Objective 1: Characterize rumen microbial populations, including cellulolytic microbes, and elucidate dynamics of these populations through the use of metagenomic approaches.
Sub-objective 1.A. Whole genome shotgun sequencing of rumen microbial milieu.
Sub-objective 1.B. Compare rumen bacterial species diversity responses to different diets.
Objective 2: Determine rumen microbial and host genetic effects associated with differences in measures of efficiency of heifers developed under divergent planes of nutrition or different diets.
Objective 3: Determine phenotypic and genetic relationships of early-in-life measures of feed consumption, growth and body composition, with subsequent reproduction and lifetime productivity.
Sub-objective 3.A. Estimate genetic and phenotypic variances and covariances of longevity, stayability, number of calves produced, and cumulative production of beef cows with early-in-life measures of growth rate, feed consumption, and indicators of body composition.
Sub-objective 3.B. Determine effects of phenotypes measured early-in-life on subsequent fertility of bulls.
Objective 4: Determine if the level of nutrition in utero and prior to puberty results in epigenetic effects on traits associated with production efficiency at later stages in life.
Sub-objective 4.A. Determine effects of feed intake prior to puberty and level of supplementation during mid to late gestation on genetic (co)variance and gene expression of the treated animals and their progeny.
Sub-objective 4.B. Determine effects of nutrient intake during gestation on phenotypes of treated animals and their progeny.
Objective 5: Develop and validate appropriate phenotypes for measuring fertility in cattle in order to determine interactions between variation in cow feed efficiency and reproductive performance.
Sub-objective 5.A. Determine factors controlling establishment and maintenance of pregnancy in cows induced to ovulate different sized follicles.
Sub-objective 5.B. Establish relationships between previous nutrition, time post-partum, resumption of estrus, and energetic efficiency in young postpartum beef cows.
Objective 6: Identify and fine map quantitative trait loci (QTL) affecting feed intake, growth and reproduction.
Sub-objective 6.A. Identify QTL affecting growth and reproduction in an advanced intercross of Red Angus, Charolais, and Tarentaise.
Sub-objective 6.B.Identify QTL with over-dominance effects on fitness
Sub-objective 6.C. Identify genes expressed in tissues of cattle.
We have proposed a series of experiments which will ultimately lead to reducing costs of beef production by:
Laying a foundation for future studies detailing relationships between rumen microbes and ruminant animals (Objectives 1 and 2) in order to further understand ways in which feed and particularly forages may be converted more efficiently to metabolically useful forms of energy;
Elucidating relationships between information available at the time selection decisions are made, typically at approximately one year of age, and lifetime performance (Objectives 3 and 6) thus facilitating selection of breeding stock for efficient low-cost production;
Collectively increasing knowledge of the phenotypic and genetic interplay between nutrition and reproduction (Objectives 2 and 4, Sub-objective 5.B) thus facilitating the economic optimization of feed level and identification of germplasm that is of less risk of reproductive failure when feed level is reduced; and
Further identifying factors controlling establishment and maintenance of pregnancy (Sub-objective 5.A), thus leading to targets for managerial interventions that increase pregnancy rate and reduce cost associated with producing replacement females.
Most of the work needed to accomplish our objectives is multi-disciplinary and contributions from more than one scientist are expected in order to bring each objective to fruition. In alphabetical order, primary collaborators responsible for accomplishment of each objective are as follows: 1) Alexander, Waterman, and our partners at the Venter Institute; 2) Grings, Roberts and Waterman; 3) Geary, MacNeil, and Roberts; 4) Geary, Grings, MacNeil and Roberts; 5) Geary, MacNeil, Roberts, and Waterman; and 6) Alexander, MacNeil, and Roberts. Results are brought to the public domain through scientific, technical, and popular press publication and through presentation and scientific and technology transfer meetings. All identified quantitative trait loci and gene expression results are contributed to appropriate public domain databases [e.g., AnimalQTLdb (http://www.animalgenome.org/QTLdb/cattle.html); Bovine QTL Viewer (http://bovineqtlv2.tamu.edu/index.html); and NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/projects/geo/query/browse.cgi)].