Next generation sequencing platforms have democratized genome sequencing. Large genome centers are no longer required to produce genome sequences costing millions. A few lanes of paired-end sequence on an Illumina Genome Analyzer, costing < $10,000, will produce more sequence than generated only a few years ago to produce the human and cow assemblies. The de novo assembly of large numbers of short reads into a high-quality whole-genome sequence is now technically feasible and will allow the whole genome sequencing and assembly of a broad spectrum of ruminant species. Next-generation sequencing instruments are also proving very useful for transcriptome or resequencing projects in which the entire RNA population produced by a tissue, or the entire genomes of individual animals are sequenced, and the produced reads are aligned to a reference assembly. We have used this strategy to examine gene expression differences in tissues from cattle differing in feed efficiency, to perform genome-wide single nucleotide polymorphism discovery for the construction of ultrahigh-density genotyping assays, and in combination with genome-wide association analysis, for the identification of mutations responsible for Mendelian diseases. The new 800K SNP bovine genotyping assays possess the resolution to map trait associations to the locations of individual genes and the 45 million polymorphisms identified in > 180X genome sequence coverage on over 200 animals can be queried to identify the polymorphisms present within positional candidate genes. These new tools should rapidly allow the identification of genes and mutations underlying variation in cattle production and reproductive traits.
The bovine corpus luteum (CL) grows very fast and regresses within a few days at luteolysis. Mechanisms controlling development and secretory function of the bovine CL may involve many factors that are produced both within and outside the CL. In the cow, luteolysis is initiated by uterine prostaglandin (PG)F2alpha released at the late luteal stage. It can also be induced by injection of exogenous PGF2alpha given at the mid luteal stage. Luteolysis consists of a phase of rapid decrease in progesterone (P4) production by the CL, followed by a phase of structural regression. Although uterine PGF2alpha is known to be the main luteolytic factor, its direct action on the CL is mediated by the products of accessory luteal cells: immune cells, endothelial cells, pericytes and fibroblasts. There are studies showing that beside endothelin-1, cytokines (tumor necrosis factor-alpha, interferons) and nitric oxide play critical roles in functional and structural luteolysis in cattle by stimulating leukotrienes and PGF2alpha', decreasing P4 secretion and apoptosis induction. Because of luteal blood flow and P4 concentrations decrease in parallel during both spontaneous and PGF2alpha-induced luteolysis, a decrease in luteal blood flow resulting in hypoxia has been proposed as one of the main luteolytic mechanisms in the cow. Hypoxia inhibits P4 synthesis in luteal cells by inhibiting the steroidogenic enzymes and promotes apoptosis of luteal cells by increasing pro-apoptotic proteins. Although reduction of luteal blood flow and hypoxia contribute to the late events of luteolysis, little is known about the physiological relevance and the cause of the transient increase in luteal blood flow and reactive oxygen species during the initial step of luteolysis.
Reduced reproductive efficiency has been reported in high-producing dairy cows. Sources of reproductive inefficiency include decreased expression of estrus, increased diameter of the ovulatory follicle and reduced fertility when cows are inseminated after estrus, increased incidence of double ovulation and twinning, and increased pregnancy loss. To overcome some of these inefficiencies, reproductive management programs have been developed that synchronize ovulation and enable effective timed artificial insemination (AI) of lactating dairy cows. Effective regulation of the corpus luteum (CL), follicles, and hormonal environment are critical for optimizing these programs. Recent programs, such as the 5-day CIDR program, Double-Ovsynch, G-6-G, and estradiol benzoate-CIDR programs were designed to more effectively control one or more physiological events. These events include synchronization of a new follicular wave at the beginning of the program, optimization of the circulating progesterone (P4) concentrations and duration of follicular dominance, optimized reductions in P4 and increases in circulating estradiol (E2) concentrations during the preovulatory period, and tightly synchronized ovulation of a follicle of optimal size and fertility for implementation of timed AI. The success of these programs has been remarkable, although there is substantial variability in effectiveness due to environmental, management, nutritional, genetic, and disease factors as well as potential variability in some aspects of reproductive physiology among commercial dairy farms. Future programs will optimize the reproductive physiology while simplifying the protocol implementation and also match specific reproductive management protocols to specific farms and even specific cows (for example primiparous vs. multiparous).
