title: Population transcriptomics reveals a potentially positive role of expression diversity in adaptation.
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.
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Xu
authors.forename: Shilai
authors.initials: S
authors.lastname: Xing
authors.forename: Caiyun
authors.initials: C
authors.lastname: Zhu
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.forename: Yangyang
authors.initials: Y
authors.lastname: Fan
authors.forename: Qian
authors.initials: Q
authors.lastname: Wang
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Song
authors.forename: Wenhui
authors.initials: W
authors.lastname: Yang
authors.forename: Fan
authors.initials: F
authors.lastname: Luo
authors.forename: Fei
authors.initials: F
authors.lastname: Shang
authors.forename: Lifang
authors.initials: L
authors.lastname: Kang
authors.forename: Wenli
authors.initials: W
authors.lastname: Chen
authors.forename: Juan
authors.initials: J
authors.lastname: Yan
authors.forename: Jianqiang
authors.initials: J
authors.lastname: Li
authors.forename: Tao
authors.initials: T
authors.lastname: Sang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D018556:Crops, Agricultural / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D010802:Phylogeny; D018515:Plant Leaves / Q000235:genetics; D006109:Poaceae / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012015:Reference Standards; D059467:Transcriptome / Q000235:genetics*
chemical_list: D012333:RNA, Messenger
keywords: Adaptation; Miscanthus lutarioriparius; artificial selection; de novo assembling; expression variation; genetic diversity; population transcriptome