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Genome-wide comparison of two poplar genotypes with different growth rates

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Abstract

The ecologically dominant and economically important genus Populus, with its available full genome sequence, has become an ideal woody species for genomic study. Rapid growth is one of the primary advantageous features of Populus, and extensive physiological research has been carried out on the growth of Populus throughout the growing period among different clones. However, the molecular information related to the mechanisms of rapid growth is rather limited. In this study, an Affymetrix poplar genome array was employed to analyze the transcriptomic changes from the pre-growth to the fast-growth phase in two poplar clones (P.deltoides × P.nigra, DN2, and P.nigra × (P.deltoides × P. nigra), NE19) with different growth rates. A total of 1,695 differently expressed genes were identified between two time points in NE19 and DN2 (two-way ANOVA, P < 0.01 and fold change ≥2). Except for genes changing in common for both clones, many transcripts were regulated specifically in one genotype. After functional analysis of the differentially expressed genes, distinct biological strategies seemed to be utilized by the two genotypes to accommodate their fast-growth phase. The faster-growing clone NE19, which has a higher photosynthetic rate and larger total leaf area, emphasized growth-related primary metabolism. However, the slower-growing DN2 tended to have more up-regulated genes involved in defense-related secondary metabolism and stress response. Emphasis of such divergent biological processes in two clones may explain their significant growth differences during the fast-growth phase.

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Abbreviations

ABA:

Abscisic acid

ANOVA:

Analysis of variance

BR:

Brassinolide

CTK:

Cytokinin

DPTF:

The database of poplar transcription factor

ETH:

Ethylene

GA:

Gibberellin

IAA:

Indole-3-acetic acid

JA:

Jasmonic acid

JGI:

Joint Genome Institute

PS I:

Photosystem I

PS II:

Photosystem II

PlnTFDB:

Plant transcription factor database

qRT-PCR:

Real-time quantitative reverse transcription PCR

SA:

Salicylic acid

TAIR:

The Arabidopsis information resource

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Acknowledgments

This work was supported by the National Basic Research Program of China (2009CB119101), National Natural Science Foundation of China (30730077, 30972339, 31070597), Program for New Century Excellent Talents in University of China (NCET-07-0083), National R&D Key Project of China (2011BAD38B01). We thank Prof. Dr. Hongwei Guo (College of Life Sciences, Peking University, Beijing, China) for helpful suggestions.

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  1. National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, People’s Republic of China

    Shuang Hao, Teng Zhao, Xinli Xia & Weilun Yin

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  1. Shuang Hao
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Correspondence to Xinli Xia or Weilun Yin.

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Hao, S., Zhao, T., Xia, X. et al. Genome-wide comparison of two poplar genotypes with different growth rates. Plant Mol Biol 76, 575–591 (2011). https://doi.org/10.1007/s11103-011-9790-0

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