General Information

  • A Review of Genetic Parameter Estimates for Wool, Growth, Meat and Reproduction Traits in Sheep

    Genetic parameters for a range of sheep production traits have been reviewed from estimates published over the last decade. Weighted means and standard errors of estimates of direct and maternal heritability, common environmental effects and the correlation between direct and maternal effects are presented for various growth, carcass and meat, wool, reproduction, disease resistance and feed intake traits. Weighted means and confidence intervals for the genetic and phenotypic correlations between these traits are also presented. A random effects model that incorporated between and within study variance components was used to obtain the weighted means and variances. The weighted mean heritability estimates for the major wool traits (clean fleece weight, fibre diameter and staple length) and all the growth traits were based on more than 20 independent estimates, with the other wool traits based on more than 10 independent estimates. The mean heritability estimates for the carcass and meat traits were based on very few estimates except for fat (27) and muscle depth (11) in live animals. There were more than 10 independent estimates of heritability for most reproduction traits and for worm resistance, but few estimates for other sheep disease traits or feed intake. The mean genetic and phenotypic correlations were based on considerably smaller numbers of independent estimates. There were a reasonable number of estimates of genetic correlations among most of the wool and growth traits, although there were few estimates for the wool quality traits and among the reproduction traits. Estimates of genetic correlations between the groups of different production traits were very sparse. The mean genetic correlations generally had wide confidence intervals reflecting the large variation between estimates and relatively small data sets (number of sires) used. More accurate estimates of genetic parameters and in particular correlations between economically important traits are required for accurate genetic evaluation and development of breeding objectives.More »
  • Alpaca Genomics

    In 2005, the alpaca became the first camelid species to have its genome sequenced, in an effort led by Dr. Warren Johnson at the National Cancer Institute. The Alpaca Genome Project, which also includes the generation of a medium-density Radiation Hybrid (RH) map for the alpaca, set the foundation for genomic studies in camelids.More »
  • Breeding Alpacas

    Breeding Alpacas is a much marketed but little known subject. Perusing industry literature, the enthusiast will see beautiful glossy images of alpaca herdsires and show ribbons, each promoting that alpaca as the perfect match for your girl. It behooves the serious owner to study the subject of alpaca breeding carefully.More »
  • Call for Participation

    I have started a DNA bank for future use mapping potentially genetic diseases and phenotypic traits in alpacas and other camelids. Now that the alpaca genome project is completed, and the first alpaca genome has been completely sequenced, we can really dive into finding the genes involved in camelid health, disease, and various phenotypes of interest to breeders.More »
  • Camelid Geneticists Chart Course for Future Research

    The purpose of the meeting was to bring together genomic scientists from the National Institutes of Health, academic geneticists, clinical veterinarians, veterinary pathologists, and organizational administrators to share thoughts and opinions on camelid genetics. The workshop was truly international in scope with attendees from Australia, Canada, Peru, and the United States. Among the disciplines represented were geneticists, molecular biologists, genomic researchers, clinical veterinarians, pathologists, academicians, and fiber specialists.More »
  • Camelid Genomes Reveal Evolution and Adaptation to Desert Environments

    Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.More »
  • Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids

    The development of high-quality chromosomally assigned reference genomes constitutes a key feature for understanding genome architecture of a species and is critical for the discovery of the genetic blueprints of traits of biological significance. South American camelids serve people in extreme environments and are important fiber and companion animals worldwide. Despite this, the alpaca reference genome lags far behind those available for other domestic species. Here we produced a chromosome-level improved reference assembly for the alpaca genome using the DNA of the same female Huacaya alpaca as in previous assemblies. We generated 190X Illumina short-read, 8X Pacific Biosciences long-read and 60X Dovetail Chicago® chromatin interaction scaffolding data for the assembly, used testis and skin RNAseq data for annotation, and cytogenetic map data for chromosomal assignments. The new assembly VicPac3.1 contains 90% of the alpaca genome in just 103 scaffolds and 76% of all scaffolds are mapped to the 36 pairs of the alpaca autosomes and the X chromosome. Preliminary annotation of the assembly predicted 22,462 coding genes and 29,337 isoforms. Comparative analysis of selected regions of the alpaca genome, such as the major histocompatibility complex (MHC), the region involved in the Minute Chromosome Syndrome (MCS) and candidate genes for high-altitude adaptations, reveal unique features of the alpaca genome. The alpaca reference genome VicPac3.1 presents a significant improvement in completeness, contiguity and accuracy over VicPac2 and is an important tool for the advancement of genomics research in all New World camelids.More »
  • Comparative Population Genomics Reveals Genetic Basis Underlying Body Size of Domestic Chickens

