Genomic Selection as a Risk Management Tool for U.S. Dairies

Introduction

Genomic selection is based on finding associations of a DNA variant (SNP, see Figure 1) and a trait such as milk production. Once the association is made, animals are genotyped (their DNA identified at the region associated with a trait) to predict the performance of that animal and its offspring. For example, one animal may have the “A” nucleotide at a DNA position, and another animal may have a “C”. Through previous research, the “A” has been identified to be associated with an increase of 100 pounds of milk production and the “C” is associated with no additional milk production (above the average). Heifers that are genotyped and have received an “A” from both their dam and sire will produce 200 pounds more milk (two A’s × 100 lbs = 200 lbs), while those that only receive one “A” from one of their parents will produce 100 pounds more milk and those that receive no “A’s” will produce no more milk than average (Figure 2). These differences in performance from the average are called predicted transmitting abilities or PTA. Genomic selection is the use of PTA based on genotypes to estimate the performance of the heifers. Her offspring’s performance is estimated in the same way. In this proposal, several thousand SNP will be used to predict the performance of the heifers based on previous research that has linked the genotypes to heifer performance. The genotypes of each heifer will also be compared to the predicted performance of all Holstein heifers in the U.S. to assist the dairy producers, workshop participants and students to make decisions on which heifers to keep or cull. 

Genomic selection is much more accurate than basing the prediction of a heifer’s performance on the performance of her dam or her sire^14-16,19. The increased accuracy of the heifer’s future milk production allows the dairy to identify heifers that are likely to produce more milk and therefore be more profitable over their lifetime. As the heifers will also produce the next generation of milking animals through their calves, this increase (or decrease) in milk production carries forward generation after generation. This proposal will measure the actual difference in milk and revenue produced from heifers selected using DNA genotypes (genomic selection) compared to heifers chosen using parent information and visual inspection (traditional selection). This real-life comparison will be used to educate present and future dairy producers, and veterinarians.

Material and Methods

For the educational workshops and financial analyses, we have collected pictures (front, side and rear views) of each of the 1200 heifers, a tissue sample, genotypes and reproductive and health records. As heifers finished their first lactation, milk yield and milk components were collected and summarized for each animal. The following provides an overview of that collection process.

Animal Data Collection. Each dairy producer collaborator provided access to approximately 200 heifers between 6 and 10 months of age (Figure 3). The age of heifers when replacement decisions are made vary by dairy, but the decision to keep or cull heifers was made prior to breeding at approximately one year of age. Pictures were taken of all heifers for use in workshops and in the undergraduate agricultural courses and were used for selection of heifers using traditional selection methods. Groups of heifers (10, 20 or 50) were given to participants/students and they ranked the heifers based on visual, pedigree information and individual information and compared how these rankings changed depending on how the animals were assessed. Participants/students were also given four bulls to evaluate and determine by using genomic information, which were to be used to mate to the heifers they chose to keep as replacements. Beef bulls were also provided as an option for offspring that will not be kept in the breeding herd. 

Following the pictures, an ear tissue sample was taken from each heifer (see Animal Assurance; WSU IACUC #6370). DNA was extracted from the tissue sample and genotyping was conducted using the Neogen Igenity Prime assay that contains over 50,000 DNA variants (SNP). The genotypes were used to predict the performance of each heifer as described in Figure 2. A graduate Animal Sciences student was involved with the sample collection needed for genotyping and data analysis.

Analysis of genotypes. The genotypes of the heifers was determined at the Neogen laboratory for three reasons: 1) Neogen donated the cost of DNA extraction required for the genotyping (a $4800 savings); 2) Neogen genotyped the animals at lower cost than we could have genotyped the animals; and 3) Neogen has a contractual relationship with the Council on Dairy Cattle Breeding that allows them to compare and rank each heifer against all other Holstein heifers that have been genotyped in the US. Without this contractual agreement between Neogen and the Council on Dairy Cattle Breeding, we would not have the ability to compare and rank the demonstration herd heifers to all US Holstein heifers.

