Research Article: Transcriptome profiling revealed diverse gene expression patterns in poplar (Populus × euramericana) under different planting densities

Date Published: May 29, 2019

Publisher: Public Library of Science

Author(s): Kun Ning, Changjun Ding, Qinjun Huang, Weixi Zhang, Chengchao Yang, Dejun Liang, Ruting Fan, Xiaohua Su, Anil Kumar Singh.

http://doi.org/10.1371/journal.pone.0217066

Abstract

Certain plant genotypes can achieve optimal growth under appropriate environmental conditions. Under high planting density conditions, plants undergo competition for uptake and utilization of light and nutrients. However, the relationship between whole-genome expression patterns and the planting density in perennial woody plants remains unknown. In this study, whole-genome RNA sequencing of poplar (Populus × euramericana) was carried out at three different sampling heights to determine gene expression patterns under high (HD) and low (LD) planting densities. As a result, 4,004 differentially expressed genes (DEGs) were detected between HD and LD, of which 2,300, 701, and 1,003 were detected at the three positions, upper, middle and bottom, respectively. Function annotation results further revealed that a large number of the DEGs were involved in distinct biological functions. There were significant changes in the expression of metabolism-related and stimulus-related genes in response to planting density. There were 37 DEGs that were found at all three positions and were subsequently screened. Several DEGs related to plant light responses and photosynthesis were observed at different positions. Meanwhile, numbers of genes related to auxin/indole-3-acetic acid, and carbon and nitrogen metabolism were also revealed, displaying overall trends of upregulation under HD. These findings provide a basis for identifying candidate genes related to planting density and could increase our molecular understanding of the effect of planting density on gene expression.

Partial Text

Tree growth is closely related to environmental conditions. For example, planting density affects population structure and yield. An optimal planting density allows effective utilization of light energy and soil nutrients, ensuring normal development of individual plants and coordinated development of the entire population. In line with this, planting density has been shown to improve grain yield [1,2], via its effect on plant size, morphology, biomass, productivity, and the extent of lodging [3,4]. The density of planting has also been found to be important in acquiring a high yield in modern corn production [5,6]. Although planting density has been shown to be important for the growth of crops, vegetables, and medicinal plants [7], little is known about the molecular-level effect of planting density on plant growth.

The ability of trees to maintain a high level of productivity under an adequate planting density is a determinant factor for increasing timber yield. With increasing establishment of poplar plantations, further research on how trees adapt to their growth environment at the molecular level is necessary to secure optimum timber yield and quality. For the nine-year-old poplar, trees grown under HD are already in a canopy closure state; the DBH was found to be highly significantly different between the two planting densities. Here, the whole-genome RNA-Seq was utilized to profile transcript levels in mature poplar trees planted under HD and LD. The results revealed that a large amount of DEGs (4,004) existed at three positions when comparing HD with LD. In addition, it was found that the vertical position had a significant effect on gene expression when comparing planting densities. Guo et al. sought out 205 genes that were considered to be differentially expressed in Arabidopsis grown under different planting densities [7]. Another study found that 221 genes exhibited differential expression in response to density stress in barley [28]. These results suggest that transcriptome profiles are influenced by changes in planting density in both annual herbaceous and perennial woody plants.

The whole-genome RNA-seq of leaves from perennial woody poplar provided insight into gene expression patterns under high and low planting densities. Overall, 4,004 DEGs emerged in the comparison of HD with LD, with 37 density-related DEGs found at all three positions. Moreover, several light-related genes, which were mostly upregulated under HD, were also observed. These genes may therefore play an important role in the response to light under different positions and planting densities. A series of AUX/IAA-related genes that showed diverse expression trends were also analyzed. Meanwhile, genes involved in carbon and nitrogen metabolism were identified. Of these genes, those displaying increased expression under HD, may be indicative of the plants’ ability to adapt to density stress. These findings could increase our molecular understanding of the effect of planting density on gene expression and provide a reference for future research on planting density-regulated genes. In the future, we hope to achieve optimal expression of the most important functioning genes by regulating planting density. This should enable us to obtain the maximum yield under high density.

 

Source:

http://doi.org/10.1371/journal.pone.0217066

 

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