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Introducing Genomics

Genomics: A Revolutionary Tool

Genomics. It all started in 2004 when researchers sequenced the cattle genome. They used a Hereford for the project and discovered the bovine is made up of 30 chromosomes and three billion bases or nucleotides...those little letters.

To visualize this, picture a cell. Among other things, a cell contains those 30 chromosomes. The chromosomes consist of deoxyribonucleic acid, which is just a big fancy word for DNA. Looking closely at DNA, you can see it is made up of nucleotides - the As, Ts, Cs and Gs. The sequences of these little letters are what contain the instructions for making proteins. Proteins are the building blocks of life, ultimately determining the phenotype of animals.

In 2007 a company named Illumina Inc. developed a bovine SNP (pronounced snip) BeadChip. This SNP chip allows us to look across all the chromosomes and evaluate the animal for 58,000 markers or those letters called nucleotides. Through extensive research carried out by the USDA (United States Department of Agriculture), we have found that only 38,000 of these markers are actually useful.

By analyzing these useful markers on a sire, the USDA can determine the sire's genetic ability in certain traits. By genomically proving animals, we can gain substantial reliability in an animal's proof for all traits. Table 1 shows those gains in reliability by three breeds that, to date, have been involved in the project. A quick side note, the American Guernsey Association has initiated some work in genomics.


Table 1. Reliability Gain Across Breeds Due to Genomics
Trait Holstein Jersey Brown Swiss
Lifetime Net Merit 28% 14% 3%
Milk 30% 6% -
Fat 30% 10% 5%
Productive Life 28% 8% 2%
PTA Type 25% 4% -


Trait Traditional Parent Average  Genomic Realised  Genomic Gain 
Table 2. Holstein Reliability Values: Comparing Traditional to Genomic
Lifetime Net Merit  37%  65%  28%
Milk  39%  69%  30%
Fat  39%  69%  30%
Productive Life  32%  60%  28%
Daughter Fertility  31%  58%  27%
PTA Type  40%  65%  25%

 If we look at Table 1, the reliability gains for Holsteins are impressive to say the least. Table 2 shows the gains over parent averages (PA) for Holstein. Whether you look at the Lifetime Net Merit (LNM) index, yield traits or type traits all the gains are close to 30 percent. This means for a newborn calf, we can accurately predict close to 70 percent reliability (equal to the reliability of a sire with about 50 milking daughters) how superior or inferior that animal will be.

Now when you evaluate the Jersey and Brown Swiss columns in Table 1, you see their gains are not as impressive. These gains are greatly dependent on the size of the population. However in a short time, maybe as soon as August, Jerseys will have gains substantial enough to implement strategic changes to their genetic programs. While global efforts are underway, it will take more time to see significant reliability increases in Brown Swiss.

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