    Domestic animals are excellent biological models widely used in developmental biology, phenotypic evolution, and medical research studies. They have been developed as different breeds exhibiting remarkable differences in morphology, physiology, behavior, and adaptations.More »
  • Connecting Gene Expression and Phenotype – Preliminary Results from RNA Sequencing of 150 Lambs

    Gene expression analysis can aid in prioritising regions or classes of variants for genomic prediction and they increase our understanding of quantitative traits. The number of reads from RNA sequencing that align to a gene can be used to quantify gene expression. We sampled liver and muscle tissues of 150 lambs at slaughter. Their dams had been managed to high, medium, and low body condition scores (BCS) during mid-to-late pregnancy and the lambs were fed three different finishing diets. Differential expression of genes (DEG) was investigated contrasting tissue, BCS, lamb diets, other treatment differences, as well as high and low lamb carcass eye muscle width (CEMW). A large number of DEG were identified between tissues, but only the low versus high BCS comparison resulted in DEG for treatments. DEG were also found when we contrasted high and low CEMW. A strong trend toward down regulation was observed in all tests, except in BCS where all DEG were overexpressed in fatter ewes.More »
  • Efficient Alpaca Breeding

    The primary goal of an alpaca breeding program is to efficiently and safely impregnate females with the least amount of stress for all parties involved. The role of the alpaca manager is to facilitate breedings to maximize a herd’s development. Doing this effectively requires some knowledge of reproductive biology, an understanding of basic genetics, and interpretation of behaviors that indicate reproductive status. Developing the ability to accurately identify aberrant aspects of reproductive performance also helps improve program efficiency. This article gives an overview of some of the reproductive techniques used in South America. In addition, some troubleshooting tips are offered in an effort to provide the North American alpaca breeder with new insight and practical ways to sleuth and avoid reproductive problems within their herd.More »
  • Explaining the Maths

    This post explains the maths behind the formula 3n × 2m (the number of unique zygotes) mentioned in last week’s post.More »
  • Genetic Analysis Reveals the Wild Ancestors of the Llama and the Alpaca

    The origins of South America's domestic alpaca and llama remain controversial due to hybridization, near extirpation during the Spanish conquest and difficulties in archaeological interpretation. Traditionally, the ancestry of both forms is attributed to the guanaco, while the vicuña is assumed never to have been domesticated. Recent research has, however, linked the alpaca to the vicuña, dating domestication to 6000–7000 years before present in the Peruvian Andes. Here, we examine in detail the genetic relationships between the South American camelids in order to determine the origins of the domestic forms, using mitochondrial (mt) and microsatellite DNA. MtDNA analysis places 80% of llama and alpaca sequences in the guanaco lineage, with those possessing vicuña mtDNA being nearly all alpaca or alpaca–vicuña hybrids. We also examined four microsatellites in wild known–provenance vicuña and guanaco, including two loci with non–overlapping allele size ranges in the wild species. In contrast to the mtDNA, these markers show high genetic similarity between alpaca and vicuña, and between llama and guanaco, although bidirectional hybridization is also revealed. Finally, combined marker analysis on a subset of samples confirms the microsatellite interpretation and suggests that the alpaca is descended from the vicuña, and should be reclassified as Vicugna pacos. This result has major implications for the future management of wild and domestic camelids in South America.More »
  • Genetic Diversity in Alpacas: Can Inbreeding Explain the High Prevalence of Congenital Defects?

