Trends in Ecology & Evolution, Journal Year: 2022, Volume and Issue: 37(12), P. 1104 - 1115
Published: July 30, 2022
Understanding the molecular mechanisms underlying phenotypic evolution is a central goal in evolutionary biology.Unfortunately, causal associations between candidate loci and phenotype are rarely established because majority of never validated with functional tools.We describe latest developments use tools, particularly RNAi clustered regularly interspaced palindromic repeats (CRISPR)-Cas, to establish links genotype phenotype, discuss some methodological challenges when applying these tools that unique emerging model organisms.Specifically, we highlight significant issue current studies ecology biology date recapitulate ecologically relevant variation, suggest gene editing species should make more HDR pathway obtain insights thereby deeper understanding genetic basis traits. Most field aiming connect validate identified using tools. Recent RNA interference (RNAi) (CRISPR)-Cas genome have dramatically increased feasibility validation. However, methods come specific applied organisms, including limited spatial control silencing, low knock-in efficiencies, throughput Moreover, many do not this limits their scope for into processes. We therefore argue by allelic replacement through homology-directed repair (HDR) would greatly benefit evolution. A fundamental aim identify genomic variation underlies micro- macroevolutionary dynamics [1.Vitti J.J. et al.Detecting natural selection data.Annu. Rev. Genet. 2013; 47: 97-120Crossref PubMed Scopus (397) Google Scholar]. In present post-genomic era, diverse datasets routinely used purpose organisms (see Glossary), ranging from genome-wide population data various association approaches differential expression analysis chromatin accessibility assays [2.Jamann T.M. al.QTL mapping high-throughput sequencing.in: Alonso J.M. Stepanova A.N. Plant Functional Genomics: Methods Protocols. 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Given circumstances, raise two worth considering investigating First, although acknowledge implementation even desirable instances, wish stress absence proper allowing avoiding language. Imprecise language degrades insights, impedes how world works, bloats false positive results [9.Siddiq M.A. al.Experimental test refutation classic case Drosophila melanogaster.Nat. 2017; 1: 25Crossref (21) Second, relying upon existing annotations without perpetuates bias. Consider hypothetical scenario, wherein intersection SNP trait, where variants associated near coding sequences several differentially expressed genes. resulting list assessed, hypotheses formed based sequence element annotations, which turn overwhelmingly closest organism melanogaster insects, mouse Mus musculus mammals, zebrafish Danio rerio fish, Saccharomyces cerevisiae yeast, Arabidopsis thaliana plants, so on). note duality approach: seems sound way forward homologous share functions over deep time, approach necessary no other possible, comes risk erroneous inferences. Model only important unknown function [10.Wu al.CRISPR/Cas9 mediated resource kinase phosphatase Drosophila.Sci. 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They then manipulate four Knockout (KO) first choice, locus annotated wing-pattern (cortex), predictably affected color. Of one had effect (Dscam3) whereas did (trehalase). Finally, KO uncharacterized unannotated demonstrated causally coloration plasticity, was named herfst. Had chosen cortex, novel missed, (the metabolic trehalase) has unpredicted patterning. conducted neuronal Dscam3 patterning might generated line inquiry fact lacks support, trehalase possibly discounted. discovery herfst provides knowledge allows reanalysis previous work. With components types will synergistically improve across broader taxonomical range interest field. 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Language: Английский
