Genome-Wide Expression and Alternative Splicing in Domesticated Sunflowers (Helianthus annuus L.) under Flooding Stress

Joon Seon Lee,Lexuan Gao,Loren H Rieseberg,Laura Melissa Guzman

doi:10.3390/agronomy11010092

Abstract

Approximately 10% of agricultural land is subject to periodic flooding, which reduces the growth, survivorship, and yield of most crops, reinforcing the need to understand and enhance flooding resistance in our crops. Here, we generated RNA-Seq data from leaf and root tissue of domesticated sunflower to explore differences in gene expression and alternative splicing (AS) between a resistant and susceptible cultivar under both flooding and control conditions and at three time points. Using a combination of mixed model and gene co-expression analyses, we were able to separate general responses of sunflower to flooding stress from those that contribute to the greater tolerance of the resistant line. Both cultivars responded to flooding stress by upregulating expression levels of known submergence responsive genes, such as alcohol dehydrogenases, and slowing metabolism-related activities. Differential AS reinforced expression differences, with reduced AS frequencies typically observed for genes with upregulated expression. Significant differences were found between the genotypes, including earlier and stronger upregulation of the alcohol fermentation pathway and a more rapid return to pre-flooding gene expression levels in the resistant genotype. Our results show how changes in the timing of gene expression following both the induction of flooding and release from flooding stress contribute to increased flooding tolerance.

Highlights

People have inhabited regions with abundant water for multiple reasons, but most of all, for successful agriculture
We found 2338 genes (1510 upregulated, 828 downregulated) from leaf tissue and 9089 genes (4417 upregulated, 4672 downregulated) from root tissue that were differentially expressed under flooding stress (E) (FDR < 0.01) (Figure 2, Table S2)
We conducted a large-scale transcriptomics study to investigate the eco-physiological responses of sunflower, an important oilseed crop, to flooding stress

Summary

Introduction

People have inhabited regions with abundant water for multiple reasons, but most of all, for successful agriculture. The association with water means that flooding typically is common as well, which can result in significant crop losses, especially for crops that lack resistance to flooding. From a plant physiological standpoint, flooding results in reduced gas exchange in submerged roots and shoots, which can slow down rates of respiration and photosynthesis [3] or lead to damage at the cellular level (e.g., in lipids, proteins and DNA) due to increased levels of reactive oxygen species (ROS) [4]. Plants that are frequently exposed to flooding, have developed several strategies to respond and adapt to flooding stress, both physiologically and morphologically. These strategies include quiescence, anaerobic energy production, rapid shoot growth to escape flooding, and the development of aerenchyma to facilitate internal gas exchange

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