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

• Published in: Journal of integrative plant biology Vol. 57; no. 3; pp. 284 - 299
• Main Authors: Xu, Qin, Xing, Shilai, Zhu, Caiyun, Liu, Wei, Fan, Yangyang, Wang, Qian, Song, Zhihong, Yang, Wenhui, Luo, Fan, Shang, Fei, Kang, Lifang, Chen, Wenli, Yan, Juan, Li, Jianqiang, Sang, Tao
• Format: Journal Article
• Language: English
• Published: China (Republic : 1949- ) Blackwell Publishing Ltd 01.03.2015; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China%Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China%Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China
• Subjects: abiotic stress; Adaptation; Adaptation, Physiological - genetics; artificial selection; biomass; Crops, Agricultural - genetics; de novo assembling; domestication; energy crops; expression variation; gene expression; Gene Expression Regulation, Plant; genes; genetic diversity; Genetic Variation; Genetics, Population; Genome, Plant; habitats; histones; leaves; methylation; Miscanthus lutarioriparius; phenotypic variation; Phylogeny; Plant Leaves - genetics; planting; Poaceae - genetics; population structure; population transcriptome; Reference Standards; RNA, Messenger - genetics; RNA, Messenger - metabolism; single nucleotide polymorphism; stress tolerance; transcriptome; Transcriptome - genetics; transcriptomics; 人口结构; 单核苷酸多态性; 基因表达; 组蛋白甲基化; 能源作物; 转录表达; 遗传多样性; 非生物胁迫; de novo assembling; genetic diversity; population transcriptome; expression variation; Miscanthus lutarioriparius; Adaptation; artificial selection
• ISSN: 1672-9072; 1744-7909; 1744-7909
• DOI: 10.1111/jipb.12287

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 Resediversity 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.