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Annual Review of Animal Biosciences

Ben J Hayes, Hans D Daetwyler
The 1000 Bull Genomes Project is a collection of whole-genome sequences from 2,703 individuals capturing a significant proportion of the world's cattle diversity. So far, 84 million single-nucleotide polymorphisms (SNPs) and 2.5 million small insertion deletions have been identified in the collection, a very high level of genetic diversity. The project has greatly accelerated the identification of deleterious mutations for a range of genetic diseases, as well as for embryonic lethals. The rate of identification of causal mutations for complex traits has been slower, reflecting the typically small effect size of these mutations and the fact that many are likely in as-yet-unannotated regulatory regions...
December 3, 2018: Annual Review of Animal Biosciences
Jose V Lopez, Bishoy Kamel, Mónica Medina, Timothy Collins, Iliana B Baums
Conservation genomics aims to preserve the viability of populations and the biodiversity of living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few genomic resources currently exist for the group. The subset of marine invertebrates includes the most ancient metazoan lineages and possesses codes for unique gene products and possible keys to adaptation. The benefits of supporting invertebrate conservation genomics research (e.g., likely discovery of novel genes, protein regulatory mechanisms, genomic innovations, and transposable elements) outweigh the various hurdles (rare, small, or polymorphic starting materials)...
November 28, 2018: Annual Review of Animal Biosciences
Edward S Rice, Richard E Green
Affordable, high-throughput DNA sequencing has accelerated the pace of genome assembly over the past decade. Genome assemblies from highthroughput, short-read sequencing, however, are often not as contiguous as the first generation of genome assemblies. Whereas early genome assembly projects were often aided by clone maps or other mapping data, many current assembly projects forego these scaffolding data and only assemble genomes into smaller segments. Recently, new technologies have been invented that allow chromosome-scale assembly at a lower cost and faster speed than traditional methods...
November 28, 2018: Annual Review of Animal Biosciences
Ilan Halachmi, Marcella Guarino, Jeffrey Bewley, Matti Pastell
Consumption of animal products such as meat, milk, and eggs in first-world countries has leveled off, but it is rising precipitously in developing countries. Agriculture will have to increase its output to meet demand, opening the door to increased automation and technological innovation; intensified, sustainable farming; and precision livestock farming (PLF) applications. Early indicators of medical problems, which use sensors to alert cattle farmers early concerning individual animals that need special care, are proliferating...
November 28, 2018: Annual Review of Animal Biosciences
Shu-Jin Luo, Yue-Chen Liu, Xiao Xu
Of all the big cats, or perhaps of all the endangered wildlife, the tiger may be both the most charismatic and most well-recognized flagship species in the world. The rapidly changing field of molecular genetics, particularly advances in genome sequencing technologies, has provided new tools to reconstruct what characterizes a tiger. Here we review how applications of molecular genomic tools have been used to depict the tiger's ancestral roots, phylogenetic hierarchy, demographic history, morphological diversity, and genetic patterns of diversification on both temporal and geographical scales...
February 15, 2019: Annual Review of Animal Biosciences
Mariana I Giassetti, Michela Ciccarelli, Jon M Oatley
The demand for food will increase to an unprecedented level over the next 30 years owing to human population expansion, thus necessitating an evolution that improves the efficiency of livestock production. Genetic gain to improve production traits of domestic animal populations is most effectively achieved via selective use of gametes from animals deemed to be elite, and this principle has been the basis of selective breeding strategies employed by humans for thousands of years. In modern-day animal agriculture, artificial insemination (AI) has been the staple of selective breeding programs, but it has inherent limitations for applications in beef cattle and pig production systems...
February 15, 2019: Annual Review of Animal Biosciences
R Michael Roberts, Harris Lewin
No abstract text is available yet for this article.
February 15, 2019: Annual Review of Animal Biosciences
Elisabetta Giuffra, Christopher K Tuggle
Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics are deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement...
November 14, 2018: Annual Review of Animal Biosciences
S Panserat, L Marandel, I Seiliez, S Skiba-Cassy
The rapid development of aquaculture production throughout the world over the past few decades has led to the emergence of new scientific challenges to improve fish nutrition. The diet formulations used for farmed fish have been largely modified in the past few years. However, bottlenecks still exist in being able to suppress totally marine resources (fish meal and fish oil) in diets without negatively affecting growth performance and flesh quality. A better understanding of fish metabolism and its regulation by nutrients is thus mandatory...
November 12, 2018: Annual Review of Animal Biosciences
Sung Woo Kim, John F Less, Li Wang, Tianhai Yan, Viswanath Kiron, Sadasivam J Kaushik, Xin Gen Lei
Feed protein supplements are one of the most expensive and limiting feed ingredients. This review offers a comprehensive analysis of how the expected expansion of animal production, driven by the rising world population and living standards for more animal-sourced foods, is creating a global shortage of feed protein supply. Because ruminants, chickens, and pigs contribute to 96% of the global supply of animal protein and aquaculture is growing fast, means of meeting the feed protein requirements of these species are elaborated...
November 12, 2018: Annual Review of Animal Biosciences
Elaine A Ostrander, Dayna L Dreger, Jacquelyn M Evans
Dogs are second only to humans in medical surveillance and preventative health care, leading to a recent perception of increased cancer incidence. Scientific priorities in veterinary oncology have thus shifted, with a demand for cancer genetic screens, better diagnostics, and more effective therapies. Most dog breeds came into existence within the last 300 years, and many are derived from small numbers of founders. Each has undergone strong artificial selection, in which dog fanciers selected for many traits, including body size, fur type, color, skull shape, and behavior, to create novel breeds...
