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Title: Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)

Abstract

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 withmore » 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.« less

Authors:
ORCiD logo [1];  [2];  [2];  [3];  [3];  [4];  [2]
  1. Univ. of Georgia, Athens, GA (United States). Dept. of Crop and Soil Sciences; Univ. of Carthage,Tunis (Tunisia). Laboratory of Bioaggressors and Integrated Protection in Agriculture
  2. Univ. of Georgia, Athens, GA (United States). Dept. of Crop and Soil Sciences
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Univ. of California, Davis, CA (United States). Plant Sciences Dept.
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1559793
Alternate Identifier(s):
OSTI ID: 1544018
Grant/Contract Number:  
AC02-05CH11231; PS02-06ER64304
Resource Type:
Accepted Manuscript
Journal Name:
BMC Evolutionary Biology (Online)
Additional Journal Information:
Journal Name: BMC Evolutionary Biology (Online); Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1471-2148
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Evolutionary Biology; Genetics & Heredity

Citation Formats

Bahri, Bochra A., Daverdin, Guillaume, Xu, Xiangyang, Cheng, Jan-Fang, Barry, Kerrie W., Brummer, E. Charles, and Devos, Katrien M. Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.). United States: N. p., 2018. Web. doi:10.1186/s12862-018-1193-2.
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.). United States. doi:https://doi.org/10.1186/s12862-018-1193-2
Bahri, Bochra A., Daverdin, Guillaume, Xu, Xiangyang, Cheng, Jan-Fang, Barry, Kerrie W., Brummer, E. Charles, and Devos, Katrien M. Thu . "Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)". United States. doi:https://doi.org/10.1186/s12862-018-1193-2. https://www.osti.gov/servlets/purl/1559793.
@article{osti_1559793,
title = {Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)},
author = {Bahri, Bochra A. and Daverdin, Guillaume and Xu, Xiangyang and Cheng, Jan-Fang and Barry, Kerrie W. and Brummer, E. Charles and Devos, Katrien M.},
abstractNote = {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.},
doi = {10.1186/s12862-018-1193-2},
journal = {BMC Evolutionary Biology (Online)},
number = 1,
volume = 18,
place = {United States},
year = {2018},
month = {6}
}

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