In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F1 bulls, 113 F1 dams, and 246 F2 progeny. A total of 37 amplicons were used to screen single nucleotide polymorphisms (SNPs) on 6 F1 bulls. Among 36 SNPs detected in 11 of these 13 genes, 19 were selected for genotyping by the Sequenom assay design on all F2 progeny. Single-marker analysis revealed seven SNPs in ATP binding cassette A1, apolipoproteins A1, B and E, phospholipid transfer protein and paraoxinase 1 genes significantly associated with nine phenotypes (P<0.05). Previously, we reported genetic networks associated with 19 complex phenotypes based on a total of 138 genetic polymorphisms derived from 71 known functional genes. Therefore, after Bonferroni correction, these significant (adjusted P<0.05) and suggestive (adjusted P<0.10) associations were then used to identify genetic networks related to the RCT pathway. Multiple-marker analysis suggested possible genetic networks involving the RCT pathway for kidney-pelvic-heart fat percentage, rib-eye area, and subcutaneous fat depth phenotypes with markers derived from paraoxinase 1, apolipoproteins A1 and E, respectively. The present study confirmed that genes involved in cholesterol homeostasis are useful targets for investigating obesity in humans as well as for improving meat quality phenotypes in a livestock production.

Quantitative or complex traits are determined by the combined effects of many loci, and are affected by genetic networks or molecular pathways. In the present study, we genotyped a total of 138 mutations, mainly single nucleotide polymorphisms derived from 71 functional genes on a Wagyu x Limousin reference population. Two hundred forty six F-2 animals were measured for 5 carcass, 6 eating quality and 8 fatty acid composition traits. A total of 2,280 single marker-trait association runs with 120 tagged mutations selected based on the HAPLOVIEW analysis revealed 144 significant associations (P < 0.05), but 50 of them were removed from the analysis due to the small number of animals (< 9) in one genotype group or absence of one genotype among three genotypes. The remaining 94 single-trait associations were then placed into three groups of quantitative trait modes (QTMs) with additive, dominant and overdominant effects. All significant markers and their QTMs associated with each of these 19 traits were involved in a linear regression model analysis, which confirmed single-gene associations for 4 traits, but revealed two-gene networks for 8 traits and three-gene networks for 5 traits. Such genetic networks involving both genotypes and QTMs resulted in high correlations between predicted and actual values of performance, thus providing evidence that the classical Mendelian principles of inheritance can be applied in understanding genetic complexity of complex phenotypes. Our present study also indicated that carcass, eating quality and fatty acid composition traits rarely share genetic networks. Therefore, marker-assisted selection for improvement of one category of these traits would not interfere with improvement of another.

Bayesian analysis was performed to examine the single-nucleotide polymorphism (SNPs) neighborhood patterns in cattle using 15,110 SNPs, each with a flanking sequence of 500 bp. Our analysis confirmed three well-known features reported in plants and/or other animals: (1) the transition is the most abundant type of SNPs, accounting for 69.8% in cattle; (2) the transversion occurs most frequently (38.56%) in cattle when the A + T content equals two at their immediate adjacent sites; and (3) C <--> T and A <--> G transitions have reverse complementary neighborhood patterns and so do A <--> C and G <--> T transversions. Our study also revealed several novel SNP neighborhood patterns that have not been reported previously. First, cattle and humans share an overall SNP pattern, indicating a common mutation system in mammals. Second, unlike C <--> T/A <--> G and A <--> C/G <--> T, the true neighborhood patterns for A <--> T and C <--> G might remain mysterious because the sense and antisense sequences flanking these mutations are not actually recognizable. Third, among the reclassified four types of SNPs, the neighborhood ratio between A + T and G + C was quite different. The ratio was lowest for C <--> G, but increased for C <--> T/A <--> G, further for A <--> C/G <--> T, and the most for A <--> T. Fourth, when two immediate adjacent sites provide structures for CpG, it significantly increased transitions compared to the structures without the CpG. Finally, unequal occurrence between A <--> G and C <--> T in five paired neighboring structures indicates that the methylation-induced deamination reactions were responsible for approximately 20% of total transitions. In addition, conversion can occur at both CpG sites and non-CpG sites. Our study provides new insights into understanding molecular mechanisms of mutations and genome evolution.

