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We validated gene expression by qRT-PCR in pools of clones and many individual genotypes.
But with conventional approaches, this inference is limited by how many individual genotypes can be sampled from the population at a time.
One way around these limitations is to examine and analyze gene expression from many individual genotypes that each contains multiple mutations and to study the covariance in phenotypes and multiple gene expression levels to hypothesize which of the gene expression changes might cause phenotypic deviations [ 38- 41].
Although firm conclusions on single genotypes are difficult because of the rarity of many individual genotypes, it is interesting to note that the crude IR of the key LR-HPV-types (HPV6,11), is almost twice as high as that of the two main HR-types (HPV16,18).
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In order to reduce the mapped region, a fine-mapping is performed in which many individuals are genotyped for markers around the QTL.
This enables us to screen many individuals with different genotypes efficiently and conduct association studies between genotype and schooling behaviour.
In cattle, many individuals with BovineHD genotypes are available.
These approaches are most powerful in model organisms, where it is possible to control the environment and genetic background, and to measure traits across many individuals with identical genotypes (Mackay et al. 2009).
Instead, the phenomenon is a simple consequence of how many novel phenotypes occur in the neighborhoods of individual genotypes.
DNA barcoding methods make high-density genotyping cost-effective by multiplexing many individual genomes into a single sequencing library (Baird et al. 2008; Andolfatto et al. 2011).
Finally, the environment can be systematically varied between many individuals of the same genotype, allowing dissection of interactions between genotype and environment, something that is not achievable in standard outbred populations.
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