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Undefined or hard to define traits: One issue with MAS is trying to associate markers with traits that do not have a clearly defined value. Usually, a trait has a substitution value that scientists refer to, but for certain instances such as fertility, these values are not defined well enough to link markers to. In addition, other traits along with their correlation to other traits shift and change over time, creating more problems with those traits. However, as more QTL maps are being recorded, and new technologies are introduced, these traits will soon be able 

 

to be assigned to a value, thus letting MAS take place. Scientists who employ MAS have problems with this because they have to use genes from the organism’s gene pool, and not from other, foreign organisms.

(Citation 18, 20)

Costs: As with all new technology, public or private funding is hard to gather. Sequencing genomes, a crucial part of Marker Assisted Selection, cost millions of dollars when it first started. However, as time went by, the cost of sequencing drastically dropped – to the point where a genome can be sequenced for only a few thousand dollars. This makes the prospect of MAS a reality – one that will soon drastically change the agricultural sector.
(Citation 19)

ISSUES

Issues: As with all new technologies or scientific breakthroughs, there are specific issues and problems the public or scientific community can have with the material. For Marker Assisted Selection, however, public perception is positive and there are remarkably few difficulties with this technology. 
Ethical Issues: One strong point of Marker Assisted Selection is that the general public has consented of its use. Why? Because unlike the popular argument for GM crops, MAS only uses the genes within the gene pool for an organism, instead of using genes from other organisms. This is just the 21st century way of selective breeding through new technologies unavailable in the past. In addition, the process of MAS can be much quicker than the process of creating GM crops, while also reducing the risks associated with gene splicing, therefore strengthening public opinion. “Bill Freese, a science policy analyst with the Center for Food Safety, a nonprofit advocacy group, calls it ‘a perfectly acceptable tool. I don’t see any food safety issue. It can be a very useful technique if it’s used by breeders who are working in the public interest,’” (Conniff). (Citation 19, 21)
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