1a. Objectives (from AD-416):
The research objectives of this proposal are to: 1) Assemble DNA samples, individual animal feed intake (FI), growth and carcass composition data for some 8,000 animals representing 8 major U.S. beef cattle breeds; 2) Genotype 2,400 animals from 6 breeds with the Affymetrix Bovine 800K Axiom assay and develop and validate across-breed molecular expected progeny differences (MEPDs) for FI, growth and carcass traits. Based upon results, recruit additional funding from industry partners to genotype additional animals; 3) Sample animals from the tails of the feed efficiency (FE) distribution from large groups (>/=300) of individually fed Angus, Hereford, Gelbvieh and composite breed cattle for basic studies of GHG emissions, gut microbiome composition and tissue-specific gene expression/network studies; 4) Test an approach to rapidly identify FE causal mutations based upon the public availability of 180X sequence coverage of the bovine genome from which over 45M polymorphisms were discovered for the design of the Illumina and Affymetrix ultrahigh-density SNP assays; 5) Develop and maintain DNA, RNA and phenotype repositories for samples acquired through project funding and publicly distribute these to the international research community; 6) Examine the roles of mitochondrial complex I and III proteins on FE of 600 animals from 3 breeds (Angus, Simmental and Gelbvieh); 7) Perform grain × forage and grow × finish feeding trials to quantify genotype × feeding regimen (nutritional environment) interactions on 900 individually fed Charolais steers and heifers. Four hundred of these animals will be genotyped with the Axiom assay; and 8) Provide research experiences for undergraduates at CoPD universities to attract these students to graduate school and prepare the next generation of well-trained, diverse scientists with expert skills and breadth of knowledge to address sustainable beef production. The extension objectives of this proposal are to: 1) Develop and deliver to a national industry-wide stakeholder audience the resources, tools, information and educational activities that will enhance their understanding of the: a) importance of FE to farm economics and resource use, b) emerging technologies for genetic improvement in FE and component traits (FI, growth, carcass composition), and c) options to use marker assisted management (MAM) systems to sustainably improve profitability; 2) Conduct a field demonstration project to demonstrate the utility of MEPDs for FE and component traits and “push” the technology into the beef industry, and 3) Deploy GS base on MEPDs for FE and component traits to the international beef industry. This tightly integrated research and extension proposal will generate basic new knowledge concerning the genetic and physiological regulation of FE. By capitalizing on a preexisting network of research and extension scientists and beef industry leaders (NBCEC WTP), we anticipate the translation of GS via MEPDs to the industry by Year 4. Existing partnerships with an international service provider (Igenity) and Breed Associations position our work for immediate international commercialization to improve global food security.
1b. Approach (from AD-416):
Proposed research activities: 1) Assemble DNA samples, individual animal feed intake, growth and carcass composition data for some 8,000 animals representing 8 US beef cattle breeds; 2) Molecular EPD estimation and validation; 3) An integrated genomic analysis of feed efficiency (FE); 4) RNA-Sequence: We will characterize transcriptome profiles for liver, small intestine, muscle, pituitary, hypothalamus and adipose tissues from high and low residual feed intake (RFI) animals; 5) Network construction: We will implement a variation of the likelihood-based causality model selection procedure to infer causal associations between genotype, gene expression and FE; 6) Test of an approach to rapidly identify mutations causal for variation in FE: Genomic regions of largest effect on FE will be investigated by strategically increasing regional SNP density; 7) Determine associations between ruminal and cecal methanogen bacterial abundance and CH4 production in vivo and in vitro from steers differing in FE; 8) Compare the metagenome within the gastro-intestinal tract of composite-breed steers differing in FE; 9) Develop and maintain DNA, RNA, and phenotype database repositories: DNA, RNA and tissue samples will be divided and stored to ensure that the valuable resources developed under this grant are preserved and made publicly available to researchers worldwide; 10) Mitochondrial Respiration Analyses: Mitochondrial metabolism will be investigated as a biomarker to produce “cleaner” FE phenotypes and strengthen the predictive ability of MEPDs; 11) Determine impact of efficiency during the growing period on performance, nutrient digestion and manure greenhouse gas emission; and 12) Perform grain x forage and grow x finish feeding trials to identify the presence of genotype × feeding regimen interactions on relative ranking for RFI. Proposed Extension Activities are: 1) Develop broadcast media; 2) Annual conferences will target industry-wide participation; 3) Youth leadership workshops will be coordinated with the Youth Beef Industry Conference; 4) Develop educational materials for distribution; 5) Develop decision support software to assist in sire selection and the evaluation of economic impacts to producers and feedlot managers implementing MAM; and 6) An industry-wide survey of stakeholders and their consultants will assess understanding of the importance of FE to sustainable resource use, understanding and adoption of DNA technologies, and of management techniques to improve resource use.
3. Progress Report:
We determined the prevalence of methanogens in the rumen and cecum of 14 steers that differed in residual gain. Procedures were developed to isolate DNA from rumen and cecum contents. Primary sets made for different groups of Archeae bacteria using sequence in the 16s rRNA 1) Total Archeae, 2) Methanobrevibacter ruminantium + Methanobrevibacter cuticularis, 3) Methanobrevibacter smithii + Methanobrevibacter wolinii + Methanobrevibacter thaueri + Methanobrevibacter gottschalkii + Methanobrevibacter woesii, 4) Methanosarcina barkeri, and 5) Methanobacterium ruminantium. In addition, two primary sets were made for total eubacteria using sequence from 16s rRNA. The sequences were cloned into vectors to be used for standard curves. Reverse Transcriptase-Polymerase Chain Reaction was used to quantify Methanogens. Three hundred sixteen calves were placed on study to determine individual feed intake and growth for an 83-day period. Two hundred sixty-five calves were born in the spring to be placed on study in the fall to measure feed intake and growth.