Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

Our plain-English summary of Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils, by T.L. Turner, E.C. Bourne, E.J. Von Wettberg, et al (Nature Genetics, 2010).

The study

• Authors: T.L. Turner, E.C. Bourne, E.J. Von Wettberg, T.T. Hu, S.V. Nuzhdin
• Journal: Nature Genetics
• Published: 2010;42(3):260-3
• Cited by: 318 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

A powerful way to map functional genomic variation and reveal the genetic basis of local adaptation is to associate allele frequency across the genome with environmental conditions. Serpentine soils, characterized by high heavy-metal content and low calcium-to-magnesium ratios, are a classic context for studying adaptation of plants to local soil conditions. To investigate whether Arabidopsis lyrata is locally adapted to serpentine soil, and to map the polymorphisms responsible for such adaptation, we pooled DNA from individuals from serpentine and nonserpentine soils and sequenced each 'gene pool' with the Illumina Genome Analyzer. The polymorphisms that are most strongly associated with soil type are enriched at heavy-metal detoxification and calcium and magnesium transport loci, providing numerous candidate mutations for serpentine adaptation. Sequencing of three candidate loci in the European subspecies of A. lyrata indicates parallel differentiation of the same polymorphism at one locus, confirming ecological adaptation, and different polymorphisms at two other loci, which may indicate convergent evolution.

In plain English

This study concerns a plant, not asbestos or human health; the article does not mention asbestos. The authors asked whether the wild plant Arabidopsis lyrata was genetically adapted to serpentine soils, which they described as high in heavy metals and low in calcium relative to magnesium. They pooled DNA from 25 plants from each of four US populations and sequenced it. Two populations grew on serpentine soil and two on granitic soil, in Pennsylvania and Maryland. Of about 8.4 million genetic variants, 96 differed in frequency by more than 80% between soil types. Metal ion transporter genes were over-represented: 12.5% of them were among the most differentiated regions, whereas such strongly soil-associated regions made up only 0.6% of all annotated genes. In Scottish plants of a related subspecies, the same calcium-channel variant separated serpentine from nonserpentine plants. Two other candidate regions also differed strongly in Scotland, but at different variants. The authors concluded that the variants most strongly linked to soil type were enriched at genome locations (loci) involved in heavy-metal detoxification and calcium and magnesium transport. They noted that such patterns can also arise from neutral demographic processes.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Genome-wide population genetic study using pooled DNA sequencing of plant populations, with follow-up sequencing of three candidate loci in Scottish populations
• Who was studied: Arabidopsis lyrata plants: 25 plants from each of four US populations (two serpentine sites in Pennsylvania and Maryland, two granitic sites in Pennsylvania), from seeds collected May to September 2006. Also a serpentine and a nonserpentine population of the European subspecies A. lyrata petraea in Scotland, collected August and September 2008.
• Exposure: Growth on serpentine soil, described as high in heavy-metal content with low calcium-to-magnesium ratios, compared with granitic (nonserpentine) soil. No asbestos exposure was studied.
• Main results:
  • Of the roughly 8.4 million polymorphisms detected in the US populations (8,433,201 after coverage filtering), 96 had allele frequency differences greater than 80% between serpentine and granitic soils.
  • 12.5% of the metal ion transmembrane transporters in the genome were among the most differentiated loci between soils, although loci strongly associated with soil type made up only 0.6% of annotated genes (binomial P = 5.85 times 10 to the minus 6).
  • At Calcium channel 1, the derived glycine had a frequency of 1.00 and 0.85 in the two US serpentine populations and 0.00 in both granitic populations. In the Scottish populations, the glycine was fixed in the serpentine population and the ancestral valine was fixed in the nonserpentine population.
  • In Scotland, FST at the magnesium transporter gene AT5G64560 was 0.966. Six microsatellite loci in the same populations had FST values from 0.017 to 0.381 (mean 0.200). The Scottish differentiation at this gene involved different polymorphisms from the US populations.
  • The three candidate loci sequenced in Scotland showed much higher differentiation than all six polymorphic microsatellites (t-test, P less than 0.0001).
  • The nonserpentine allele matched the reference A. lyrata genome at 18 of the 20 candidates in Table 1 and at 80% of the 96 most differentiated polymorphisms.
  • A scan for copy number variation found 94 candidate duplications and 373 candidate deletions in the serpentine populations.
• The authors' conclusion: The authors concluded that the polymorphisms most strongly associated with soil type were enriched at heavy-metal detoxification and calcium and magnesium transport loci, providing numerous candidate mutations for serpentine adaptation.
• Limitations the authors state:
  • The authors noted that associations between genetic and environmental variation can also result from neutral demographic processes, for example if gene flow is higher between similar environments.
  • Discarding mismatches seen only once removed most sequencing errors but also removed rare genetic variation.
  • Some apparent deletions may instead be regions of high divergence where serpentine reads could not be aligned.
  • The authors stated that the evolutionary significance of the nonrandom gene content of copy number variant regions is unclear.

Topics

The National Library of Medicine indexes this study under subjects our site covers: Chrysotile.

Medical terms in this study, explained in our Lexicon: Serpentine Group.

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