Widespread adoption of artificial insemination as a breeding practice has allowed for expanded use of desirable genetics from specific sires and greatly influenced production traits in dairy cattle populations worldwide. In fact, the average dairy cow in the US in 2009 produced 4.5 times more milk than in 1940 when commercialization of artificial insemination began. While many factors have contributed to this rapid increase in levels of milk production, genetic gain through expanded utilization of germlines from specific sires has been a major contribution. In comparison, use of artificial insemination in beef cattle populations has been limited due to challenges with implementing intensive management strategies required for success. Thus, there is need for alternative reproductive tools to expand use of desirable male genetics in the beef cattle industry. The process of sperm production, termed spermatogenesis, is supported by a tissue-specific stem cell population referred to as spermatogonial stem cells (SSCs). These unique cells have the capacity for infinite self-renewal and long-term regeneration of spermatogenesis following transplantation. In rodents, methods for isolating, culturing, and transplanting SSCs have been devised. For beef cattle, transplanting SSCs isolated from a donor male into the testes of recipient males in which donor-derived spermatogenesis occurs and offspring with donor genetics are produced from natural breeding has great potential as an alternative to artificial insemination. This potential reproductive strategy would allow for expansive use of genetics from desirable sires that overcomes the logistical challenges of artificial insemination. Translation of the methods devised for rodents to cattle is at the forefront of development. Devising means for isolating an SSC-enriched cell fraction from donor testes and identifying conditions that support long-term maintenance and proliferation of bovine SSCs in vitro are two tools that would greatly accelerate the pace at which transplantation will become a commercially viable option for cattle industries. Recent studies showed that expression of THY1 by SSCs is a conserved phenotype between rodents and cattle, and selection of the THY1 + fraction from donor testes can be used for isolating an SSC-enriched germ cell population. In addition, the conditions devised for expanding the number of rodent SSCs in vitro continues to serve as the basis for developing conditions that support bovine SSCs. With these tools in hand major advances in developing implementable reproductive tools with SSCs for commercial cattle production will be made in the coming decade.
The pattern of intrauterine growth and size at birth, in particular, programmes the structure and function of tissues later in life in many species, which has important implications for the incidence of adult-onset generative diseases in human populations. In mammals, the main determinant of intrauterine growth is the placental supply of nutrients which, in turn, depends on the size, morphology, transport characteristics and endocrine function of the placenta. However, compared to somatic tissues, little is known about the developmental programming of the placenta. This review examines the epigenetic regulation of placental phenotype with particular emphasis on the nutrient transfer capacity of the ovine placenta and environmental factors shown to cause developmental programming of other tissues. Overall, the placenta is responsive to environmental factors and uses a number of different strategies to adapt its phenotype to help support fetal growth during adverse intrauterine conditions. It is, therefore, not just a passive conduit for nutrient transfer to the fetus but alters its nutrient supply capacity dynamically to optimise fetal nutrient acquisition. Thus, the placental epigenome provides both a memory of environmental conditions experienced during development and an index of the future well being of the offspring.
The ovulatory process is extraordinary in that it constitutes a hormone-induced injury. Gonadotropin delivered via the follicular vascular wreath stimulates secretion of plasminogen activator by contiguous ovarian surface epithelial cells. A consequent elevation in interstitial plasmin activates collagenases and cleaves tumor necrosis factor alpha from its anchors on endothelium. Collagen fibril degradation and cellular death at the apex of the preovulatory follicle are hallmarks of impending ovulation. Follicular contractions rupture the weakened fabric at the apex, and the ovum, which has been disconnected from the underlying granulosa, is expelled; these components of the cascade are prostaglandin-mediated. Ovulation is required for fertility; unfortunately, it imparts a cancer risk to the ovarian surface epithelium. DNA-damaging reactive oxygen species are generated by inflammatory cells attracted into the vicinity of the ovulatory stigma. An ischemia-reperfusion flux coincident with ovulation and wound repair also contributes to genotoxicity. Potentially mutagenic lesions in DNA are normally reconciled by TP53 tumor suppressor-dependent cell-cycle arrest and base excision repair mechanisms; it is a unifocal escape that could be problematic. Epithelial ovarian cancer is a deadly insidious disease because it typically remains asymptomatic until it has metastasized to vital abdominal organs.