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Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)
BACKGROUND: Advances in genomic technologies have expanded our ability to accurately and exhaustively detect natural genomic variants that can be applied in crop improvement and to increase our knowledge of plant evolution and adaptation. Switchgrass (Panicum virgatum L.), an allotetraploid (2n = 4×...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6000970/ https://www.ncbi.nlm.nih.gov/pubmed/29898656 http://dx.doi.org/10.1186/s12862-018-1193-2 |
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author | Bahri, Bochra A. Daverdin, Guillaume Xu, Xiangyang Cheng, Jan-Fang Barry, Kerrie W. Brummer, E. Charles Devos, Katrien M. |
author_facet | Bahri, Bochra A. Daverdin, Guillaume Xu, Xiangyang Cheng, Jan-Fang Barry, Kerrie W. Brummer, E. Charles Devos, Katrien M. |
author_sort | Bahri, Bochra A. |
collection | PubMed |
description | BACKGROUND: Advances in genomic technologies have expanded our ability to accurately and exhaustively detect natural genomic variants that can be applied in crop improvement and to increase our knowledge of plant evolution and adaptation. Switchgrass (Panicum virgatum L.), an allotetraploid (2n = 4× = 36) perennial C4 grass (Poaceae family) native to North America and a feedstock crop for cellulosic biofuel production, has a large potential for genetic improvement due to its high genotypic and phenotypic variation. In this study, we analyzed single nucleotide polymorphism (SNP) variation in 372 switchgrass genotypes belonging to 36 accessions for 12 genes putatively involved in biomass production to investigate signatures of selection that could have led to ecotype differentiation and to population adaptation to geographic zones. RESULTS: A total of 11,682 SNPs were mined from ~ 15 Gb of sequence data, out of which 251 SNPs were retained after filtering. Population structure analysis largely grouped upland accessions into one subpopulation and lowland accessions into two additional subpopulations. The most frequent SNPs were in homozygous state within accessions. Sixty percent of the exonic SNPs were non-synonymous and, of these, 45% led to non-conservative amino acid changes. The non-conservative SNPs were largely in linkage disequilibrium with one haplotype being predominantly present in upland accessions while the other haplotype was commonly present in lowland accessions. Tajima’s test of neutrality indicated that PHYB, a gene involved in photoperiod response, was under positive selection in the switchgrass population. PHYB carried a SNP leading to a non-conservative amino acid change in the PAS domain, a region that acts as a sensor for light and oxygen in signal transduction. CONCLUSIONS: Several non-conservative SNPs in genes potentially involved in plant architecture and adaptation have been identified and led to population structure and genetic differentiation of ecotypes in switchgrass. We suggest here that PHYB is a key gene involved in switchgrass natural selection. Further analyses are needed to determine whether any of the non-conservative SNPs identified play a role in the differential adaptation of upland and lowland switchgrass. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12862-018-1193-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6000970 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-60009702018-06-26 Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.) Bahri, Bochra A. Daverdin, Guillaume Xu, Xiangyang Cheng, Jan-Fang Barry, Kerrie W. Brummer, E. Charles Devos, Katrien M. BMC Evol Biol Research Article BACKGROUND: Advances in genomic technologies have expanded our ability to accurately and exhaustively detect natural genomic variants that can be applied in crop improvement and to increase our knowledge of plant evolution and adaptation. Switchgrass (Panicum virgatum L.), an allotetraploid (2n = 4× = 36) perennial C4 grass (Poaceae family) native to North America and a feedstock crop for cellulosic biofuel production, has a large potential for genetic improvement due to its high genotypic and phenotypic variation. In this study, we analyzed single nucleotide polymorphism (SNP) variation in 372 switchgrass genotypes belonging to 36 accessions for 12 genes putatively involved in biomass production to investigate signatures of selection that could have led to ecotype differentiation and to population adaptation to geographic zones. RESULTS: A total of 11,682 SNPs were mined from ~ 15 Gb of sequence data, out of which 251 SNPs were retained after filtering. Population structure analysis largely grouped upland accessions into one subpopulation and lowland accessions into two additional subpopulations. The most frequent SNPs were in homozygous state within accessions. Sixty percent of the exonic SNPs were non-synonymous and, of these, 45% led to non-conservative amino acid changes. The non-conservative SNPs were largely in linkage disequilibrium with one haplotype being predominantly present in upland accessions while the other haplotype was commonly present in lowland accessions. Tajima’s test of neutrality indicated that PHYB, a gene involved in photoperiod response, was under positive selection in the switchgrass population. PHYB carried a SNP leading to a non-conservative amino acid change in the PAS domain, a region that acts as a sensor for light and oxygen in signal transduction. CONCLUSIONS: Several non-conservative SNPs in genes potentially involved in plant architecture and adaptation have been identified and led to population structure and genetic differentiation of ecotypes in switchgrass. We suggest here that PHYB is a key gene involved in switchgrass natural selection. Further analyses are needed to determine whether any of the non-conservative SNPs identified play a role in the differential adaptation of upland and lowland switchgrass. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12862-018-1193-2) contains supplementary material, which is available to authorized users. BioMed Central 2018-06-14 /pmc/articles/PMC6000970/ /pubmed/29898656 http://dx.doi.org/10.1186/s12862-018-1193-2 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Bahri, Bochra A. Daverdin, Guillaume Xu, Xiangyang Cheng, Jan-Fang Barry, Kerrie W. Brummer, E. Charles Devos, Katrien M. Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.) |
title | Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.) |
title_full | Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.) |
title_fullStr | Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.) |
title_full_unstemmed | Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.) |
title_short | Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.) |
title_sort | natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (panicum virgatum l.) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6000970/ https://www.ncbi.nlm.nih.gov/pubmed/29898656 http://dx.doi.org/10.1186/s12862-018-1193-2 |
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