The genomic prediction information (PTA) was provided to us and to the dairy producers by Neogen for use in this project to choose replacement heifers using genomic selection. All heifers at each dairy were ranked by using pedigree information and genomic information. This allowed the comparison of the profitability of different percentiles (top 25% versus bottom 25%) using different sources of information. Replacement decisions to keep or cull heifers were made by the dairy producers prior to the heifers being bred. Replacement heifers were followed through one lactation. 

Financial Analysis

Objective 1: Identified the profitability difference between replacement heifers chosen with genomic selection compared to those chosen with traditional selection on a per heifer basis.

Profitability analysis included expenses (the cost of health events such as treatment costs, costs associated with the number of inseminations required to achieve pregnancy, and feed costs) and revenues (revenue from first lactation milk sales)(see Equation 1). Individual heifer production data was collected through each participating farm’s records database, which maintained all dairy production records. Feed costs, milk price and milk component premiums were determined through public reports and held constant across dairies to isolate and evaluate the net profitability attributed to selection. The total profit made for heifers ranked in the top 25% and bottom 25% based on Genomic Selection and Traditional Selection groups were compared.

Objective 2: Identify return on investment for the cost of genomic selection on a per heifer, per dairy and across dairies basis.

To calculate the return on investment, we first determined the difference in profitability from what the genomic predicted revenue was for milk  and what the actual milk income was, after correction for the heifer being in her first lactation. The return on investment was calculated to determine the value of using genomic selection for each dairy and across all dairies. The calculate the return on investment, we compared the difference in the actual and genomic predicted profits and divided it by the cost of genotyping to determine how much was returned in revenue for each dollar spent on genomic testing. A related analysis evaluated the difference in the profitability of the top and bottom 25% of heifers based on their genomic selection and on traditional selection predictions. 

Objective 3: Determine the reduction in financial risk (variability in profits) on a per dairy and across dairies basis that results from an increased accuracy of prediction of replacement heifer performance through genomic selection. Objectives 1 and 2 kept milk price constant to isolate the effects of genomic and traditional selection. The primary factor affecting dairy financial risk is variation in milk price. Equation 2 evaluates the effect of selection profit when milk prices vary. The range of milk prices producers have received over the past five years ranges from $13.00 to $21. Profits for each selection group will be calculated iteratively for the range of milk prices received over the past five years.

Objective 4: Develop a model to project the one and ten-year difference in dairy farm profitability and nutrient (manure) load contributed to the environment between traditional versus genomic selection to determine the added sustainability of using genomic selection.

Predicted dairy farm profitability. A model will be developed to predict the ten-year difference in dairy farm profitability and nutrient (manure) load contributed to the environment between traditional versus genomic selection to determine the added sustainability of using genomic selection. This model will be based on data collected on the first lactation. The hypothesis is that production efficiency gains from Genomic Selection heifers will result in less animals needed to meet a constant level of production, therefore, resulting in significantly less manure, thus improving economic sustainability while increasing profitability. This hypothesis is based on studies conducted and USDA statistics over the past 10 years that has shown that genomic selection has improved milk production with fewer cows⁸. 

The model will simulate milk production gain for each selection method and the projected milk production gains of the offspring over the ten-year period. Total milk production for each dairy will be held constant and herd inventory number will be adjusted to maintain this level of production. The net present value for genomic and traditional selection profits will be calculated to account for the time value of money. Total manure and nutrients produced over the 10-year period will be estimated using USDA NRCS manure characteristics^21,22. For example, the average US Holstein cow produces 28,050 pounds of milk per lactation so 100 cows would produce 2.8 million pounds of milk in one lactation²³. This analysis will identify how many heifers will be required to meet the average milk yield for 100 US Holstein cows in the Genomic Selection and Traditional Selection groups and how that number would impact the environment through the amount of nutrients (manure) in pounds that would be produced^17,21,22,24.