Cataloging Natural Allelic Variations in Switchgrass (Panicum virgatum L.) NAM Parental Genomes

Switchgrass has been identified as a potential species for cellulosic ethanol production by the U.S. Department of Energy. Application of molecular breeding techniques to improve biomass production for this species are limited because only limited markers/linkage maps are available. A Nested Association Mapping (NAM) population of switchgrass was developed for deciphering natural allelic variations for biomass yield and quality traits. Fifteen diverse parents were crossed to a recurrent parent, AP13. Subsequently, 10 F₁s from each family were chain crossed to develop a NAM population of 2,000 genotypes. We observed significant within and among population variation for morphological characteristics and biomass yield in the NAM population. All 15 parental genotypes were sequenced via shotgun sequencing in collaboration with the JGI. On average we received 28-66 Gb high-quality sequence data from each parent. Alignment of the parental sequences with the reference AP13 genome revealed that up to 98.87% of the genomic sequences can be mapped to the reference genome. We cataloged 12.54 million SNPs in the 18 chromosomes of a tetraploid switchgrass genome. On an average one SNP was identified for every 80 (in Chromosome I-a) to 100 bp (in Chromosome VIII-b) of chromosome sequence in the NAM parental genomes. Regional fluctuations were observed in the SNP density within each chromosome. The parent, PI 421521-2, produced the highest number (12.45 million) of SNPs whereas, the least SNPs (9.33 million) were observed in PI 442535. Detail results of the SNP analysis will be present in the poster.