news from illumina. error rates are probably going to be an issue at the lower read densities.
http://www.sandiegouniontribune.com/news/2016/jan/11/illumina-2016-jp-morgan/
https://www.illumina.com/company/news-center/press-releases/press-release-details.html?newsid=2128277
sequencing is soon going to be soon cheap enough that larger end users will be able to afford an instrument. in general, sequencing is getting cheaper and will continue to go down as it finds price equilibrium for utility for wider useful adoption.
the $ will probably be in supplying reagent kits and qualtiy data rather than sending in samples.
there will be a higher expectation of useful data rathter than just mating high percentile animals.
the user will be able to essentially be closer to collecting phenotypic data, sequence individuals and cull or sort quickly rather everyone wasting time sending in samples.
the expectations of useful data will increase.
breed organizations will probably be able to generate breed specific utility quicker due to more power in the hands of individuals indentifying useful animals, developing markers, panels, whatever, and identify crossing them by whatever means possible.