In vitro fertilization of ovulated bovine oocytes was a t tempted with fresh or frozen semen after capacitation in vitro. Sperm incubations and oocyte cultures were performed in a Krebs Ringer bicarbonate medium containing Na pyruvate, glucose and .3% bovine serum albumin. High ionic strength (HIS) medium was prepared by adding NaC1 to provide an osmolarity of 370 to 380 nOsmol/kg. Donor cows were treated with prostaglandin F2a and a series of follicle-stimulating hormone injections and ovulated oocytes were recovered 72 h after prostaglandin treatment. Fresh or frozen semen was: 1) placed directly into a microdrop of standard medium (SM) under oil; 2) washed by centrifugation with SM and placed in a microdrop of SM or 3) pretreated with HIS for 10 min, washed and placed into a microdrop of SM. In all cases, spermatozoa were preincubated for 3 h at a concentration of ~106 cells/ml before addit ion of oocytes. Oocytes were incubated with spermatozoa for 6 h, transferred to fresh medium and cultured for 24 h. When spermatozoa were placed directly into a microdrop, three of 34 (9%) oocytes were penetrated, but none divided. Spermatozoa washed with SM penetrated 20 of 45 (44%) oocytes and three (7%) divided. Spermatozoa incubated in HIS penetrated 14 of 47 (30%) oocytes and five (11%) divided. The washing of spermatozoa with standard medium was equally as effective as incubation with high ionic strength medium in inducing in vitro capacitat ion of bovine spermatozoa.

Elucidation of the retinoid signaling circuitry in the testis is critical to understanding how male germ cells develop to spermatozoa. Retinoic acid receptor A protein (RARA) is an essential mediator of retinoid signaling in the testis, as shown by a sterility phenotype observed for retinoic acid receptor A gene (Rara) knockout male mice. The seminiferous tubules of Rara knockout mice showed varying degrees of germ-cell degeneration. A dramatic increase in apoptosis of early meiotic prophase spermatocytes was observed in these tubules compared to the wild-type tubules. Germ-cell loss was dependent on the stages of the spermatogenic cycle: germ-cell loss was negligible in stages I-V, but severe after stages VIII and IX of the spermatogenic cycle. Using spermatogonial transplantation, the individual function of RARA in Sertoli cells or germ cells was determined. The wild-type donor germ cells, transplanted into Rara knockout testes, colonized and proliferated in the RARA-deficient microenvironment. The donor-derived cells were mostly early meiotic prophase spermatocytes, with few more advanced germ cells detected. Conversely, when Rara-deficient germ cells were injected into the microenvironment that express RARA, establishment of donor-derived germ-cell colonies was rare, but remarkably, once colonized, Rara-deficient germ cells progressed normally through spermatogenesis. These results together suggest that RARA may function in Sertoli cells to promote the survival and development of early meiotic prophase spermatocytes, whereas RARA in germ cells functions to increase the proliferation and differentiation of spermatogonia, prior to meiotic prophase.

Mitochondrial transcription factor A (TFAM), a nucleus-encoded protein, regulates the initiation of transcription and replication of mitochondrial DNA (mtDNA). Decreased expression of nuclear-encoded mitochondrial genes has been associated with onset of obesity in mice. Therefore, we hypothesized genetic variants in TFAM gene influence mitochondrial biogenesis consequently affecting body fat deposition and energy metabolism. In the present study, both cDNA (2259 bp) and genomic DNA (16,666 bp) sequences were generated for the bovine TFAM gene using a combination of in silico cloning with targeted region PCR amplification. Alignment of both cDNA and genomic sequences led to the determination of genomic organization and characterization of the promoter region of the bovine TFAM gene. Two closely linked A/C and C/T single nucleotide polymorphisms (SNPs) were found in the bovine TFAM promoter and then genotyped on 237 Wagyu x Limousin F2 animals with recorded phenotypes for marbling and subcutaneous fat depth (SFD). Statistical analysis demonstrated that both SNPs and their haplotypes were associated with marbling (P = 0.0153 for A/C, P = 0.0026 for C/T, and P = 0.0004 for haplotype) and SFD (P = 0.0200 for A/C, P = 0.0039 for C/T, and P = 0.0029 for haplotype), respectively. A search for transcriptional regulatory elements using MatInspector indicated that both SNPs lead to a gain/loss of six putative-binding sites for transcription factors relevant to fat deposition and energy metabolism. Our results suggest for the first time that TFAM gene plays an important role in lipid metabolism and may be a strong candidate gene for obesity in mammals.