November 12, 2018: Annual Review of Animal Biosciences
Wan-Sheng Liu
Mammalian sex chromosomes evolved from an ordinary pair of autosomes. The X chromosome is highly conserved, whereas the Y chromosome varies among species in size, structure, and gene content. Unlike autosomes that contain randomly mixed collections of genes, the sex chromosomes are enriched in testis-biased genes related to sexual development and reproduction, particularly in spermatogenesis and male fertility. This review focuses on how sex chromosome dosage compensation takes place and why meiotic sex chromosome inactivation occurs during spermatogenesis...
November 9, 2018: Annual Review of Animal Biosciences
Constance E Clare, Amey H Brassington, Wing Yee Kwong, Kevin D Sinclair
One-carbon (1C) metabolism comprises a series of interlinking metabolic pathways that include the methionine and folate cycles that are central to cellular function, providing 1C units (methyl groups) for the synthesis of DNA, polyamines, amino acids, creatine, and phospholipids. Sadenosylmethionine is a potent aminopropyl and methyl donor within these cycles and serves as the principal substrate for methylation of DNA, associated proteins, and RNA. We propose that 1C metabolism functions as a key biochemical conduit between parental environment and epigenetic regulation of early development and that interindividual and ethnic variability in epigenetic-gene regulation arises because of genetic variants within 1C genes, associated epigenetic regulators, and differentially methylated target DNA sequences...
November 9, 2018: Annual Review of Animal Biosciences
Marko Rudar, Marta L Fiorotto, Teresa A Davis
Skeletal muscle growth during the early postnatal period is rapid in the pig and dependent on the capacity of muscle to respond to anabolic and catabolic stimuli. Muscle mass is driven by the balance between protein synthesis and degradation. Among these processes, muscle protein synthesis in the piglet is exceptionally sensitive to the feeding-induced postprandial changes in insulin and amino acids, whereas muscle protein degradation is affected only during specific catabolic states. The developmental decline in the response of muscle to feeding is associated with changes in the signaling pathways located upstream and downstream of the mechanistic target of rapamycin...
November 2, 2018: Annual Review of Animal Biosciences
Joel Armstrong, Ian T Fiddes, Mark Diekhans, Benedict Paten
Rapidly improving sequencing technology coupled with computational developments in sequence assembly are making reference-quality genome assembly economical. Hundreds of vertebrate genome assemblies are now publicly available, and projects are being proposed to sequence thousands of additional species in the next few years. Such dense sampling of the tree of life should give an unprecedented new understanding of evolution and allow a detailed determination of the events that led to the wealth of biodiversity around us...
October 31, 2018: Annual Review of Animal Biosciences
Aimee J Silla, Phillip G Byrne
Anthropogenic environmental change has led to unprecedented rates of species extinction, presenting a major threat to global biodiversity. Among vertebrates, amphibians have been most severely impacted, with an estimated 41% of species now threatened with extinction. In response to this biodiversity crisis, a moral and ethical obligation exists to implement proactive interventionist conservation actions to assist species recovery and decelerate declines. Conservation breeding programs have been established for several threatened amphibian species globally, aiming to prevent species' extinction by maintaining genetically representative assurance colonies ex situ while providing individuals for population augmentation, translocation, and reestablishment in situ...
October 25, 2018: Annual Review of Animal Biosciences
I Martin Sheldon, James G Cronin, John J Bromfield
Bacteria are ubiquitous in the bovine uterus after parturition, but 50 years ago, cows tolerated these bacteria and few animals developed uterine disease. Now, up to 40% of dairy cattle develop postpartum uterine disease. Uterine disease causes infertility by compromising the function of not only the endometrium but also the ovary. Animals defend themselves against pathogens using tolerance and resistance mechanisms. Tolerance is the ability to limit the disease severity induced by a given pathogen burden. Resistance is the ability to limit the pathogen burden and is usually the function of immunity...
October 25, 2018: Annual Review of Animal Biosciences
Yusuke Nakane, Takashi Yoshimura
Organisms use changes in photoperiod for seasonal reproduction to maximize the survival of their offspring. Birds have sophisticated seasonal mechanisms and are therefore excellent models for studying these phenomena. Birds perceive light via deep-brain photoreceptors and long day-induced thyroid-stimulating hormone (TSH, thyrotropin) in the pars tuberalis of the pituitary gland (PT), which cause local thyroid hormone activation within the mediobasal hypothalamus. The local bioactive thyroid hormone controls seasonal gonadotropin-releasing hormone secretion and subsequent gonadotropin secretion...
October 17, 2018: Annual Review of Animal Biosciences
Mateus Contar Adolfi, Rafael Takahiro Nakajima, Rafael Henrique Nóbrega, Manfred Schartl
In vertebrates, sex organs are generally specialized to perform a male or female reproductive role. Acquisition of the Müllerian duct, which gives rise to the oviduct, together with emergence of the Amh/Amhr2 system favored evolution of viviparity in jawed vertebrates. Species with high sexspecific reproductive adaptations have less potential to sex reverse, making intersex a nonfunctional condition. Teleosts, the only vertebrate group in which hermaphroditism evolved as a natural reproductive strategy, lost the Müllerian duct during evolution...
October 10, 2018: Annual Review of Animal Biosciences
James E Jim Womack
I abandoned my original career choice of high school teaching to pursue dentistry and soon abandoned that path for genetics. The latter decision was due to a challenge by a professor that led to me reading Nobel speeches by pioneer geneticists before I had formal exposure to the subject. Even then, I was 15 years into my career before my interest in rodent genomes gave way to mapping cattle genes. Events behind these twists and turns in my career path comprise the first part of this review. The remainder is a review of the development of the field of bovine genomics from my personal perspective...
October 8, 2018: Annual Review of Animal Biosciences
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