    Genome research has progressed rapidly in recent years and DNA-based selection tools are now available in a number of domesticated species. To date, advanced genomics technologies have not been developed in alpacas (Vicugna pacos). Therefore, breeders select for traits of economic importance (fleece phenotypes) using traditional techniques such as line breeding. Alpacas have experienced a history of population bottlenecks including the mass destruction of alpacas and llamas during the 16th Century, therefore traditional breeding may exacerbate an already depleted gene pool. Alpaca veterinarians report a prevalence of congenital defects much higher than any other livestock species. This study investigated levels of genetic diversity at genome-wide markers in Australian alpacas. Samples have been collected from unrelated individuals with normal and defective phenotypes including choanal atresia, polydactyly, cyclopia, syndactyly, vulval atresia and anal atresia. Multi-locus heterozygosity and inbreeding coefficients were estimated using microsatellite data from 53 or 22 loci. In addition, pedigrees were examined in order to detect pedigree inbreeding. Inbreeding coefficients estimated from genomic data reveal that individuals with congenital defects do not have significantly higher molecular inbreeding levels than healthy individuals. These results suggest that high levels of inbreeding cannot explain the high prevalence of congenital abnormalities in alpacas. This study is the first to report on the genetic variability of Australian alpacas and represents an important first step in the use of genomics to inform alpaca breeding practices.More »
  • Genetics for Alpaca Breeders

    Humans and alpacas share many things in common, along with the rest of the animal kingdom, including how they pass their genes on to the next generation. Humans have over 20,000 genes spread across 23 pairs of chromosome and some 3 billion base pairs of DNA. Alpacas likely have between 15,000 and 20,000 genes (just a guess at this point) spread across 37 pairs of chromosomes and unknown billions of base pairs of DNA. The first complete alpaca genome was sequenced in 2008, so many of these statistics will shortly become known.More »
  • Grand Challenge Animal Reproduction-Theriogenology: From the Bench to Application to Animal Production and Reproductive Medicine

    Reproductive physiology and procreation has always fascinated human kind. Therefore, it is not surprising that scientific research in reproduction is one of the oldest and most established field in biology. Advancement in reproductive sciences has been possible because of the curiosity of scientists of various backgrounds (biologists, animal scientists, and veterinarians). At the turn of the twentieth century, advances in reproductive research were mostly driven by needs for improved animal production and prevention of venereal diseases. The body of knowledge in animal reproduction has seen an exponential growth in the last 50 years. In recent years, the field of study expanded beyond laboratory species and production animals to include wildlife conservation and management. As this field of research grew, scientists felt the importance of organizing in international societies dedicated to this area. One of the oldest of these societies is the Society for the Study of Reproduction. In the veterinary field, reproductive physiology and pathology became known as “Theriogenology” thanks to the efforts of the founding members of a veterinary specialty under the name of the American College of Theriogenologists, recognized in 1971 by the American Veterinary Medical Association as an integral part of the veterinary curriculum (1). Similar specialty colleges were also started in Europe (European College of Animal Reproduction), Australia, and New Zealand (College of Veterinary Scientists, Animal Reproduction). In addition to these specialty colleges, other international societies have emerged including Society for Theriogenology, International Embryo Transfer Society, European Society for Domestic Animal Reproduction, and European Society for Small Animal Reproduction. All these society have now well-established regular meetings to provide a forum for communication of recent research and their application to the health and welfare of animals. This paper attempts to highlight some of the major milestones and challenges in reproductive research.More »
  • Heritabilities, Phenotypic Correlations and Genetic Correlations for Major Traits in Sheep

    Heritabilities, phenotypic correlations and genetic correlations for major traits in sheep.More »
  • Just How Random is Genetic Inheritance?

    Mating two superior animals together does improve your chance of producing superior offspring, but because of the completely random nature of gene assortment there is no way to predict which particular combination of genes will end up in which gamete. There is no way to control which egg is fertilised by which sperm, and ultimately chance and even luck still factor in the genome you are dealt. Some gamete combinations may be so detrimental that the embryo dies very early on. Two animals who together produced a superb animal may never do so again, but at the same time a disappointing mating outcome doesn’t mean future ones will be. So yes, there absolutely is a lot of randomness in genetic inheritance — far, far more than you may have thought. It is important to be aware of this randomness, and how, because of it, you do not have as much control over your breeding as you may think. But this is a blog about better breeding, and just knowing what you can’t control is a big step on the way to being a better breeder. We will be going deeper and deeper in our understanding, covering genes, statistics and selection strategies along the way.More »
  • Punnet Squares: Two Genes