The launch of large-scale chicken expressed sequence tags (EST) projects has placed the chicken in the lead for the number of EST sequences in agriculturally important animals. More than 451,000 chicken ESTs derived from over 158 libraries have been deposited in the NCBI dbEST database as of December 2003. But how many genes these ESTs represent and how they are expressed in different chicken tissues/organs remain undetermined. In the present research, we developed a human gene-based strategy for census of chicken orthologous genes and identification of their expression patterns. Among 34,157 human coding genes used in the study, BLAST analysis revealed that 11,066 genes provisionally matched 248,628 chicken ESTs. Based on the average EST abundance of the orthologous genes, the current public repository of chicken ESTs could represent ∼20,000 provisional genes. Analysis of gene expression in 14 single tissues/organs showed that approximately 15% of genes were expressed exclusively in single tissue/organ whereas the remaining ∼85% of genes were co-expressed in two or more tissues/organs. A majority (91.15%) of genes expressed in chicken embryos were also expressed at post-hatch stages, indicating that most genes activated in chicken embryos could serve housekeeping functions. Self-organizing maps (SOM) analysis organized 8807 provisional genes in selected chicken tissues into 98 clusters with each cluster being indicative of common regulatory factors and pathways. A total of 969 provisional orthologous genes were identified as preferentially expressed genes (PEGs) in various chicken tissues/organs (LOD>3.0). No doubt, the present study on gene expression patterns will provide insight into dynamics of metabolic pathways and tissue/organ programming and reprogramming in chickens.

A total of 98 898 expressed sequence tags (ESTs) derived from embryos and reproductive tissues in pigs were identified in the GenBank "est_others" database. Pig embryos were collected at 11, 12, 13, 14, 15, 20, 30, and 45 days after gestation. The reproductive tissues were sampled from testis, ovary, endometrium, hypothalamus, anterior pituitary, uterus, and placenta. A gene-oriented approach was developed to annotate these porcine EST sequences to census the genes expressed from these sources. Of the 33 308 mRNA sequences from the human genes used as references (data accessed on 1 November 2002), 9410 had the porcine EST homologs expressed in embryos and 11795 had the EST homologs expressed in reproductive tissues. The entire genome contributes at least 28.3% of its genes to embryo development and 35.4% of its genes to reproduction. Using the EST entry numbers as indicators of gene expression, we determined that the gene expression patterns differ significantly between embryos and reproductive tissues in pigs. The basic active genes were identified for each source, but most of them are not coexpressed abundantly. Few genes were expressed on the Y chromosome (P < 0.01), but they may represent counterparts of the double-dose genes that remain active in an inactivated X chromosome in females but are needed for proper development and growth. The census provides a panel of transcripts in a broad sense that can be used as targets to study the mechanisms involved in embryo development and reproduction in pigs and other mammals, including humans.

Objective: To compare sperm chromatin structural changes seen in media only culture or in coculture with bovine oviduct epithelial cells.Design: Three freshly ejaculated and three cryopreserved sperm samples in media culture or in oviduct epithelial cell coculture. Sperm in each treatment were evaluated by the sperm chromatin structure assay during a 72-hour time course.Setting: An academic research laboratory.Patient(s): Normospermic donors with children.Intervention(s): Semen collection through masturbation after 48 hours of abstinence.Main Outcome Measure(s): The sperm chromatin structure assay using flow cytometry to detect the susceptibility of sperm in either treatment to denaturation of DNA in situ.Result(s): The sperm chromatin structure assay data differed for sperm type (fresh or cryopreserved), over time, and between treatments within 6 hours of culture. In oviduct epithelial cell coculture, fresh sperm chromatin structure assay values for fresh sperm were stable, whereas in control medium higher chromatin degeneration levels were seen by 10 hours. For cryopreserved sperm, chromatin degeneration had increased by 1 hour postthaw in both treatments, although levels were higher in the control treatment thereafter.Conclusion(s): Sperm chromatin structural changes occur over time in culture. Such changes were observed within 2 hours for cryopreserved sperm. Coculture of sperm with oviduct epithelial cells results in a stabilizing effect for sperm against chromatin changes. (C) 1998 by American Society for Reproductive Medicine.

