Differential gene expression of ewes varying in tolerance to dietary nitrate.

Ruminants consuming diets with increased concentrations of nitrate (NO(3)(-)) can accumulate nitrite (NO(2)(-)) in the blood, resulting in toxicity. In a previous experiment, ewes identified as highly tolerant to subacute dietary NO(3)(-) were able to consume greater amounts of NO(3)(-) than lowly tolerant ewes without exhibiting signs of toxicity. We hypothesized that highly tolerant and lowly tolerant ewes differ in their ability to metabolize NO(3)(-) and thereby differ in the expression of hepatic genes involved in NO(3)(-) metabolism. Therefore, our objective was to identify hepatic genes differentially expressed between ewes classified as lowly tolerant and highly tolerant after administration of a subacute quantity of dietary NO(3)(-). Analysis of the Bovine Oligonucleotide Microarray data identified 100 oligonucleotides as differentially expressed (P < 0.05) between lowly tolerant and highly tolerant ewes. Functional analysis of the genes associated with these oligonucleotides revealed 2 response clusters of interest: metabolic and stress. Genes of interest within these 2 clusters (n = 17) and nonclustered genes with the greatest fold changes (FC; n = 5) were selected for validation by real-time reverse-transcription PCR. Relative expression, genomic regulation, and FC agreed between microarray and real-time reverse-transcription-PCR analyses, and FC differences (P < 0.05) between lowly tolerant and highly tolerant ewes were confirmed for 12 genes. Metabolic genes that were downregulated (P ≤ 0.032) in lowly tolerant ewes vs. highly tolerant ewes included aldehyde oxidase 1, argininosuccinate lyase, putative steroid dehydrogenase, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase1, and sterol carrier protein 2. In contrast, the metabolic gene homeobox was upregulated (P = 0.037) in lowly tolerant ewes. The glutathione peroxidase 3 and inter-α (globulin) inhibitor H4 genes in the stress response cluster were upregulated (P ≤ 0.045) in lowly tolerant ewes. Genes with the greatest FC, but did not cluster within the functional analysis included haptoglobin, which was upregulated (P = 0.024) in lowly tolerant ewes, and fatty acid desaturase 2 and thyroid hormone responsive, both of which were downregulated (P ≤ 0.019) in lowly tolerant ewes. Results from this study indicate that hepatic gene expression differs in ewes identified as lowly tolerant and highly tolerant to increased dietary NO(3)(-).

A software tool for the graphical visualization of large and complex populations.

Pedigree drawing is an essential tool in genetic and genealogical studies. A genetic analysis of a disease often starts with drawing a pedigree to show the overall population structure, the relationship among individuals, and gene flows from generation to generation. Such a graphical presentation of a pedigree is valuable for understanding the nature of the disease such as inheritance mode and familial trends and of the disease, for tracing the source of a detrimental gene, and for identifying the founders of the population. A genealogy study typically requires a pedigree drawing to show relationships among individuals. However, as the size and complexity of a pedigree increase, drawing a clear pedigree becomes a challenge. Pedigraph has been created to solve this problem. We developed a software tool named Pedigraph capable of creating artistic graphical pedigree drawings of large and complex populations with flexible options for pedigree analysis. Preliminary tests show that this software tool has great potential to be a useful tool for research in breeding, genetics and genomics in plants, animals, and zoo species, as well as a useful tool for studying history and human populations.

Allelic variation and genetic linkage of avian microsatellites in a new turkey population for genetic mapping.

Efforts to build a comprehensive genetic linkage map for the turkey (Meleagris gallopavo) have focused on development of genetic markers and experimental resource families. In this study, PCR amplification was attempted for 772 microsatellite markers that had been previously developed for three avian species (chicken, quail and turkey). Allelic polymorphism at 410 markers (53.1% of total examined) was determined by genotyping ten individuals (six F1 parents and four grandparents) in a new resource population specifically developed for genetic linkage mapping. Of these 410 markers, 109 (26.6%) were polymorphic in the tested individuals, with an average of 2.3 alleles per marker. Higher levels of polymorphism were found for the turkey-specific markers (61.1%) than for the chicken (22.7%) or quail-specific markers (33.3%). To test the fidelity of the matings, demonstrate the power of these families for linkage analysis, and determine genetic linkage relationships, 86 polymorphic markers were genotyped for up to 224 birds including founder grandparents, parents and F2 progeny. Linkage relationships for many of the chicken markers elucidated in the turkey were comparable to those observed in the chicken. These data demonstrate that the new UMN/NTBF resource population will provide a solid foundation for constructing a comparative genetic map of the turkey.