    Every sperm or egg has only one copy of each gene So each sperm from the male could have either the G or the S allele from the whitespot gene and it can have either B or B from the color gene.More »
  • Systematics, Taxonomy and Domestication of Alpaca and Llama: New Chromosomal and Molecular Evidence

    Four camelid species exist in South America: two wild, the guanaco (Lama guanicoe) and the vicuña (Vicugna vicugna), and two domestic, the alpaca (Lama pacos) and the llama (Lama glama). However, the origin of the domestic species has been a matter of debate. In the present study, variations in chromosome G banding patterns and in two mitochondrial gene sequences have been used to study the origin and classification of the llama and alpaca. Similar patterns in chromosome G band structure were observed in all four Lamini species, and these in turn were similar to the bands described for camels, Camelus bactrianus. However, fine and consistent differences were found in the short arms of chromosome 1, separating camels, guanacos and llamas from vicuñas and alpacas. This pattern was consistent even in a hybrid guanaco x alpaca. Equivalent relationship showed the complete cytochrome b gene sequences, and the minimum expansion tree of the partial control region sequence, grouping guanaco with llama and vicuña with alpaca. Phylogenetic analyses showed V. vicugna and L. guanicoe as monophyletic groups. Analysis of both gene sequences revealed two clades within vicuña, concordant with the two described subspecies, but the results for guanaco did not confirm existence of the four previously proposed subspecies. The combined analysis of chromosomal and molecular variation showed close genetic similarity between alpacas and vicuñas, as well as between llamas and guanacos. Although directional hybridization was revealed, our results strongly support the hypothesis that the llama would have derived from L. guanicoe and the alpaca from V. vicugna, supporting reclassification as V. pacos.More »
  • Testicular Length as an Indicator of the Onset of Sperm Production in Alpacas under Swedish Conditions

    The popularity of alpacas (Vicugna pacos) is increasing in Sweden as well as in other countries; however, knowledge about optimal management practices under Swedish conditions is still limited. The wide age range reported when the onset of puberty can occur, between 1 and 3 years of age, makes management decisions difficult and may be influenced by the conditions under which the alpacas are kept. The aim of this study was to find out when Swedish alpacas can be expected to start producing sperm, by using testicular length and body condition score as a more precise indirect indicator than age.More »
  • Ultrastructural Observations on the Placenta of the Alpaca (Lama pacos)

    The alpaca is one of the four South American species of the family Camelidae. Its placenta, like that of other camelids, is diffuse and epitheliochorial in type. The chorionic epithelium is thrown into unbranched villi or folds which are closely apposed to corresponding undulations of the uterine epithelium, and the fetal-maternal interface consists of an intricate interdigitation of fetal and maternal microvilli. In late gestation both chorionic and uterine epithelia are deeply indented by placental capillaries, so that the minimum intercapillary distance across the diffusion pathway may be as little as 2 μm. This distance appears to be less than that found in the epitheliochorial placenta of any other species of domestic ungulate in late gestation: it may be one of several adaptations to pregnancy at high altitude. Delivery of the fetal membranes occurs some 45 minutes after the birth of the fetus. The placenta is non-deciduate.More »
  • What’s Next in Genomics? Functional Annotation of Animal Genomes

    The last five years has witnessed the completion of reference genome projects for each of the major livestock species, along with the application of high throughput SNP genotyping to fast track gene discovery and genomic prediction. This paper explores one possible new direction in genomics and its possible impact on animal science. An international project has been initiated that aims to identify the genomic regions responsible for gene regulation, thereby providing functional annotation of animal genomes FAANG). This seeks to increase our ability to interpret variation in genome sequence and predict the resulting phenotypic consequence. This has large implications for animal science and in particular animal breeding, given a key objective of genomic prediction is to use molecular data (currently SNP) to predict genetic merit. To successfully annotate the regulatory elements in genomic sequence, the FAANG Consortium has been created to provide coordination and standardisation in data collection, uality control and analysis. Aspects of the consortium are described, along with information on Australia’s current and future contributions.More »