Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops

doi:10.3389/fpls.2017.00578

	Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops
	Yan, Juan ; Song, Zhihong 1,2,3; Xu, Qin 1,2; Kang, Lifang 1,2; Zhu, Caiyun 3,4; Xing, Shilai 3,4; Liu, Wei 1,2; Greimler, Josef 5; Zuest, Tobias 6; Li, Jianqiang ; Sang, Tao1,2,4
	2017
发表期刊	MOLECULAR ECOLOGY
ISSN	0962-1083
卷号	26 期号:21 页码:5911-5922
摘要	The use of transcriptome data in the study of the population genetics of a species can capture faint signals of both genetic variation and expression variation and can provide a broad picture of a species' genomic response to environmental conditions. In this study, we characterized the genetic and expression diversity of Miscanthus lutarioriparius by comparing more than 16,225 transcripts obtained from 78 individuals, belonging to 10 populations distributed across the species' entire geographic range. We only observed a low level of nucleotide diversity (pi = 0.000434) among the transcriptome data of these populations, which is consistent with highly conserved sequences of functional elements and protein-coding genes captured with this method. Tests of population divergence using the transcriptome data were consistent with previous microsatellite data but proved to be more sensitive, particularly if gene expression variation was considered as well. For example, the analysis of expression data showed that genes involved in photosynthetic processes and responses to temperature or reactive oxygen species stimuli were significantly enriched in certain populations. This differential gene expression was primarily observed among populations and not within populations. Interestingly, nucleotide diversity was significantly negatively correlated with expression diversity within populations, while this correlation was positive among populations. This suggests that genetic and expression variation play separate roles in adaptation and population persistence. Combining analyses of genetic and gene expression variation represents a promising approach for studying the population genetics of wild species and may uncover both adaptive and nonadaptive processes.
关键词	gene expression Miscanthus nucleotide diversity population genetics transcriptome
学科领域	Plant Sciences
DOI	10.3389/fpls.2017.00578
收录类别	SCI
语种	英语
WOS关键词	WATER-USE EFFICIENCY ; RNA-SEQ DATA ; ALLELE FREQUENCY ; LOCAL ADAPTATION ; LOESS PLATEAU ; DIVERSITY ; SELECTION ; REVEALS ; DIFFERENTIATION ; DIVERGENCE
WOS记录号	WOS:000399370100001
出版者	WILEY
文献子类	Article
出版地	HOBOKEN
EISSN	1365-294X
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31000147, 31400284, 41501418] ; Project for Autonomous Deployment of the Wuhan Botanical Garden [55Y755271G02]
作者邮箱	lijq@wbgcas.cn ; sang@ibcas.ac.cn
作品OA属性	Green Published, gold
引用统计	被引频次：15[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/22196
专题	系统与进化植物学国家重点实验室
作者单位	1.Chinese Acad Sci, Wuhan Bot Garden, Key Lab Plant Germplasm Enhancement & Specialty A, Wuhan, Hubei, Peoples R China 2.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing, Peoples R China 3.Chinese Acad Sci, Inst Bot, Beijing Bot Garden, Beijing, Peoples R China 4.Univ Chinese Acad Sci, Beijing, Peoples R China 5.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 6.Univ Vienna, Dept Bot & Biodivers Res, Vienna, Austria 7.Univ Bern, Inst Plant Sci, Bern, Switzerland
推荐引用方式 GB/T 7714	Yan, Juan,Song, Zhihong,Xu, Qin,et al. Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops[J]. MOLECULAR ECOLOGY,2017,26(21):5911-5922.
APA	Yan, Juan.,Song, Zhihong.,Xu, Qin.,Kang, Lifang.,Zhu, Caiyun.,...&Sang, Tao.(2017).Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops.MOLECULAR ECOLOGY,26(21),5911-5922.
MLA	Yan, Juan,et al."Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops".MOLECULAR ECOLOGY 26.21(2017):5911-5922.

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