié. En raison des pratiques de sélection contraires à l’éthique, la nécessité de développer des tests moléculaires tels que des tests de vérification de l’identification ou des tests d’identité d’espèce est de plus en plus importante. Les recherches futures sont primordiales pour assurer la conservation des populations sauvages et aider les éleveurs à améliorer leurs stratégies de sélection.The Technology and Human Resources for Industry Programme (THRIP), which forms part of the Department of Trade and Industry of the South African government project ID number TP13082831254, Lumegen Laboratories as well as the Technology Innovation Agency, SABDI grant (407/01 SABDI 16/1016).http://www.tandfonline.com/loi/tost202020-03-01hj2019Animal and Wildlife Science

Development of an SNP-based parentage verification panel for lovebirds

Please read abstract in the article.File S1 NGS sequencing, SNP discovery initial SNP panel selection, samples genotyped and construction of SNP‐based parentage verification panel.File S2 MAF and HO values of each SNP.File S3 Suggested relationships and parentage verification results.The Technology Innovation Agency, SABDI grant (407/01 SABDI 16/1016).https://onlinelibrary.wiley.com/journal/136520522020-12-01hj2019Animal and Wildlife Science

Development of an SNP

File S1 NGS sequencing, SNP discovery initial SNP panel selection, samples genotyped and construction of SNP‐based parentage verification panel.File S2 MAF and HO values of each SNP.File S3 Suggested relationships and parentage verification results.Please read abstract in the article.The Technology Innovation Agency, SABDI grant (407/01 SABDI 16/1016).https://onlinelibrary.wiley.com/journal/136520522020-12-01hj2019Animal and Wildlife Science

Draft de novo genome sequence of Agapornis roseicollis for application in avian breeding

In aviculture, lovebirds are considered one of the most popular birds to keep. This African parakeet is known for its range of plumage colors and ease to tame. Plumage variation is the most important price-determining trait of these birds, and also the main selection criterion for breeders. Currently, no genetic screening tests for traits of economic importance or to confirm pedigree data are available for any of the nine lovebird species. As a starting point to develop these tests, the de novo genome of Agapornis roseicollis (rosy-faced lovebird) was sequenced, assembled, and annotated. Sequencing was done on the Illumina HiSeq 2000 platform and the assembly was performed using SOAPdenovo v2.04. The genome was found to be 1.1 Gb in size and 16,044 genes were identified and annotated. This compared well with other previously sequenced avian genomes, such as the chicken, zebra finch, and budgerigar. To assess genome completeness, the number of benchmarking universal single-copy orthologs were identified in the genome. This was compared to other previously assembled avian genomes and the results indicated that the genome will be useful in the development of genetic screening tests to aid lovebird breeders in selecting breeding pairs.http://www.tandfonline.com/loi/labt202018-10-16hj2017Animal and Wildlife Science

Dense sampling of bird diversity increases power of comparative genomics

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.Peer reviewe

Author Correction: Dense sampling of bird diversity increases power of comparative genomics

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online