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

文献类型：期刊论文

作者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, Tao11
刊名PLANT GENOME
出版日期2017
卷号10期号:2
ISSN号1940-3372
DOI10.2135/cropsci2016.08.0673
文献子类Article
英文摘要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.
学科主题Agriculture
出版地MADISON
WOS关键词ENERGY CROP ; ARABIDOPSIS-THALIANA ; C-4 PHOTOSYNTHESIS ; DOG DOMESTICATION ; FINGER PROTEINS ; COLD TOLERANCE ; X GIGANTEUS ; DIVERSITY ; SEQUENCE ; GENE
语种英语
WOS记录号WOS:000408534800007
出版者CROP SCIENCE SOC AMER
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]
源URL[http://ir.ibcas.ac.cn/handle/2S10CLM1/22289]  
专题植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文
作者单位1.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
2.[Kang, Li-Fang
3.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China
4.Chinese Acad Sci, Inst Bot, Beijing Bot Garden, Beijing 100093, Peoples R China
5.Chinese Acad Sci, Wuhan Bot Garden, Key Lab Plant Germplasm Enhancement & Spacialty A, Wuhan 430074, Hubei, Peoples R China
6.[Yan, Juan
7.Fan, Yang-Yang
8.[Zhu, Cai-yon
9.Liu, Wei
10.Xu, Qin
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).

入库方式： OAI收割

来源：植物研究所

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