The objective of this study was to test the hypothesis that incubating equine cumulus-oocyte complexes (COCs) in medium containing 50% or 100% homologous preovulatory follicular fluid would improve cumulus expansion and nuclear maturation. Oocytes were incubated in one of three media: 1) supplemented TCM-199 (control), 2) 50% (v/v) follicular fluid in control medium or 3) 100% follicular fluid. Cumulus expansion was evaluated subjectively, and nuclear maturation was evaluated by staining oocytes with Hoechst 33258. The hypothesis that incubating COCs in medium containing follicular fluid would improve cumulus expansion was supported. More (P < 0.05) compact COCs incubated in 50% or 100% follicular fluid developed a moderately to completely expanded cumulus after 24 and 36 h of incubation and more (P < 0.05) expanded COCs incubated in 100% follicular fluid developed a moderately to completely expanded cumulus after 36 h of incubation compared to control medium. The hypothesis that incubating COCs in medium containing follicular fluid would improve nuclear maturation was not supported. Although more (P < 0.05) compact COCs incubated in 50% follicular fluid reached polar body-stage compared to those in control medium, the nuclear maturation rate in the control medium was lower than it was when the same medium was used in a preliminary experiment (described in main text); therefore, the apparent superiority of 50% follicular fluid must be interpreted cautiously. Based on these results, future studies are warranted to further address the value of adding preovulatory follicular fluid to equine IVM culture systems.

Sheep affected with ovine GM1 gangliosidosis are normal at birth and develop clinical signs, initially ataxia, commencing at approximately 5 months of age, which progresses rapidly to recumbency. Superovulation and embryo transfer techniques were applied to a flock of carrier sheep of ovine GM1 gangliosidosis to increase the numbers of carrier and affected animals. A recipient ewe with 3 at-risk fetuses died at 4 months of gestation (normal ovine gestation is 5 months), and spectrofluorimetric assay of cerebral lysosomal beta-galactosidase of the fetuses showed that 2 were carriers and one was an affected fetus. The affected fetus had marked cytoplasmic enlargement and vacuolization of central and peripheral nervous system neuronal soma and of hepatocytes and renal epithelial cells. Lectin histochemistry indicated abnormal storage of complex carbohydrates, with terminal saccharide moieties consisting of beta-galactose, N-acetylneuraminic acid, and N-acetylgalactosamine. This case underlines the need for prenatal initiation of therapy and also demonstrates that vacuolization alone is not the cause of clinical signs in this lysosomal storage disease in that clinical signs do not commence until at least 5 months after vacuolization is histologically apparent.

Knowledge regarding the timing of embryonic expression of the mammalian genome is of relevance for the development of preimplantation diagnostic methods for human genetic diseases. For development of preimplantation diagnosis of lysosomal storage diseases, it will be necessary to know at which embryonic stage the genes for lysosomal enzymes are expressed. In previous studies by other investigators, it has been shown that lysosomal alpha- and beta-galactosidase and beta-glucuronidase in murine embryos increase 50- to 100-fold in activity between the two-cell and late blastocyst stage. We describe here expression of lysosomal beta-galactosidase in preimplantation ovine (two-cell through midblastocyst) and porcine (two-cell through late blastocyst) embryos. Expression of beta-galactosidase in ovine and porcine preimplantation embryos followed a similar rate of increase as that described for murine embryos. Activity of beta-galactosidase increased over 10-fold between the two- to four-cell and midblastocyst stages in ovine embryos, and 300-fold between the two- to four-cell and late blastocyst stages in porcine embryos. Activity expressed on a per cell basis was relatively constant in ovine embryos, as has been described in murine embryos, and increased approximately 5-fold on a per cell basis in porcine embryos. Activity of beta-galactosidase in ovine and porcine embryos initially was greater than 12-fold on a per cell or per embryo basis than in murine embryos evaluated. The knowledge of beta-galactosidase embryonic expression may provide the basis for preimplantation diagnosis of genetic beta-galactosidase deficiency in these species.

