J Integr Plant Biol. ›› 2015, Vol. 57 ›› Issue (3): 284-299.DOI: 10.1111/jipb.12287

• Molecular Ecology and Evolution • Previous Articles     Next Articles

Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

Qin Xu1†, Shilai Xing1†, Caiyun Zhu1†, Wei Liu1, Yangyang Fan2, Qian Wang1, Zhihong Song2, Wenhui Yang2, Fan Luo1, Fei Shang2, Lifang Kang2, Wenli Chen1, Juan Yan3, Jianqiang Li3 and Tao Sang1,2*   

  1. 1State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
    2Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
    3Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, China
  • Received:2014-06-29 Accepted:2014-09-19 Published:2014-09-23
  • About author:These authors contributed equally to this work.
    *Correspondence: E-mail: sang@ibcas.ac.cn

Abstract:

While it is widely accepted that genetic diversity determines the potential of adaptation, the role that gene expression variation plays in adaptation remains poorly known. Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius. RNA-seq was conducted for 80 individuals of the species, with half planted in the energy crop domestication site and the other half planted in the control site near native habitats. A leaf reference transcriptome consisting of 18,503 high-quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA-seq data. The population structure and genetic diversity of M. lutarioriparius were estimated based on 30,609 genic single nucleotide polymorphisms. Population expression (Ep) and expression diversity (Ed) were defined to measure the average level and the magnitude of variation of a gene expression in the population, respectively. It was found that expression diversity increased while genetic diversity decreased after the species was transplanted from the native habitats to the harsh domestication site, especially for genes involved in abiotic stress resistance, histone methylation, and biomass synthesis under water limitation. The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.

 

Xu Q, Xing S, Zhu C, Liu W, Fan Y, Wang Q, Song Z, Yang W, Luo F, Shang F, Kang L, Chen W, Yan J, Li J, Sang T (2015) Population transcriptomics reveals a potentially positive role of expression diversity in adaptation. J Integr Plant Biol 57: 284–299. doi: 10.1111/jipb.12287

Key words: Adaptation, artificial selection, de novo assembling, expression variation, genetic diversity, Miscanthus lutarioriparius, population transcriptome

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