Genome-Wide Association Study of Natural Variation in Arabidopsis Exposed to Acid Mine Drainage Toxicity and Validation of Associated Genes with Reverse Genetics

Bandana Ghimire,Venkata Lakshmi Abburi,Padma Nimmakayala,Arjun Ojha Kshetry,Umesh K Reddy,Thangasamy Saminathan,Abiodun Bodunrin,Suhas Shinde

doi:10.3390/plants10020191

Abstract

Acid mine drainage (AMD) is a huge environmental problem in mountain-top mining regions worldwide, including the Appalachian Mountains in the United States. This study applied a genome-wide association study (GWAS) to uncover genomic loci in Arabidopsis associated with tolerance to AMD toxicity. We characterized five major root phenotypes—cumulative root length, average root diameter, root surface area, root volume, and primary root length—in 180 Arabidopsis accessions in response to AMD-supplemented growth medium. GWAS of natural variation in the panel revealed genes associated with tolerance to an acidic environment. Most of these genes were transcription factors, anion/cation transporters, metal transporters, and unknown proteins. Two T-DNA insertion mutants, At1g63005 (miR399b) and At2g05635 (DEAD helicase RAD3), showed enhanced acidity tolerance. Our GWAS and the reverse genetic approach revealed genes involved in conferring tolerance to coal AMD. Our results indicated that proton resistance in hydroponic conditions could be an important index to improve plant growth in acidic soil, at least in acid-sensitive plant species.

Highlights

Soil contamination is a major global environmental issue, severely affecting crop production worldwide, along with bio-accumulation of toxic chemicals in our food
This study used genome-wide association study (GWAS) to uncover genomic loci in Arabidopsis associated with tolerance to acid mine drainage (AMD) toxicity, which is a global problem in agricultural production
This study identified genetic loci responsible for acidity tolerance using a GWAS approach in the model plant Arabidopsis

Summary

Introduction

Soil contamination is a major global environmental issue, severely affecting crop production worldwide, along with bio-accumulation of toxic chemicals in our food. Anthropogenic activities are the major source of soil contamination [1]. Coal mining has been performed industrially in the Appalachian Mountains since the mid-1800s. Today, it continues to serve as a significant contributor to the regional economy and the United States’ energy portfolio Administration [3]. West Virginia is the second-largest coal-producing state in the United States after Wyoming (https://www.eia.gov). Coal is mined in West Virginia and the other Appalachian Mountains by both underground mining and mountaintop removal methods. Mountain-top mining is a form of surface mining that involves removing the topsoil layer and exposing the coal seams. The extensive mountain-top mining and coal processing activities in Appalachia and across the world have left a legacy of contaminated mine spoils

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