Application of Parentage Testing by DNA on Western Ranges with Large Beef Herds

Final Report for SW02-030

Project Type: Research and Education
Funds awarded in 2002: $23,013.50
Projected End Date: 12/31/2003
Matching Federal Funds: $12,000.00
Region: Western
State: Nevada
Principal Investigator:
Ben Bruce
Department of Animal Biotechnology
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Project Information

Abstract:

Extensive ranching operations in the West are unable to identify the sires and the dams of calves, precluding selection or culling of animals based on performance or undesirable traits. DNA technology for parent testing in cattle is viable, but has not been applied to large herds. This research developed satisfactory field sampling techniques for DNA testing in large herds. Time problems emerged with lab procedures in processing large sample numbers, taking too long for the information to be used in culling animals effectively. The techniques show promise, but more rapid methods for large sample number need to be developed.

Project Objectives:

Develop sampling techniques, data storage, and data application techniques for determining the parentage of calves, particularly in large herds.
Develop methods for selection on the basis of parentage and performance parameters within the cow herd.
Develop curricular materials for producers such that these techniques may be successfully applied.

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Introduction:

Ranchers with large beef cow herds grazing vast Western rangelands find it difficult if not impossible to keep individual cow records identifying sires and dams of calves. This lack of information costs the producer greatly in production efficiency and in revenues. Beef producers that are able to positively identify sires and dams of calves can discover which bulls are siring the most profitable calves and the number of calves each bull is siring. Producers could determine if certain bulls are siring calves with dystocia problems at birth (for animals kept under close supervision, such as first calf heifers), which bulls are siring replacement quality heifer calves if some sires produce calves with more health problems. Producers could also determine how many of these effects are dam related. Any markers that are currently identified for positive traits or negative traits could also be incorporated. With this information, bull and cow cull decisions may be more effectively managed. This would increase the fecundity of the herd, increase income, and put less pressure on natural resources as profit margins could be maintained with fewer cows and bulls. By placing calves in a retained ownership program or by other arrangement, carcass data could be retrieved and quality of meat monitored. This also has application in traceability for food safety programs and future genetic adjustments to improve the end product.
The technology to use DNA typing for discovering parentage is now mainstream. The technology has yet to see adaptation to the ranching industry on a large scale. While cost has been a limiting factor, these tests are becoming more affordable. The lack of application is due to non-existent techniques in the application of this testing. This proposed research would develop techniques to use this technology, test the technology on two large range livestock operations, and establish protocol for teaching its application to ranchers.
The validity of DNA for fingerprinting or parentage typing with beef cattle has been studied. Betsch and Weber (1994) outlined some general uses for DNA in all agriculture and Burns (2001) the basic theory of its use. It has been found by a number of researchers to be a valid and highly accurate method of parent testing in beef cattle (Vankan and burns, 1997; Stockburger et al, 1999). Paternity testing without knowledge of dams genotypes has resulted in an unacceptably high exclusion rate (Dodds, et al, 1996), but the use of more loci, such as use of 23 loci, allow for near 100% proper sire identification even if there is no data on the dams (Inoue- Murayama, et al, 1997). Williams (et al, 1997) has shown that DNA is very accurate in identifying individual animals, and is a technique that can be used when animals’ identification is in dispute.
Some scientists have tried varying levels of analysis with DNA, with multiple sire herds and subsets of the animals in the herd. The use of extreme offspring only (the top 10% and the bottom 10%) give performance accuracies equal to that of a random sampling of 65% of the offspring (Goddard and Goddard, 1997). Work has been done with accuracies of multiple sire matings, with accuracy varying from 75% to 100% (11 markers used). When sire, calf, and dam are tested the accuracy is 99% compared to 88-99% (Vankan and Burns, 1997). However the use of up to 23 markers dramatically increases the accuracy, but also increases the costs.
There are a variety of tissues suggested to be sampled ranging from hair (Healy et al 1995) to blood to fleshy tissue samples. Some simple sample collections have been developed for sheep (Demeny et al 1997) and cost analysis done (Barnett et al 1997). It was found that for sheep pedigrees costs would have to be $10- $15 to be widely adopted. This kind of information, for cattle on a large scale, is unavailable.
The most popular current use of DNA in livestock is for parent testing (Davis and Denise, 1998). However, there is little information on field application of parent testing, and the benefits in bull and cow selection when related to calf performance, on beef cattle, particularly in large herds. Some work has been done on the depth (number of animals necessary to sample), but the most information for the least amount of money has not been tested. There is a clear need for procedures to be developed with large extensively managed herds, including sampling, sample storage, and how to use the information garnered
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Research

