Annual Review of Animal Biosciences最新文献

Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is 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. A scientific community-driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.

Prenatal exposure to excess steroids or steroid mimics can disrupt the normal developmental trajectory of organ systems, culminating in adult disease. The metabolic system is particularly susceptible to the deleterious effects of prenatal steroid excess. Studies in sheep demonstrate that prenatal exposure to excess native steroids or endocrine-disrupting chemicals with steroidogenic activity, such as bisphenol A, results in postnatal development of numerous cardiometabolic perturbations, including insulin resistance, increased adiposity, altered adipocyte size and distribution, and hypertension. The similarities in the phenotypic outcomes programmed by these different prenatal insults suggest that common mechanisms may be involved, and these may include hormonal imbalances (e.g., hyperandrogenism and hyperinsulinemia), oxidative stress, inflammation, lipotoxicity, and epigenetic alterations. Animal models, including the sheep, provide mechanistic insight into the metabolic repercussions associated with prenatal steroid exposure and represent valuable research tools in understanding human health and disease. Focusing on the sheep model, this review summarizes the cardiometabolic perturbations programmed by prenatal exposure to different native steroids and steroid mimics and discusses the potential mechanisms underlying the development of adverse outcomes.

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. To gain this knowledge, these new genomes must be compared through genome alignment (at the sequence level) and comparative annotation (at the gene level). However, different alignment and annotation methods have different characteristics; before starting a comparative genomics analysis, it is important to understand the nature of, and biases and limitations inherent in, the chosen methods. This review is intended to act as a technical but high-level overview of the field that should provide this understanding. We briefly survey the state of the genome alignment and comparative annotation fields and potential future directions for these fields in a new, large-scale era of comparative genomics.

All mammalian uteri contain glands that synthesize or transport and secrete substances into the uterine lumen. Uterine gland development, or adenogenesis, is uniquely a postnatal event in sheep and pigs and involves differentiation of glandular epithelium from luminal epithelium, followed by invagination and coiling morphogenesis throughout the stroma. Intrinsic transcription factors and extrinsic factors from the ovary and pituitary as well as the mammary gland (lactocrine) regulate uterine adenogenesis. Recurrent pregnancy loss is observed in the ovine uterine gland knockout sheep, providing unequivocal evidence that glands and their products are essential for fertility. Uterine gland hyperplasia and hypertrophy during pregnancy are controlled by sequential actions of hormones from the ovary and/or pituitary as well as the placenta. Gland-derived histotroph is transported by placental areolae for fetal growth. Increased knowledge of uterine gland biology is expected to improve pregnancy outcomes, as well as the health and productivity of mothers and their offspring.

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. In mammals, the eyes are believed to be the only photoreceptor organ, and nocturnal melatonin secretion triggers an endocrine signal that communicates information about the photoperiod to the PT to regulate TSH. In contrast, in Salmonidae fish the input pathway to the neuroendocrine output pathway appears to be localized in the saccus vasculosus. Thus, comparative analysis is an effective way to uncover the universality and diversity of fundamental traits in various organisms.

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 sex-specific 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. They developed for gamete release complete independence from the urinary system, creating optimal anatomic and developmental preconditions for physiological sex change. The common and probably ancestral role of Amh is related to survival and proliferation of germ cells in early and adult gonads of both sexes rather than induction of Müllerian duct regression. The relationship between germ cell maintenance and sex differentiation is most evident in species in which Amh became the master male sex-determining gene.

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. Wearable technologies dominate the market. In less-value-per-animal systems like sheep, goat, pig, poultry, and fish, one sensor, like a camera or robot per herd/flock/school, rather than one sensor per animal, will become common. PLF sensors generate huge amounts of data, and many actors benefit from PLF data. No standards currently exist for sharing sensor-generated data, limiting the use of commercial sensors. Technologies providing accurate data can enhance a well-managed farm. Development of methods to turn the data into actionable solutions is critical.

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). Here we review best conservation genomics practices in the laboratory and in silico when applied to marine invertebrates and also showcase unique features in several case studies of acroporid corals, crown-of-thorns starfish, apple snails, and abalone. Marine conservation genomics should also address how diversity can lead to unique marine innovations, the impact of deleterious variation, and how genomic monitoring and profiling could positively affect broader conservation goals (e.g., value of baseline data for in situ/ex situ genomic stocks).