# Presentation: 050694

## Slide 1

## Slide 2

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Production Efficiency**
_**Explanation:**_**  Cow-calf and feeding systems: use of feed energy, reproduction, and longevity**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  End Product Quality**
_**Explanation:**_**  Pre-harvest molecular characterization and interventions in conventional systems and emerging systems; post-harvest quality assessment**

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Information Systems for Phenotypic and DNA**
_**Explanation:**_**  Establish open systems architecture platforms for quantitative and molecular investigations**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Animal Well-Being/Welfare**
_**Explanation:**_**  Adaptability - e.g., heat, fescue tolerance, etc.**

## Status:  New and needs to be investigated

**Priority Rating:  Medium**
_**Issue:**_**  Transgenics**
_**Explanation:**_**  Conduct discovery research, food production currently lower priority**

## Status:  New and needs to be investigated

**Priority Rating:  Medium**
_**Issue:**_**  Rumen microflora**
_**Explanation:**_**  initiate developing platform for characterization and future use**

## Slide 9

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Nutrient Intake and utilization**
_**Explanation:**_**  Basic research in this area is paramount. Need to look at triad of nutrients-microbes-host genetics. Priority should be rumen, but all areas of gut need to be explored. Need ways to measure and capture information. Gene expression/regulation studies **

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Reproductive efficiency**
_**Explanation:**_**  Need to investigate triad of nutrition-immune system-genetics. Make selection tools more accurate.  study expression/regulation of important genes. Evaluate economic impact.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Genetic Improvement and Genomic Tools**
_**Explanation:**_**  Need wider range phenotypes. ARS should remain repository of data. Emphasize health, fertility and well-being. Incorporate molecular data into genetic evaluations. Continue aggressive genomic program.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Animal behavior/ well-being**
_**Explanation:**_**  Important to develop standard methods and measures.  Important to educate producers and practitioners how to recognize problems.  **

## Status:  Needs to be investigated further

**Priority Rating:  Medium**
_**Issue:**_**  Conserve and Characterize Germplasm**
_**Explanation:**_**  Keep current repositories.  There is a need to both conserve germplasm and to characterize it.  May need to expand current repositories to include non-domestic breeds.**

## Status:  Needs to be investigated further

**Priority Rating:  Low**
_**Issue:**_**  Growth and Development**
_**Explanation:**_**  Focus should be on heifer growth. Also, mammary gland growth and regeneration in terms. Studies of structural conformation needs of high producing cows would also be interesting.  **

## Status:  Needs to be investigated further

**Priority Rating:  Low**
_**Issue:**_**  Product Quality**
_**Explanation:**_**  Work in this area should focus on improving the nutritional value of milk and enhancing important milk components.**

## Status:  Should no longer be investigated

**Priority Rating:  N/A**
_**Issue:**_**  Integrated Systems**
_**Explanation:**_**  Panel felt this was an important area, but that important decision making tools should be incorporated into other objectives and programs.**

## Slide 18

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Infrastructure needs**
_**Explanation:**_**  ****Continued support and research for functional genomics including continued genome funding for additional coverage and SNPs research.  Needs exist for facility(s) to house a production unit of relevant size & population for genetics/genomics studies that can be accessed by the genetics/genomics community. Priority for increased support of training and development programs for bioinformatics personnel.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Biological efficiency**
_**Explanation:**_**  ****This includes nutrient utilization & efficiency, seasonality, longevity, male reproduction, energy efficiency, other repro components (pregnancy success, piglet survivability, maternal ability), and alternative feed ingredients.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Swine Well-being**
_**Explanation:**_**  This includes research into useful measures and mechanisms that explain why they are relevant measures of animal well being. Also includes efforts to mitigate problems in swine well being once useful measures are defined.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Environmental impacts of swine production**
_**Explanation:**_**  This includes nutritional and genomic research on the retention of nutrients versus shedding of nutrients into the environment for odor abatement and pollution mitigation.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Pork Quality**
_**Explanation:**_**  Relevant factors and their interactions that predict pork quality are not fully known. Tools to predict pork quality and product tenderness pre-harvest are also needed. **

## Slide 24

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Reproductive efficiency limits profitability **
_**Explanation:**_**  Lifetime reproductive efficiency focusing on uterine health/embryonal and fetal survival, and assisted reproduction technologies including germplasm conservation should be emphasized.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Characterize genetic variation among breeds, animals within breeds, and alleles in distinct production environments **
_**Explanation:**_**  This characterization should emphasize fitness traits, lifetime productivity, meat and wool quality, and disease and parasite resistance/tolerance.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Suboptimal nutrient intake, utilization, and partitioning limits all aspects of production; nutrition is the largest cost factor in production**
_**Explanation:**_**  This should include elements from previous action plan, including grazing behavior, rumen microbiology.**