The objective of this study was to determine if porcine endometrial cell contact would enhance the in vitro development of porcine embryos relative to endometrial cell culture supernatants or ovarian fibroblast contact. One hundred forty-nine embryos of various developmental stages were collected from 10 excised gilt reproductive tracts. Embryos were washed three times and placed randomly into one of four treatments: Minimal Essential Medium + 5% heat-treated fetal calf serum (complete MEM), porcine endometrial cell coculture (pEM), porcine endometrial cell supernatant (pEMS) and porcine ovarian fibroblast coculture (pOF). All cultures were conducted in 96 well microtiter plates, one embryo per well, at 37 C in a 5% CO2 in humidified air atmosphere. Observations for stage of development were made every 12 h by phase contrast microscopy (100X). Embryos in the pEM and pOF treatments had significantly greater (P less than .05) mean embryonic development scores (1.59 +/- .22 and 1.44 +/- .18, respectively) than embryos cultured in complete MEM only or pEMS (.63 +/- .13 and .48 +/- .15, respectively). The results of this study indicate that cell to embryo contact enhances in vitro development of porcine embryos.

The following paper briefly reviews the morphology of the bovine embryo and presents a retrospective analysis of bovine embryo transfer results accumulated from April to December of 1982 at a commercial embryo transfer center. Of particular interests were bovine embryo morphology, assessment of embryo quality, and recipient-donor, recipient-embryo synchrony requirements.

The effects of surgically tansectioning the muscular branch of the great sciatic nerve on ovine semitendinosus muscle weight, grams of fat, iodine number and fat percentage were studied. Twelve lambs were randomized into four treatment time periods. Time periods utilized postsurgery were: 48, 75, 110 and 138 d. Overall, highly significant decrease in absolute muscle weight was observed for the dener-vated muscle compared to the contralateral control. A muscle by section interaction was caused by a difference in relative weight loss between the proximal and distal sections. An increase in absolute muscle weight over time indicated that both the denervated and control muscle continued to grow during the experimental period. No difference in fat content between the denervated and control muscle was observed. An interaction between time and muscle was found due to a reduction in grams of fat in the denervated muscle for the first treatment time period. In denervated and control muscle lipid unsaturation increased with time, and a highly significant decrease in unsaturation was observed for denervated muscle compared to control muscle. Proximal and distal sections of the semitendinosus muscle differed (P<.05) in degree of saturation, the proximal section being more saturated. Also, an interaction between time and section was observed for degree of saturation. This was due to treatment time period two, where the degree of unsaturation was less for the distal section. Fat percentage increased in the distal section of denervated muscle.

The objective was to determine the effect of various cell types on the development of bovine embryos in vitro. Morulae were collected from beef and dairy cows 4 to 5 d after the onset of estrus (d 0). Embryos were randomly allocated to nine treatments: (1) microdrops of Ham's F-10 medium (HF-10) under paraffin oil (HF-10); (2) HF-10 over a substratum of collagen without paraffin oil (HF-10/clg); (3) HF-10 with bovine uterine fibroblasts grown on a collagen substratum (HF-10/clg-fib); (4) Minimal Essential Medium (MEM) without paraffin oil (MEM); (5) microdrops of MEM under paraffin oil (MEM/oil); (6) MEM with bovine uterine fibroblasts (MEM/Buf; (7) MEM with bovine testicular fibroblasts (MEM/Btes); (8) MEM exposed to uterine fibroblasts for 24 h to condition the medium (MEM/Con), and (9) MEM with 1 mm cubes of bovine endometrial tissue (MEM/End). In all cases, media were supplemented with 10% (v/v) heat-treated fetal calf serum. Observations were made at 24 h intervals, with the stage of embryo development recorded. Morulae developed into expanded blastocysts more frequently (P less than .05) in HF-10, MEM, MEM/oil, MEM/Buf, MEM/Btes and MEM/Con than in HF-10/clg, HF-10/clg-fib and MEM/End. More (P less than .01) blastocysts hatched in MEM/Buf and MEM/Btes than in the other media. In addition, nine of 12 (MEM/Buf), eight of 11 (MEM/Btes) and two of two (HF-10/clg-fib) hatched blastocysts attached to the fibroblast monolayers, an observation that was uncommon in treatments without cells. These data suggest that the co-culture of bovine embryos with bovine fibroblasts in a superior system for promoting embryo hatching and attachment in vitro.