Genomics….Questions and Answers
Why is genomics so publicized today?
The term genomics has appeared in headlines in every major dairy publication over the last nine months. Scientific advancements in DNA sequencing technology have allowed USDA to create a more accurate genetic evaluation for animals much earlier in their lifespan. This scientific breakthrough may literally be the most impactful event in the A.I. industry since the introduction of frozen semen.
What is a genomic evaluation?
An animal’s genetic evaluation is composed of several components. An animal’s pedigree, the performance of that animal, the performance of the progeny of that animal, and now the DNA makeup of that animal all contribute to its genomic evaluation. Each of these components is weighted differently within the official evaluation depending on the amount of available information. To put it simply, genomics adds the actual DNA makeup of an animal to the animal’s genetic evaluation based on performance levels of other animals with similar DNA makeup. The combined genetic evaluation is referred to as a genomic evaluation.
Does genomic data apply to all breeds?
Genomic data applies to the Holstein and Jersey breed and potentially the Brown Swiss breed in the future. The reason for just the two breed genomic adjustments is simply the reliability genomics brings to the table for these two breed’s accuracy in their evaluations. It has taken nearly 4,500 highly reliable proven Holstein sires to be genotyped to build SNP relationship estimates that increase the reliability of sires of lower reliability levels. This is how you can see 25 – 30 percent reliability adjustments on young Holstein sires. Jersey has approximately 1,200 highly reliable proven sires in their genotype data base to achieve the 10 – 20 percent reliability boosts they can achieve on younger sires. To date, no other breed has near enough proven sires genotyped to make adjustments of economic significance.
Is Select Sires convinced that genomic technology will really impact my business?
YES! Sound science backs this process, utilizing similar tools that scientists involved with human and plant genome development have found beneficial. Several studies by USDA and additional investigation by Select Sires’ sire development team have shown the predictive power genomics delivers to facilitate more logical genetic decisions earlier in an animal’s lifespan. All Holstein and Jersey sire selection decisions at Select Sires include the animal’s genomic information.
Was IGENITY testing an advantage for Select Sires?
Another resounding YES! The IGENITY® dairy profile provided a learning curve for the Select Sires family about SNPs (Single Nucleotide Polymorphisms) and how the data could be incorporated into a sire selection scheme. Additionally, the results from the IGENITY profile show a positive relationship with the USDA genomic evaluations. This gives Select Sires a three year sire selection head-start within the industry. That’s right! Select Sires has been utilizing SNP technology as part of our sire selection and development process since 2006! IGENITY also continues to provide valuable parentage verification testing to assure our sire proofs are filled with accurate parentage data.
So, what exactly is a SNP?
A Single Nucleotide Polymorphism (SNP) is a single base difference that marks a difference in DNA from one animal to another. Research advancements have made SNP technology affordable for commercial use allowing the dairy industry to develop genomic tools. Chromosomes contain two strands of DNA that contain sequences of four different base pairs (Adenine, Thymine, Guanine, Cytosine). Cattle have 30 different chromosome pairs containing roughly 3 billion of these DNA base pairs. Since it is much too costly to identify the sequence of all 3 billion of these base pairs, a subset of these bases in the form of SNPs are measured. Illumina Inc., in partnership with USDA has developed a microchip to test for 50,000 of these SNPs in an effort to condense these 3 billion base pairs into an affordable genotyping tool.
Are all traits measured by USDA and breed associations affected by genomics?
USDA will adjust 29 different genetic traits within an animal’s summary through the use of genomics. This includes five yield traits (Milk, Fat, Percent Fat, Protein, Percent Protein), seven fitness traits (Productive Life, Somatic Cell Score, Daughter Pregnancy Rate, Sire Calving Ease, Daughter Calving Ease, Sire Stillbirths, Daughter Stillbirths), 16 conformation traits (PTAT and 15 linear type traits), and Net Merit Dollars. Since all these traits vary in heritability, we’ve always seen a variation in the reliability of each of these figures. Genomics will affect each trait’s reliability differently, and in actuality the biggest winners will be the fitness traits as their accuracies will see the largest increases.
Is the whole world moving to incorporate genomics into genetic evaluations?
While in various forms, again the answer is yes. Most countries that provide seed stock use a similar genotyping method to capture the SNPs for analysis. The difference lies in the computations used by each country, similar to differences that currently exist when comparing country to country proofs. These unique differences which exist today are handled as best as possible through the Interbull evaluation system. However, at this time genomic data will only be applied to an animal’s USDA proof. Interbull has no system in place to handle genomic evaluations. Therefore, PTA data without genomic adjustments will be used in other countries as a sire’s “official” data for publication. The same is true for imported semen from other countries. Imported bulls that have not been genotyped in the U.S., will only have their within country, non-genomic adjusted proof used as their official MACE summary.
Does this mean that parent averages of the past have no value?
