Cargando…

Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China

Drought has become a critical environmental stress affecting on plant in temperate area. As one of the promising bio-energy crops to sustainable biomass production, the genus Miscanthus has been widely studied around the world. However, the most widely used hybrid cultivar among this genus, Miscanth...

Descripción completa

Detalles Bibliográficos
Autores principales: Nie, Gang, Tang, Lu, Zhang, Yajie, Huang, Linkai, Ma, Xiao, Cao, Xin, Pan, Ling, Zhang, Xu, Zhang, Xinquan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5432562/
https://www.ncbi.nlm.nih.gov/pubmed/28559912
http://dx.doi.org/10.3389/fpls.2017.00801
_version_ 1783236655093645312
author Nie, Gang
Tang, Lu
Zhang, Yajie
Huang, Linkai
Ma, Xiao
Cao, Xin
Pan, Ling
Zhang, Xu
Zhang, Xinquan
author_facet Nie, Gang
Tang, Lu
Zhang, Yajie
Huang, Linkai
Ma, Xiao
Cao, Xin
Pan, Ling
Zhang, Xu
Zhang, Xinquan
author_sort Nie, Gang
collection PubMed
description Drought has become a critical environmental stress affecting on plant in temperate area. As one of the promising bio-energy crops to sustainable biomass production, the genus Miscanthus has been widely studied around the world. However, the most widely used hybrid cultivar among this genus, Miscanthus × giganteus is proved poor drought tolerance compared to some parental species. Here we mainly focused on Miscanthus sinensis, which is one of the progenitors of M. × giganteus providing a comparable yield and well abiotic stress tolerance in some places. The main objectives were to characterize the physiological and photosynthetic respond to drought stress and to develop simple sequence repeats (SSRs) markers associated with drought tolerance by transcriptome sequencing within an originally collection of 44 Miscanthus genotypes from southwest China. Significant phenotypic differences were observed among genotypes, and the average of leaf relative water content (RWC) were severely affected by drought stress decreasing from 88.27 to 43.21%, which could well contribute to separating the drought resistant and drought sensitive genotype of Miscanthus. Furthermore, a total of 16,566 gene-associated SSRs markers were identified based on Illumina RNA sequencing under drought conditions, and 93 of them were randomly selected to validate. In total, 70 (75.3%) SSRs were successfully amplified and the generated loci from 30 polymorphic SSRs were used to estimate the genetic differentiation and population structure. Finally, two optimum subgroups of the population were determined by structure analysis and based on association analysis, seven significant associations were identified including two markers with leaf RWC and five markers with photosynthetic traits. With the rich sequencing resources annotation, such associations would serve an efficient tool for Miscanthus drought response mechanism study and facilitate genetic improvement of drought resistant for this species.
format Online
Article
Text
id pubmed-5432562
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-54325622017-05-30 Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China Nie, Gang Tang, Lu Zhang, Yajie Huang, Linkai Ma, Xiao Cao, Xin Pan, Ling Zhang, Xu Zhang, Xinquan Front Plant Sci Plant Science Drought has become a critical environmental stress affecting on plant in temperate area. As one of the promising bio-energy crops to sustainable biomass production, the genus Miscanthus has been widely studied around the world. However, the most widely used hybrid cultivar among this genus, Miscanthus × giganteus is proved poor drought tolerance compared to some parental species. Here we mainly focused on Miscanthus sinensis, which is one of the progenitors of M. × giganteus providing a comparable yield and well abiotic stress tolerance in some places. The main objectives were to characterize the physiological and photosynthetic respond to drought stress and to develop simple sequence repeats (SSRs) markers associated with drought tolerance by transcriptome sequencing within an originally collection of 44 Miscanthus genotypes from southwest China. Significant phenotypic differences were observed among genotypes, and the average of leaf relative water content (RWC) were severely affected by drought stress decreasing from 88.27 to 43.21%, which could well contribute to separating the drought resistant and drought sensitive genotype of Miscanthus. Furthermore, a total of 16,566 gene-associated SSRs markers were identified based on Illumina RNA sequencing under drought conditions, and 93 of them were randomly selected to validate. In total, 70 (75.3%) SSRs were successfully amplified and the generated loci from 30 polymorphic SSRs were used to estimate the genetic differentiation and population structure. Finally, two optimum subgroups of the population were determined by structure analysis and based on association analysis, seven significant associations were identified including two markers with leaf RWC and five markers with photosynthetic traits. With the rich sequencing resources annotation, such associations would serve an efficient tool for Miscanthus drought response mechanism study and facilitate genetic improvement of drought resistant for this species. Frontiers Media S.A. 2017-05-16 /pmc/articles/PMC5432562/ /pubmed/28559912 http://dx.doi.org/10.3389/fpls.2017.00801 Text en Copyright © 2017 Nie, Tang, Zhang, Huang, Ma, Cao, Pan, Zhang and Zhang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Nie, Gang
Tang, Lu
Zhang, Yajie
Huang, Linkai
Ma, Xiao
Cao, Xin
Pan, Ling
Zhang, Xu
Zhang, Xinquan
Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China
title Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China
title_full Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China
title_fullStr Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China
title_full_unstemmed Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China
title_short Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China
title_sort development of ssr markers based on transcriptome sequencing and association analysis with drought tolerance in perennial grass miscanthus from china
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5432562/
https://www.ncbi.nlm.nih.gov/pubmed/28559912
http://dx.doi.org/10.3389/fpls.2017.00801
work_keys_str_mv AT niegang developmentofssrmarkersbasedontranscriptomesequencingandassociationanalysiswithdroughttoleranceinperennialgrassmiscanthusfromchina
AT tanglu developmentofssrmarkersbasedontranscriptomesequencingandassociationanalysiswithdroughttoleranceinperennialgrassmiscanthusfromchina
AT zhangyajie developmentofssrmarkersbasedontranscriptomesequencingandassociationanalysiswithdroughttoleranceinperennialgrassmiscanthusfromchina
AT huanglinkai developmentofssrmarkersbasedontranscriptomesequencingandassociationanalysiswithdroughttoleranceinperennialgrassmiscanthusfromchina
AT maxiao developmentofssrmarkersbasedontranscriptomesequencingandassociationanalysiswithdroughttoleranceinperennialgrassmiscanthusfromchina
AT caoxin developmentofssrmarkersbasedontranscriptomesequencingandassociationanalysiswithdroughttoleranceinperennialgrassmiscanthusfromchina
AT panling developmentofssrmarkersbasedontranscriptomesequencingandassociationanalysiswithdroughttoleranceinperennialgrassmiscanthusfromchina
AT zhangxu developmentofssrmarkersbasedontranscriptomesequencingandassociationanalysiswithdroughttoleranceinperennialgrassmiscanthusfromchina
AT zhangxinquan developmentofssrmarkersbasedontranscriptomesequencingandassociationanalysiswithdroughttoleranceinperennialgrassmiscanthusfromchina