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Taken together, our results suggest the necessity and importance of biochemical approaches to verify the functional alterations in genetic variants, although in silico predictions may still be useful for screening putatively damaging genetic variations for functional studies.
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Whenever genetic variation for functional traits is determined solely by a mutational input of beneficial alleles (as opposed to standing levels of genetic variation), as it is the case for the majority of the investigated host traits in A. millepora, the rate of environmental change to which a population might be able to adapt to might be as low as one percent per generation [52], [53].
Integrating different sources of genetic variation for functional studies is a reasonable approach to better understand the genetic basis for complex traits [ 53].
Proteins are not rigid macromolecules and they exhibit certain degree of flexibility to allow structural variations critical for functional mechanisms [19].
MSH6 variations chosen for functional assessment were mainly picked from the LOVD database.
The map u is stationary for Φ if it is a critical point of (Phi (u)) with respect to any compact supported variation of u, and u is stable if the second variation for the functional (Phi (u)) is nonnegative.
The Lpro aa sequence displayed significant variation for a functional protein: 46.6 % for the serotype A alignment and 29.6 % for the serotype O isolates (Table 2).
Some of the structural variation found might be causal for functional variation, which influences important agronomic traits of the potato such as tuber starch and sugar content.
The resulting files were first annotated using SNPEff (version 2.0.5) for variation functional impact, and then for known disease-causing variants as classified in ClinVar database (clinical significance = "4", probable pathogenic or "5", pathogenic) and in the professional version of Human Gene Mutation Database (HGMD) (Disease mutation –"DM" variants).
Another useful resource for investigating candidate SNPs is the ECCO database (Nguyen et al. 2014), which enables researchers to interrogate sequence variation of functional elements for each of 19 tissues/cell types.
This yielded a database comprising ∼5 million aligned sequences, allowing interrogation of sequence variation of functional elements for each of the 19 tissues/cell types in commonly used mouse strains.
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