Materials and methods:

Two ranches were used in the study. One ranch is a producer ranch, and the other is the University of Nevada Reno Gund Research and Demonstration Ranch. The private ranch involved 200 cows and six bulls and an artificial insemination program. The University ranch will contribute 300 head of cows and fifteen bulls.
In the fall of 2001, as cows were pregnancy checked and calves weaned, samples for DNA were collected from all cows, bulls, calves, and any replacement animals. Any available records on cows, bulls, and calves were collected. Animals that were not identified with ear tags were tagged and tag numbers recorded to match DNA sample numbers.
During the subsequent year, records on cows, bulls, and retained replacement heifers were kept. They included health records (disease, dystocia, etc) and reproductive records. As calves were weaned, weaning weights were recorded Sampling systems were developed that are easy for the ranchers with large numbers of animals to use. The systems developed are systems of biological collection and systems of record keeping and sampling tubes, etc. Various forms of prefabricated collection vessels and pre-labeling systems were investigated to make sample collection as easy as possible.
A small part of flesh is needed for DNA analysis. Currently an ear-notching tool is used to extract a small particle of flesh from the ear. Hole punchers normally used to prepare for tag insertion were tested for potential in collection of samples.
The major effort of the research was on the informatics portion, i.e., cataloging, organizing, analyzing, and using the data retrieved as well as DNA analysis. Systems were investigated as to method of dispersion, storage, retrieval, and use of the data.
The goal of the project is to be able to present to producers a system of biological sampling, an appropriate sample handling system (sorting, storing of collection vessels, etc.), an appropriate record keeping and distribution system, and management and economical advantage of DNA typing at various levels within the herd.

Research results and discussion:

Use of the ear tag hole-puncher or an ear notcher proved satisfactory in the field for collecting appropriate samples for DNA analysis. No tool had a particular advantage, and seemed best left to the individual. Samples could be very rapidly taken, within a few seconds. The biggest challenge was the organization and labeling of sampling tubes. With two people working, one taking and placing the sample in the collection vessel, and the other labeling with the proper number, taking of samples posed no problems. Using this method several hundred samples could be collected in a half day.
There is a need for an adequate chute capable of head catching. While it is possible to sample in a crowed alleyway, it is much more difficult. Another advantage with the chute is the ability to permanently place collection vessels and have a table, etc., for organization and storage of filled vessels.
The difficulty in this project came with the speed of the DNA analysis. Collection of samples came in the fall at weaning. The goal was to sample all cows, calves, and bulls, and then to do parent matching. This information would have shown which bull sired the most calves, (or none at all), the heavier calves, and those of which sex. The cow information would have been used to cull cows with light weight or poor doing calves (assuming most dry cows were already found and culled). This was done for over 1400 total animals.
Complete DNA analysis is not yet available. To be useful the information was needed to timely cull cows and select bulls for the next season. The problem is in two parts. One is lab analysis, and the other in mathematics. Since many of these cows were related, the number of markers to be identified had to be increased from the standard eight or so. The possible permutations mathematically to examine and to identify parentage are enormous. In this case, there were approximately 600 calves, from a potential of 650 cows with 40 bulls. The number of possible combinations was 600 x 650 x40, which equals 15.6 million. And that number then has to be multiplied by the number of markers chosen for each DNA analysis. This is a markedly different problem than identifying parentage when one parent is known and other choices are from a few animals.
Some things can be done in the field to help this problem. Most ranches, even those with large numbers, have their cattle divided into smaller herds. Keeping those groups intact and sampling by small herds instead lumping them all into one large group as was done in this study can dramatically reduced the number of mathematical permutations. As familiarity with the ranch and the herd grows, reducing the number of markers needed may be possible with knowledge of which ones play a more major role in being able to identify parentage.

Research conclusions:

While the results show promise and given that sampling difficulties may be overcome with large groups of animals, the speed of retrieving results needs to be resolved.

Participation Summary

Educational & Outreach Activities

Participation Summary:

Education/outreach description:

When the final DNA analysis data become available, the results will be published in producer bulletins and given at producer meetings (late 2004 or 2005).

Project Outcomes

Project outcomes:

Because the results show that practical application at this point in time is difficult, there is no economic analysis to be done.

Farmer Adoption

Enthusiasm for this project and the techniques explored remain high, adoption by producers will be for only isolated cases in which speed is not an issue. When the technology matures to satisfy timely needs for selection, adoption will probably be fairly high.

Recommendations:

Areas needing additional study

Speed of getting the DNA analysis completed and animals properly sorted need to be resolved.

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.