Haplotypes Phased from Population Transcriptomes Detecting Selection in the Initial Adaptation of Miscanthus lutarioriparius to Stressful Environments

doi:10.2135/cropsci2016.08.0673

	Haplotypes Phased from Population Transcriptomes Detecting Selection in the Initial Adaptation of Miscanthus lutarioriparius to Stressful Environments
	Zhu, Cai-yon ; Liu, Wei ; Kang, Li-Fang ; Xu, Qin ; Xing, Shi-Lai ; Fan, Yang-Yang ; Song, Zhi-Hong ; Yan, Juan ; Li, Jian-Qiang ; Sang, Tao4
	2017
发表期刊	PLANT GENOME
ISSN	1940-3372
卷号	10 期号:2
摘要	Adaptation is a characteristic that enhances the survival or reproduction of organisms; selection is the critical process leading to adaptive evolution. Therefore, detecting selection is important in studying evolutionary biology. Changes in allele frequency are fundamental to adaptive evolution. The allele frequency of entire genes at the genomic scale is more intensive and precise for analyzing selection effects, compared with simple sequence repeat and single nucleotide polymorphism (SNP) alleles from nuclear gene fragments. Here, we analyzed 29,094 SNPs derived from 80 individuals of 14 Miscanthus lutarioriparius L. Liou ex S. L. Chen & Renvoize populations planted near their native habitat (Jiangxia, Hubei Province, JH) and a stressful environment (Qingyang, Gansu Province, QG) to detect selection during initial adaptation. The nucleotide diversity of over 60% of genes was decreased in QG compared with JH, suggesting that most genes were undergoing selection in the stressful environment. We explored a new approach based on haplotype data inferred from RNA-seq data to analyze the change in frequency between two sites and to detect selection signals. In total, 402 and 51 genes were found to be targets of positive and negative selection, respectively. Among these candidate genes, the enrichment of abiotic stress-response genes and photosynthesis-related genes might have been responsible for establishment in the stressful environment. This is the first study assessing the change in allele frequency at the genomic level during adaptation. The method in which allele frequency detects selection during initial adaptation using population RNA-seq data would be useful for developing evolutionary biology.
学科领域	Agriculture
DOI	10.2135/cropsci2016.08.0673
收录类别	SCI
语种	英语
WOS关键词	ENERGY CROP ; ARABIDOPSIS-THALIANA ; C-4 PHOTOSYNTHESIS ; DOG DOMESTICATION ; FINGER PROTEINS ; COLD TOLERANCE ; X GIGANTEUS ; DIVERSITY ; SEQUENCE ; GENE
WOS记录号	WOS:000408534800007
出版者	CROP SCIENCE SOC AMER
文献子类	Article
出版地	MADISON
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31400284, 31500186] ; National Key Research and Development Program of China [2016YFC0500905] ; Science and Technology Service Network Initiative of the Chinese Academy of Sciences [KFJ-EW-STS-119]
作者邮箱	yanj@wbgcas.cn ; sang@ibcas.ac.cn
引用统计	被引频次：2[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/2S10CLM1/22289
专题	系统与进化植物学国家重点实验室
作者单位	1.[Zhu, Cai-yon 2.Liu, Wei 3.Xu, Qin 4.Xing, Shi-Lai 5.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 6.Fan, Yang-Yang 7.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 8.[Kang, Li-Fang 9.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China 10.Chinese Acad Sci, Inst Bot, Beijing Bot Garden, Beijing 100093, Peoples R China 11.[Yan, Juan 12.Chinese Acad Sci, Wuhan Bot Garden, Key Lab Plant Germplasm Enhancement & Spacialty A, Wuhan 430074, Hubei, Peoples R China
推荐引用方式 GB/T 7714	Zhu, Cai-yon,Liu, Wei,Kang, Li-Fang,et al. Haplotypes Phased from Population Transcriptomes Detecting Selection in the Initial Adaptation of Miscanthus lutarioriparius to Stressful Environments[J]. PLANT GENOME,2017,10(2).
APA	Zhu, Cai-yon.,Liu, Wei.,Kang, Li-Fang.,Xu, Qin.,Xing, Shi-Lai.,...&Sang, Tao.(2017).Haplotypes Phased from Population Transcriptomes Detecting Selection in the Initial Adaptation of Miscanthus lutarioriparius to Stressful Environments.PLANT GENOME,10(2).
MLA	Zhu, Cai-yon,et al."Haplotypes Phased from Population Transcriptomes Detecting Selection in the Initial Adaptation of Miscanthus lutarioriparius to Stressful Environments".PLANT GENOME 10.2(2017).

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