In 2009, several countries began to incorporate DNA information of the cows and bulls in the official genetic evaluations of dairy cows of the Holstein breed. In Spain, it is planned to have our own prediction equations in 2011.
Alberdi Juan Pena
CONAFE Technical Department
Images Albéitar
selection is to use genomic information available from the DNA of cows or bulls as additional data to predict genetic values \u200b\u200band genetic values \u200b\u200bbased on those "improved" to make selection decisions. The big advantage is that the DNA information can be at the birth of the animal, from a blood sample.
Sequencing and SNP
DNA is composed of two parallel chains of chemical bases called nucleotides. These can be of four types: adenine (A), guanine (G), cytosine (C) and thymine (T). When in 2000 the human genome was sequenced, which had been achieved was to know the exact order in which they appeared the four nucleotides in the chromosomes of a few individuals (Figure 1).
Transcendence have sequenced the genome of several individuals is due to most of the genome is the same in all people. The variations are due to changes that have been occurring in the DNA over time, but they represent a small fraction of the total bases of the genome. A SNP (single nucleotide polymorphism) is a variation in DNA sequence affecting a single base (Figure 2). They are called "snips" and are the most frequent type of variation in DNA, make up 90% of all human genomic variation. Any DNA base could be replaced by any other, but, in practice, most SNPs have only two variants or alleles.
Then the human genome in 2004 sequenced the bovine genome. From this information, in late 2007 began marketing a chip that allows to know at an affordable price (around 200 euros) the exact information presents each bull or cow in 54,000 SNPs ("50K"). This was the starting gun for the race of genomic selection.
When we speak of the genotype of a bull in this context of genomic selection, we refer to the information presented bull in the 54,000 SNP chip integrated into the business, but in fact the term encompasses the total genotype of animal DNA.
What have effect on the characters SNP we observe?
SNPs need not be part of the genes. But, if they are well distributed throughout the genome, many of them will be coming to areas of DNA responsible for traits of interest, ie, are associated with genes. The aim will be to identify these associations between the SNPs and the different characteristics of interest to study in individuals. Therefore it is said that the SNP are "genetic markers." Figure 3 shows an example of the effect of a SNP in the genetic merit of kilograms of milk. We can consider the "Effect" of this SNP is due to be transmitted together with a certain gene that affects production of kilograms of milk.
If you send a sample of blood or hair to the lab , one can know what information
have that animal in each of the 54,000 SNPs.
genomic Reviews
genomic assessments are to establish a "formula" or "predictive equations by which, from the information you have an individual animal in each of the thousands of SNPs considered, predicted genetic merit in each of the characters. The evidence thus obtained are called genomic value "direct", they are not based only in the genotypes of the bulls. Direct genomic These values \u200b\u200bare subsequently incorporated into traditional genetic evaluations increasing reliability (Figure 4).
order to calculate the direct genomic values \u200b\u200bin a country is necessary to have the genotypes bulls that are tested in this country and associate evidence to the genotypes, for the "formulas" that predict the genetic merit from the genotypes. This group of bulls that are calculated "formulas" for predicting direct genomic value is called "reference population." A key aspect is that the larger the number of bulls genotyped for the study of association between tests and SNP, the more confidence will genomic evaluations.
These formulas must be found for each population because associations between SNPs and genes are not necessarily the same in different populations. We also have to periodically re-estimate them.
Several countries have already started in 2009 to incorporate information from DNA in the official genetic evaluations for dairy Holstein. In Spain is scheduled to have our own prediction equations in 2011.
Reliability of genomic values \u200b\u200b
Currently, the genetic value of any newborn animal is calculated as the average of tests on their parents and their reliability is around 30%. But if you send a sample of blood or hair to the lab, you will know what information we have that animal in each of the 54,000 SNPs. And applying formulas available, it will calculate a value genomic "direct." This information is available at the birth of the animal. By combining pedigree index and direct genomic value, reliability increases by an average of 30 points over the pedigree of the index, so you go from a 30% reliability at 60% reliability. If we are in the case of a newborn bull (Fig. 4), this reliability will preselect better what young bulls put growth test. But also five years old, when her first batch of daughters, the bull reached in half a 83% confidence, rising to 88% by the direct genomic data value.
In the case of a cow, if not available genotype in their second lactation, would reach a reliability of 51%, less than 60% is reached at birth when the animal was genotyped. This makes it radically changes the information available to select mothers of sires.
cited values \u200b\u200bfor the reliabilities refer to the Canadian total merit index (LPI) according to the Canadian Dairy Network (2009) and give us an idea of \u200b\u200bthe impact of genomic reliabilities evaluations of bulls and cows.