## Slide 28

## Status:  Needs to be investigated further

**Priority Rating:  Low**
_**Issue:**_**  Reproductive Efficiency **
_**Explanation:**_**  Considered to be the responsibility of the breeder companies.  (Most important for broiler and turkey industries.)**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Conserve, characterize and use of genetic resources**
_**Explanation:**_**  Populations are valuable and should be maintained.  Recommend combining this with the Genomic Tools component.**

## Status:  Should no longer be investigated

**Priority Rating:  Low**
_**Issue:**_**  Genetic improvement **
_**Explanation:**_**  Specifically referring to (1) developing breeding objectives  and (2) accelerating selection response.  Recommend moving (3) health and well-being and (4) transgenic poultry under Genomic Tools.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Genomic tools and Genetic resources**
_**Explanation:**_**  Extremely important for all three commodities. Combined the relevant sections of Components 2, 3 and 4.  **

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Nutrient intake and use**
_**Explanation:**_**  Fundamental problem in poultry production.**

## Status:  Should no longer be investigated

**Priority Rating:  Low**
_**Issue:**_**  Growth and development**
_**Explanation:**_**  Primary breeders should be working on this issue not ARS. **

## Status:  Needs to be investigated further

**Priority Rating:  Medium**
_**Issue:**_**  Product quality**
_**Explanation:**_**  Need to continue on genetic/nutrition interaction aspect only.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Scientific measures of well-being and stress**
_**Explanation:**_**  This is a front-line issue for industry.**

## Slide 37

## Slide 38

## Status:     

**Priority Rating:  High**
_**Issue:**_**  Enhance lifetime profitability (longevity)**
_**Explanation:**_**   Research should be directed at increasing dairy, swine, beef and sheep lifetime profitability through increased longevity.**

## Status:     

**Priority Rating:  High**
_**Issue:**_**  How do we measure welfare/well-being?**
_**Explanation:**_**  A need exists to identify objective measures of welfare/well-being including productivity, physiology, immunology and mental health; in order to enhance well-being. **

## Status:     

**Priority Rating:  High**
_**Issue:**_**  Continue research into production practices that ensure well-being while minimizing pain.**
_**Explanation:**_**  All potentially aversive production practices should be evaluated in order to optimize well-being. **

## Status:     

**Priority Rating:  High**
_**Issue:**_**  Animal's ability to adapt or environment adapted to animal**
_**Explanation:**_**  A need to determine if an animal is adapted to its current environment needs to be assessed and environmental modification explored as necessary **

## Slide 43

## Status:     

**Priority Rating:  High**
_**Issue:**_**  National Phenotypic/Genotypic Repository**
_**Explanation:**_**  Collection of existing phenotypic, genotypic, pedigree, and QTL data along with DNA, RNA, tissue samples will facilitate comprehensive data analysis. The repository would be publicly available. ARS coordinates activity due to long term commitment.**

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Paucity of Scientists with Quantitative Training**
_**Explanation:**_**  Expertise in quantitative genetics, statistics, and population genetics is in short supply. There is an aging faculty that represents a critical mass with this expertise. Training grants are urgently needed to meet the rapidly growing demand.**

## Status:     

**Priority Rating:  High**
_**Issue:**_**  Development of Statistical Analysis Techniques for Application to Genetic Evaluation**
- _**Explanation:**_**  Incorporation of genetic marker information into genetic evaluations is an urgent need. Research on statistical methodology to accommodate high-density SNPs is a major constraint to application of genomics research. Needs to be species neutral.**

## Status:     

**Priority Rating:  Medium**
_**Issue:**_**  Preservation of Unique Germplasm**
_**Explanation:**_**  There is need to maintain unique genetic lines in species where cryopreservation is not feasible. There was a conclusion that appropriately characterizing the problem is essential to gaining public support (e.g., relating to avian influenza).**

## Slide 48

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Alternative Feed Needs**
_**Explanation:**_**  Biofuel production is utilizing feedstuffs (corn, fats) commonly used as feedstuffs by livestock and poultry.  Alternative feedstuffs are needed.  This necessitates characterization of composition and nutrient availability.**

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Associative Effects Among Nutrients**
_**Explanation:**_**  The impact of associative effects among nutrients or feeds on feed utilization is not characterized so we can predict outcomes from different diets.  Need to understand mechanism and effects across gut compartments. **

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Nutrient x Genetic Interaction (multiple species)**
_**Explanation:**_**  Do different genetic lines utilize nutrients differently?  Different requirements?  Impact of nutrition on gene expression, "programming"?**

## Status:     

**Priority Rating:  Low**
_**Issue:**_**  Systems evaluation for impact of byproducts**
_**Explanation:**_**  Utilization of feedstuffs for biofuels appears likely to have an impact on diet formulation, farm profitability, nutrient management, product salability and societal concerns.**

