Cheap, Easy, and Fast Genotyping!

Many recent developments in the agricultural industry can be traced back to genetic development. From the improvement of corn hybrids to Holstein pedigrees, genetics are import to most cutting edge farmers. These advancements have been made using many different technologies from simple selection and breeding systems to genetic modification of a few key genes in corn and soybeans.  A recent technological advance has made a huge impact on the field of genetic analysis of crops and livestock, it has taken an expensive complicated and timely analysis of a genome and made it simple, fast and inexpensive. This advancement is the genetic SNP Chip or snip chip, although the more accurate name is a micro array. This is simply a glass or silicone chip with 100’s of thousands of small dots of DNA distributed over its surface. These dots are made up of short sections of DNA selected from key regions of the genome or spaced equally throughout the genome.  When the gene chip is used to analyse a sample the sample is treated with enzymes that cut the genome into short pieces, and some sort of traced that makes it glow. This mixture of millions of tiny pieces of DNA is flushed over the chip and any pieces that match those on the chip bond with them and stick in place. the rest are washed off leaving those that have bonded behind. Then the chip is scanned to record which dots are glowing. This shows which pieces of DNA that are present on the chip are present in the sample.

This technology has been produced in two forms in the livestock industry. Their is a Bovine chip that has 54,000 different unique sections of the bovine genome,  selected from studies on the most important and variable sections of the bovine genome.  This chip is capable of distinguishing the differences between any breed of cow as well as any other ruminant including giraffes, and has even been used on bones of an ancient extinct bison found in china. Thats why they have developed a second chip that only looks at 384 places on the genome and only looks at those of greatest importance to the cattle industry. The most amazing part of these chips is their cost, averaging around $250 for the 54,000 bit chip and only $40-50 for the 384 bit chip.  This has made the technology accessible to a large number of researchers, private companies, breed associations and even individual farmers.

Bovine SNP Chip

This ability to gather genetic data on large numbers of cattle for relatively cheap has the possibility of completely changing the breeding selection process for many farmers. This allows farmers to take into account the entire genetic background of a sire rather then a few key traits analyzed by pedigree or offspring. This also means that decisions are made according to the characteristics of the sire itself not an assumption of the genes it may or may not have received from its ancestors.  This is the most obvious use of the technology, for the selection of genetics within elite herds of beef and dairy cattle. I think that there is the possibility of even more interesting and useful uses of this technology in other farm sectors. The use of this technology in rare breeds could allow for animals to be screened for in breeding to avoid genetic defects in limited gene pools, as well as to simply improve these limited gene pools to produce more productive animals that may be useful for incorporation into commercial production. This would also be useful in other niche industries such as raising beefalo, a cross of buffalo and beef breeds.   This could help in that any similar genetic traits between the two species could be selected through this system, as well as any negative traits that may not be avoidable vis traditional means due to the limited background knowledge available on the buffalo. It is these niche industries that I believe could benefit most from the adoption of this new technology.



3 Responses to Cheap, Easy, and Fast Genotyping!

  1. Owen says:

    I agree that genetics have moved us ahead light years in livestock development.

    However, I’ve heard people raise concerns about SNP technology narrowing the gene pool too much.

    What do you think? Will the breed associations police narrowing gene pools, or is concern even required?

    • I agree that concern is required and that the narrowing of gene pools is an issue that must be recognized. I also see the technology as being capable of vastly expanding our gene pools by bringing formally minor breeds into greater use within mainstream agriculture and for the selection of unique traits and breeds to be used in commercial hybrid breeding programs thus incorporating new genetics into commercial gene pools.

      I believe that their are enough farmers with enough foresight that will work to expand the gene pool and develop new uses and opportunities for this technology that in the long run the narrowing of the gene pool will not be a critical issue.

      Thanks for the question!

      • Owen says:

        I think the expansion of the gene pool is an excellent point for the industry to bring forward, to quell some of the concerns I’ve heard. Thanks for your response.

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