Genomic Variation Analysis of Switchgrass (Panicum virgatum L.) NAM (Nested Association Mapping) Parents
Ali, Shahjahan, M. Saha, L. Bartley, D. Serba, and H. Bhandari.  2016.  Proceedings, Crop Science Society of America, Annual Meeting (6-9 Nov, 2016), Phoenix, AZ.

NAM (Nested Association Mapping) has been established as an efficient and powerful method for association mapping and QTL analysis. It offers benefits of both bi-parental and association mapping to dissect complex traits. We have generated 2,000 pseudo F2 NAM population by crossing 15 switchgrass low land ecotypes with a common parent, AP13. This population is currently being evaluated in Ardmore, OK and Knoxville, TN locations along with pseudo F1 and parents. We used whole genome sequencing approach to delineate allelic variations with in NAM parental genomes. Genomic shotgun sequencing NAM parental genomes produced 28-66 Gb high-quality sequence data. Alignment of these sequences with the reference genome, AP13 (v3.0), revealed that up to 99.00% of the genomic sequences mapped to the AP13 genome. The parent, NFGA16_05, produced the highest number (9.94 million) of polymorphic loci whereas, the least polymorphic loci (6.43 million) were observed in NFGA09_02. We cataloged 27.78 million bi-allelic SNPs in the 18 chromosomes of a tetraploid switchgrass genome. On an average one SNP was identified in every 48 to 64 bp of chromosome sequence of the NAM parental genomes. The ration of intronic to exonic SNPs was 1.72. We have identified 1.09 million nonsynonymous SNPs in the exonic regions of NAM parental genomes with 7,128 SNP dense genes.