Molecular Biology and Evolution
Molecular Biology and Evolution
5 years ago

A highly specific genome-wide association study integrated with transcriptome data reveals the contribution of copy number variations to specialized metabolites in Arabidopsis thaliana accessions.

Shinozaki, Tanaka, Matsuda, Nakabayashi, Hanada, Fujimoto, Shirai, Seki, Okamoto, Saito, Shimizu
Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication events contribute to the diversity of specialized metabolites within species. We identified metabolome quantitative trait genes (mQTGs) associated with quantitative metabolite variations and examined the relationship between mQTGs and CNVs. We obtained 1,335 specialized metabolite signals from 53 worldwide A. thaliana accessions using liquid chromatography-quadrupole time-of-flight mass spectrometry. In this study, genes associated with specialized metabolites were inferred by either a generally authorized genome-wide association study (GWAS) approach or a novel analysis of the association between gene expression and metabolite accumulation. Genes qualified by both analyses are defined to be mQTGs. The integrated method enabled us to detect mQTGs with a low false positive rate (= 5.71 × 10-4). We also identified 5,654 genes associated with 1,335 specialized metabolites. Of these genes, 4.4% were affected by CNVs, which was more than expected (χ2 test: P < 0.01). This result suggests that CNVs contribute to variations in specialized metabolites within a species. To assess the contribution of CNVs to adaptive evolution in A. thaliana, we examined the selective sweeps around the mQTGs. We observed that the mQTGs with CNVs tended to undergo selective sweeps. These observations imply that variations in specialized metabolites caused by CNVs contribute to the adaptive evolution of A. thaliana.

Publisher URL: http://doi.org/10.1093/molbev/msx234

DOI: 10.1093/molbev/msx234

You might also like
Discover & Discuss Important Research

Keeping up-to-date with research can feel impossible, with papers being published faster than you'll ever be able to read them. That's where Researcher comes in: we're simplifying discovery and making important discussions happen. With over 19,000 sources, including peer-reviewed journals, preprints, blogs, universities, podcasts and Live events across 10 research areas, you'll never miss what's important to you. It's like social media, but better. Oh, and we should mention - it's free.

  • Download from Google Play
  • Download from App Store
  • Download from AppInChina

Researcher displays publicly available abstracts and doesn’t host any full article content. If the content is open access, we will direct clicks from the abstracts to the publisher website and display the PDF copy on our platform. Clicks to view the full text will be directed to the publisher website, where only users with subscriptions or access through their institution are able to view the full article.