Increased reliability which provides genomic selection becomes particularly valuable characters such as longevity or fertility, known later in life of the daughters of the bulls. Just for this reason the tests take too long to have high reliabilities. In addition, these characters have low heritability, and because of that, they need to add much greater number of daughters that the characters of production to achieve the same reliability. That's why a 30-point increase in the reliability of these characters is equivalent to a larger number of daughters.
How will it affect growth test programs and farmers?
For growth test programs, increasing the reliability of birth is very interesting in the preselection of young bulls and stallions mothers because it will increase the average genetic merit bulls finally be tested . But progeny testing and data collection should be maintained to obtain high reliabilities tests and to re-estimate the prediction equations from time to time. At the same time, it will be even more important collection new data, the incidence of disease, as it would be possible to establish genomic evaluations on some of the population and that could then be applied to any animal genotyping.
One potential radical change is the selection of mothers of sires, since the birth of a calf and may have a genetic index that is more reliable than that obtained now in the second lactation. In addition, currently the reliability of many functional traits in cattle is particularly low and because genomic information will increase greatly in the genotyped animals. All this will improve the selection of mothers of sires and also expand the range of families to consider.
As farmers, they will suffer a great commercial pressure for use of so-called "genomic bulls." These bulls have daughters and no test is based on pedigree index and DNA information.
Some of them may have very high tests but they all have quite low reliabilities (60% average of all characters). The risk of these bulls is to use or pay as bulls tested for high reliability. Although using groups of bulls can reduce the risk of low reliability of the evidence does not prevent some of the bulls in group eventually showing a test based on daughters significantly lower than the genomic test to predict. Moreover, in many countries, including Spain, is required at least 80% reliability to appear on lists of top bulls. Moreover, Interbull still considering validation of genomic national assessments and how to convert genomic tests between countries.
However, an advantage, especially interesting for the functionalities of low reliability, is that proven bulls may achieve higher reliability with its first batch of daughters. This is because the information provided by these is added the information provided in the bull's DNA. And the increase in the reliabilities of the functionalities will increase its relative weight in the selection indices, such as ICO.
Conclusions
genomic selection is already being implemented in Holstein cattle in several countries but it is necessary to maintain the data collection and testing of progeny testing to continue providing high reliability and also to re-estimate the prediction equations from time to time and with increasing number of bulls . For now, the reliabilities of genomic testing bulls are still low to compete with the bulls with daughters in the face of widespread use by farmers, but the information of the SNP also contributes to greater reliability of the first test progeny of the bulls. This will apply greater focus on characters that so far were of low reliability, and longevity and fertility.
This technology is very recent and current developments all be improved. The next marketing a half-chip density and lower cost can generalize the use of genomic selection by farmers. In the coming years will continue to receive new commercial applications for SNP analysis and develop new statistical methods for analysis and new applications. Keep in perspective that we are only at the beginning of a new way of working in the area of \u200b\u200bselection.
| New chips |
| mid-2010 is already announced the commercialization of a new chip "high density" with more than 750,000 SNPs, including all the SNP chip "high density "50K. Since the cost of genotyping an animal for the 50K chip or for more than 750,000 SNPs is too high for widespread use in the population, Illumina and USDA also have just developed a chip "medium density" with 3,072 SNPs ( "3K") under the criterion of being able to predict from it the 50K SNP chip. SNP 100 also includes checks to make kinship in all breeds of cattle. If the price is attractive enough could be used more widely by farmers in dairy cattle. Some applications may be the screening of mothers of sires, making selection decisions on replacement heifers, verification or identification of kinship or used in genomic linkage programs. But from these 3072 SNPs were able to estimate the 50,000 SNP chip quite precisely standard, which will make it even more interesting as it could allow a reliable estimate genomic tests that are closer to the 50K chip. |
Bibliografía
Eggen, A. Different chips for different population segments. Interbull Workshop on the Use of Genomic Information in Genetic evaluations. Paris, March 4-5, 2010.
National Cancer Institute. US National Institute of Health. Understanding Cancer Series: Genetic Variation (SNPs). http://www.cancer.gov/cancertopics/understandingcancer/geneticvariation.
VanRaden, P.M., Wiggans, G.R., Van Tassell, C.P., Sonstegard, T.S., and Schenkel, F. Benefits from cooperation in genomics. Interbull Bull. 39:67–72. 2009.
Weigel, KA, Campos, G., Vazquez, AI, Van Tassell, CP, Rosa, GJM, Gianola, D., O'Connell, JR, VanRaden, PM, and Wiggans, GR and Its Genomic selection effects on dairy cattle breeding programs. Proc. 9th World Congr. Genet. Appl. Livest. Prod, Leipzig, Germany, Aug. 1-6. (Submitted Feb. 2010 )
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