Abstract
Population genomics integrates advances in sequencing technologies, bioinformatics tools, statistical methods and software into research on evolutionary and population genetics. Its application has provided novel approaches that have significantly advanced our understanding of new and long-standing questions in evolutionary processes. This has allowed the disentangling of locus-specific effects from genome-wide effects and has shed light on the genomic basis of fitness, local adaptation and phenotypes. “-Omics” tools have provided a comprehensive genome-wide view of the action of evolution. The specific features of the Phaseolus genus have made it a unique example for the study of crop evolution. The well-documented history of multiple domestications in Phaseolus vulgaris L. (common bean) and its further adaptation to different environments have provided the opportunity to investigate evolutionary issues, such as convergent evolution in the same species across different domestication events. Moreover, the availability of the P. vulgaris reference genome now allows adaptive variations to be easily mapped across the entire genome. Here, we provide an overview of the most significant outcomes obtained in common bean through the use of different computational tools for analysis of population genomics data.
Highlights
According to neutral theory, the great majority of evolutionary changes at the molecular level involve random fixation of selectively neutral alleles through cumulative effects of sampling drift and under the input of novel mutations [1,2]
Using a maximum-likelihood approach, they performed a origin of common bean, Rendón-Anaya et al [49]single nucleotide polymorphisms (SNPs) alsoand proposed an chloroplast early dissemination and speciation phylogenetic analysis based on genome-wide on a 55-kb genome fragment
The new “-omics” technologies can help to fine-tune the molecular basis of these adaptation strategies, an aspect that is ongoing in the BEAN_ADAPT Project. This project is based on a multidisciplinary approach with the aim to extend the genetic basis of the phenotypic adaptation of P. vulgaris and its sister species P. coccineus in Europe and outside of their centers of origin
Summary
The great majority of evolutionary changes at the molecular level involve random fixation of selectively neutral (or nearly neutral) alleles through cumulative effects of sampling drift and under the input of novel mutations [1,2]. The availability of high-throughput sequencing platforms and high-density DNA markers has allowed parallel analyses of many loci on relatively large sample sizes and exploiting several statistical methods [20] These advances have expanded the detection and conservation of important genetic variations to provide a comprehensive genome-scale view of the actions of evolution [21], even in non-model organisms [22]. The integration of quantitative trait locus (QTL) mapping and the analysis of the “selective sweep” effects allowed the target genomic regions that were under selection to be narrowed down [28] All of these recent genomics advances described above were widely applied in population genetics studies of the common bean, and a new epoch began for this crop. We will review P. vulgaris studies that have addressed evolutionary questions
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