Actually parent averages are still critical to developing a genomic evaluation. This is why Select Sires is dedicated to proper identification throughout all sire development schemes. Nearly one half of a genomic evaluation for a young animal is still the former parent average as we’ve all known from the past. This 35-40 percent reliability evaluation will now simply have the addition of the animal’s DNA makeup added to it, to achieve a genomic evaluation that grows in reliability depending on the trait being analyzed. For most production traits the genetic evaluation will receive a boost in accuracy with the addition of genomic data resulting in a reliability of 65-70 percent.
Will genomics eliminate the need for young sire testing programs?
Select Sires’ Program for Genetic Advancement™ (PGA™) is still vital in fully and properly evaluating each sire marketed under the Select Sires brand. As stated earlier, genomic data will affect which bulls are ultimately sampled through the PGA, but it will still take our industry-leading sampling program to bring you breed-leading, proven graduates at 85-90 percent reliability which you’ve become accustomed to. In a nutshell, the more data that can be added to an animal’s summary, the more accurate or reliable the summary will become! With genomic evaluations for young sires at a higher reliability, it would stand to reason that the graduation rate of young sires will improve bringing to question the continued need to sample over 300 Holstein young sires per year. In Select Sires’ case however, maintaining a larger sampling program will allow for further expansion of the Select Sires brand world-wide. Select Sires has seen extreme growth in the world-wide marketplace in the past several years and more proven sires are needed to keep pace with this ever growing demand for the brand.
So what are the methods used for genotyping?
Currently genomic testing can be done using whole blood or hair samples. A simple, clean sample is taken from the animal in question, the sample is properly identified with an official identification number and the sample is forwarded to the proper provider for genotyping and further genomic analysis.
Can anyone have their animals genotyped, how and where?
All Holstein and Jersey females are eligible for genomic testing with their respective breed association. Breeders interested in genomic testing should contact their breed association. The association will provide a kit with instructions for proper DNA collection and documentation. Following sample collection, this kit will be sent to a DNA lab for SNP50 testing. Next, USDA-AIPL will compute genomic values from these genotypes and those values become the animal’s official genetic evaluation. These values are then sent back to the owner of the animal and the respective breed association. The cost of testing is about $240-250.
The testing of males is a different story. Nearly 10 years ago, seven NAAB member organizations, including Select Sires, began a collaborative effort with USDA and the Cooperative Dairy DNA Repository (CDDR) to begin storing samples from every young bull entering their progeny testing programs for the purpose of future DNA research. This was the beginning of today’s genomic technology! A part of this collaborative effort includes an exclusivity agreement with the seven organizations that is in place until March 2013.
How do I know an animal has been genotyped?
If an animal has been genomically tested, the evaluation will have a ‘G’ preceding the PTA, TPI™ or JPI™ value. Another obvious signal to determine if an animal’s genotype has been included in his summary is to assess the reliability of that animal’s evaluation. Young stock will have reliability values near 65 percent or higher. Proven animals will also receive a boost in reliability with genomic testing. The proven Select Sires lineup will, on average, see a 5 percent reliability jump since all bulls have been genotyped.
How will genomics affect sire acquisition at Select Sires?
All young Holstein and Jersey young bulls will be genomic tested prior to on-farm pickup at a young age. These genomic evaluations will help determine the monetary value of these quality young sires and help determine their genetic potential before they enter the PGA. All sire fathers used for mating options will be genotyped to further assure that early proven sires have quality data and the true genetic potential we feel comfortable investing in. Female genomic testing will also add to the success in choosing quality bull mothers, particularly at a much earlier age than in the past. This movement toward younger parents of our young sires, will increase the genetic progress by reducing generation interval.
Will all Select Sires animals be genomic tested?
All proven lineup Holstein and Jersey sires have already been genomic tested and are labeled as such. In addition, all Holstein and Jersey young sires, regardless of how they are marketed, are labeled with a ‘G’ preceding their evaluation if they have undergone genomic testing. This assures users of the Select Sires brand that they are purchasing the most up to date genetic estimates available when they buy of a straw of code 7 or 507 semen.
With higher reliabilities on genomic-tested young sires wouldn’t it be prudent to use more of them and abandon lower-end proven bulls?
First off, we need to reemphasize the fact that until a bull is fully proven through the PGA, variation, even of a bull’s genomic prediction can and will occur. While DNA technology as it stands today provides greater accuracy, there is still much to be learned. Therefore, be assured the graduates of the PGA program are still the industry standard to which all genetic progress is measured. Young sires should always be used as groups of young bulls. Select Sires remains steadfast in their belief of 70 percent proven sire usage and 30 percent young sire usage in herd breeding programs. However, the very elite genomic unproven outliers may have merit for some additional use while again picking more than one young bull to use at a time is prudent. These elite genomic-tested young sires have tremendous genetic potential that should outperform the bottom-end proven bulls you may be using today. However, we still would recommend no more than 10 percent of these elite genomic young sires act as replacements to the proven products the PGA consistently delivers at a much higher accuracy.
TMProgram for Genetic Advancement, and PGA are trademarks of Select Sires Inc. ®IGENITY is a registered trademark of Merial.
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