Single Nucleotide Polymorphism (SNP) Variation in Switchgrass (Panicum virgatum) for Genes Involved in Biomass Production

Switchgrass (Panicum virgatum L.), an allotetraploid perennial C4 grass 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 SNP variation in 372 genotypes belonging to 36 accessions for 11 genes involved in biomass production. Fifty four primer pairs, each spanning ~1 kb regions, were designed against the 11 genes. Amplicons were pooled per genotype and sequenced. A total of 332 M of raw Illumina reads were generated of which 162 M mapped to the switchgrass reference sequence (average coverage: 50X). Only 216 of the 11,682 SNPs detected in 53,739 bp of sequence data remained 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 the accessions. On average, 2/3 of SNPs in exons were non-synonymous and, of these, 50% resulted in non-conservative amino acid substitutions. One of the 21 non-conservative amino acid substitutions is located in a PAD domain in Phytochrome B, a gene involved in photoperiod response.  PAD domains act as sensors for light and oxygen. This amino acid substitution locally changed the polarity and charge, and may modify the three-dimensional structure of the protein and, hence, possible also its activity. Correlation of this SNP with flowering time phenotypes was observed. Further analyses are needed to determine whether Phytochrome B plays a role in the differential adaptation of upland and lowland switchgrass.