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

Author
item BAHRI, BOCHRA - University Of Georgia
item DAVERDIN, GUILLAUME - University Of Georgia
item Xu, Xiangyang
item CHENG, JAN-FANG - Joint Genome Institute
item BARRY, KERRIE - Joint Genome Institute
item BRUMMER, CHARLES - University Of California
item DEVOS, KATRIEN - University Of Georgia

Submitted to: BMC Evolutionary Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/1/2017
Publication Date: 6/14/2018
Citation: Bahri, B.A., Daverdin, G., Xu, X., Cheng, J., Barry, K.W., Brummer, C.E., Devos, K.M. 2018. Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.). BMC Evolutionary Biology. 18:91 20 p. https://doi.org/10.1186/s12862-018-1193-2.
DOI: https://doi.org/10.1186/s12862-018-1193-2

Interpretive Summary: Switchgrass, an allotetraploid (2n = 4x = 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. We studied single nucleotide polymorphism (SNP) variation in 12 genes putatively involved in biomass production, and 251 SNPs were identified in 36 accessions. The most frequent SNPs were fixed in homozygous state in these accessions. Sixty percent of the exonic SNPs were non-synonymous and, of these, 45% led to amino acids with altered properties. Our results also suggested that PhyB, a gene involved in photoperiod response, was under positive selection in the switchgrass population. PhyB carried a SNP leading to an amino acid change, and may play a role in the differential adaptation of upland and lowland switchgrass. The SNPs identified in this study can be widely used in switchgrass breeding aimed at improving biomass.

Technical Abstract: Switchgrass (Panicum virgatum L.), an allotetraploid (2n = 4x = 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. We studied single nucleotide polymorphism (SNP) variation in 372 switchgrass genotypes belonging to 36 accessions for 12 genes putatively involved in biomass production. A total of 11,682 SNPs were mined from about 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 fixed in homozygous state in the accessions. Sixty percent of the exonic SNPs were non-synonymous and, of these, 45% led to amino acids with altered properties. 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. 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.