Variation in Arabidopsis flooding responses identifies numerous putative “tolerance genes”

Abstract

Plant survival in flooded environments requires a combinatory response to multiple stress conditions such as limited light availability, reduced gas exchange and nutrient uptake. The ability to fine-tune the molecular response at the transcriptional and/or post-transcriptional level that can eventually lead to metabolic and anatomical adjustments are the underlying requirements to confer tolerance. Previously, we compared the transcriptomic adjustment of submergence tolerant, intolerant accessions and identified a core conserved and genotype-specific response to flooding stress, identifying numerous 'putative' tolerance genes. Here, we performed genome wide association analyses on 81 natural Arabidopsis accessions that identified 30 additional SNP markers associated with flooding tolerance. We argue that, given the many genes associated with flooding tolerance in Arabidopsis, improving resistance to submergence requires numerous genetic changes. KEYWORDSDark; genome wide association; submergence; hypoxia Flooding is a natural phenomenon that shapes plant ecosystems and also negatively affects crop yields in agricultural areas. [1][2][3] The frequency and intensity of floods are expected to increase with the current climate change and floods are cataloged as one of the most expensive natural disasters to cause widespread crop-damage. 3 The dramatic negative impact of submergence on plants, mainly caused by reduced gas exchange underwater, provides us with a major challenge to understand and improve crop tolerance to flooding. Interestingly, many species occur naturally on floodplains and have evolved a suite of traits to thrive and survive during periods of flooding. 4 These survival strategies can be roughly divided into 2 classes, firstly cessation of growth to retain valuable resources needed for regrowth when the flood recedes, and secondly the creation of improved aeration through the development of adventitious roots and active shoot growth toward the water surface to snorkel for air and light. 5 The molecular mechanisms of these traits in wild species are gradually being elucidated. 6-8 However, these thriveand-survive traits are naturally not, or only to a limited extent, present in crops, and incorporation of these traits will be challenging. An exception is SUB1A rice, where a naturally occurring allele confers a growth cessation strategy and subsequent tolerance when completely submerged. 9 Despite a lack of specialist traits in other species and crops, large intra-species variation in flooding-tolerance does exist, which could potentially point to key players that modulate tolerance and serve as a basis for crop improvement.Such within species variation was explored by Vashisht et al. (2011) to uncover a relatively large variation in flooding tolerance among 86 Arabidopsis accessions. 11 A completely submerged plant is challenged with a compound environmental stress consisting of reduced light availability and limited gas exchange. Therefore, the authors estimated tolerance to both the compoun...

GWAS on multiple traits identifies mitochondrial ACONITASE3 as important for acclimation to submergence stress

“…Many traits related to abiotic stress such as salt, drought, heat, and freezing tolerance have been analyzed by GWAS in Arabidopsis ( Baxter et al, 2010 ; Li et al, 2010 ; Verslues et al, 2014 ; Horton et al, 2016 ). A GWAS using 81 Arabidopsis accessions identified 30 significant SNP markers ( p < 10 −4 ) associated with a survival score after submergence ( Vashisht et al, 2016 ).…”

A Comprehensive Transcriptomics Analysis Reveals Long Non-Coding RNA to Be Involved in the Key Metabolic Pathway in Response to Waterlogging Stress in Maize

“…The cause of these changes is the dramatic reprogramming of gene expression and RNA molecules, including coding RNA (mRNA) and non-coding RNA (ncRNA) that has been quantified with the development of deep high-throughput sequencing [4,5]. Numerous investigations into Arabidopsis [6][7][8], rice [9], maize [10,11], poplar (Populus × canescens) [12], and cotton (Gossypium hirsutum) [13] have been conducted to elucidate changes in the gene transcription of mRNA in response to low oxygen or flooding stress; these studies have revealed the similarity in transcriptome responses among species [14,15]. However, knowledge of ncRNA involved in hypoxia responses is largely unknown.…”

Association of Candidate Genes With Submergence Response in Perennial Ryegrass

“…Through genome-wide association analysis combined with biparental QTL mapping approaches, candidate gene HXK6 encoding a hexokinase was identified, with its role in mediating seed germination and contributing to the differences in coleoptile growth between Japonica and Indica varieties under submerged condition (Hsu and Tung, 2015). In Arabidopsis thaliana , genome wide association analysis on 81 natural accessions detected 77 genes (within 10 kb of the associated SNP markers) significantly associated with submergence response and involved in many physiological processes including carbon starvation and fermentation (Vashisht et al, 2016). These genes are important regulators for controlling diverse plant responses to submerged conditions.…”