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Improvement of Forage **
_**Explanation:**_**  There is a need to improve fiber digestibility to improve nutrient utilization.  This may entail changing the plant, better understanding the role of rumen microbes and effects of the rest of the diet.**

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Anti-nutritional Factors in Feedstuffs**
_**Explanation:**_**  How do we detect and reduce anti-nutritional factors (e.g., mycotoxins, factors in endophyte infected tall fescue, soy) and understand their effects on nutrient utilization.  Do we have the appropriate tools to assess them?  **

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Impact of Microflora**
_**Explanation:**_**  What is the effect of gut microflora?  Ruminal, small intestine, hindgut?  Potential improvements through use of "probiotics", adjuvants or diet components?  **

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Metabolism Studies / Evaluation of Feedstuffs**
_**Explanation:**_**  We need to reassess/assess nutrient requirements of animals (different genetics than 30 yr ago).  Revision/evaluation of feed analysis methods for nutritional relevance is needed.  In vitro methods need to be tied to in vivo response.**

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Increase utilization and decrease losses**
_**Explanation:**_**  Further evaluation of nutrient (e.g., N, P) inclusion in diets to reduce nutrient excretion.**

## Slide 58

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Limited ability to define and assess well being and stress of animals under production in pasture based systems**
_**Explanation:**_**  Limited data concerning the well being of animals in pasture based production systems exist. **
**Agreement on defining well being & limited methods for assessing animal stress constrain researchers from developing protocols for reducing this stress.**

## Status:  New and needs to be investigated

**Priority Rating:  Medium**
_**Issue:**_**  Limited empirical data concerning how utilization of grazing systems affect productive longevity of animals.**
_**Explanation:**_**  There is the assumption that animals completing their production cycles in extensive systems have increased productive longevity versus those in intensive systems of production.**

## Status:     

**Priority Rating:  N/A**
_**Issue:**_**  Limited information on combining nontraditional and conventional management systems to increase resource utilization.**
_**Explanation:**_**  Combient Modeling**
**Example:  Convential concentrated dry lot dairy with maxed nutrient credits might consider moving certain aspects of operation to pasture based systems (e.g., dry cows, cows with mastitis, heifers).**

## Status:  Needs to be investigated further

**Priority Rating:  Medium**
_**Issue:**_**  There is limited empirical data quantifying the potential synergistic benefits of integrated grazing systems utilizing multiple forage-animal species.**
_**Explanation:**_**  Empirical data exists concerning the benefits of these systems under limited situations. **
**Synergistic benefits of these systems are still not well defined, thereby limiting development of management protocols to fully capture all resource inputs.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Consistent product delivery from pasture finished meat animals suffers from a lack of predictability of input (e.g., forages) quanties & qualities.**
_**Explanation:**_**  Year round delivery of quality meat products from pasture finished meat animals requires improved understanding seasonal forage quality fluctuation & G*E interaction impacts on product quality & quantity.**

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Lack of data concerning how to switch from convential farming to organic farming while maintaining economic viability.**
_**Explanation:**_**  Farmers considering a transition to organic farming need information to guide them in making appropriate decisions during the transition to ensure sustainability of the new operation.**

## Status:  Needs to be investigated further

**Priority Rating:  High**
_**Issue:**_**  Optimum supplementation of grazing dairy animals (includes: cattle, goats, sheep)**
_**Explanation:**_**       **

## Status:  New and needs to be investigated

**Priority Rating:  High**
_**Issue:**_**  Limited empirical data concerning effects of forage-based management and environment on equine health & production.**
_**Explanation:**_**  Horses are effected by many of the same issues affecting other grazing species (e.g., fescue toxicosis, salmonella, reproductive effieciency, etc.).  However, horses have not routinely been recognized by ARS or other agencies for research funding.**

## Status:  New and needs to be investigated

**Priority Rating:  Medium**
_**Issue:**_**  Limited empirical data effects of forage-based management and environment on grazing monogastric animal (e.g., chickens, pigs) health and production.**
_**Explanation:**_**  Much of the information available for grazing ruminant animals does not exist for these animals which are filling a niche market.  Thus, development of sustainable production systems for these animals on pasture is particularly difficult.**

## Status:     

**Priority Rating:  N/A**
_**Issue:**_**  Animal Identification & Disease Survey**
_**Explanation:**_**  After discussing this topic, it was decided that it was an APHIS issue & that APHIS would contact ARS if they needed ARS to research particular components.**

## Status:     

**Priority Rating:     **
_**Issue:**_**  How do we retain for the producer the value added to niche products?**
_**Explanation:**_**  This was not fully discussed.  May not be a researchable issue - but rather a marketing issue.**