RNA-Seq Profiling Shows Divergent Gene Expression Patterns in Arabidopsis Grown under Different Densities.

Di Guo,Zhenyi Wang,Li Wang,Jinpeng Wang,Xiaoming Song,Min Yuan,Weina Ge,Xiyin Wang

doi:10.3389/fpls.2017.02001

Di Guo, Zhenyi Wang + Show 6 more

Open Access

https://doi.org/10.3389/fpls.2017.02001

Copy DOI

Abstract

Plants growing under high-density (HD) conditions experience increased competition for water, nutrients, and light, possibly leading to changes in size, biomass, morphology, and productivity. However, no research has focused on the relationship between whole-genome expression patterns and growth density. Here, we performed whole-genome RNA sequencing to examine the gene expression patterns in Arabidopsis grown under low and high densities. Of the 20,660 detected genes, the expression levels of 98 were enhanced and 107 were repressed under HD growth. Further analysis revealed that changes in density influenced metabolism- and stimulus-related genes the most. Furthermore, HD growth led to a shade avoidance phenotype, represented by upward growth and a reduction in rosette leaves. Moreover, a cluster of glutaredoxin genes, GRXS3, 4, 5, 7, and 8, were significantly down-regulated under high density, suggesting that high density affects plant growth mainly by nitrate limitation.

Highlights

Most plant studies have been conducted using individual potted plants under controlled conditions (Hecht et al, 2016), and much physiological and molecular data have been derived from this
30 million reads of raw tags were obtained for each sample (Supplementary Table S1), with the GC distribution close to theoretical distribution (Supplementary Figure S2)
Among those genome-mapped reads, about 90% were mapped to gene region, and more than 99% were mapped onto exons (Supplementary Table S4)

Summary

Introduction

Most plant studies have been conducted using individual potted plants under controlled conditions (Hecht et al, 2016), and much physiological and molecular data have been derived from this. Sowing density is important as plants grown under high-density (HD) conditions compete with each other for water, nutrition, and light, which often leads to changes in plant size, biomass, morphology, and productivity (Hecht et al, 2016). Research about plant density refers to productivity, organ development, nutrition absorption, water heterogeneity, shade avoidance, and flowering (Lemaire et al, 2005; Hagiwara et al, 2010; Li et al, 2011, 2016; El-Zaeddi et al, 2016; Roig-Villanova and Martinez-Garcia, 2016; Song et al, 2016). Plant density affects organ development (Hecht et al, 2016; Song et al, 2016).

Methods

Results

Conclusion