Whole-Genome Comparative Analysis of Cultivated S. bicolor and its Perennial Relative S. propinquum using a Next-Generation Sequencing Approach

Currently, 70% of global land regions used for crop production supports annual species, and two-thirds of this land is at high-risk for soil erosion.  Perennial relatives of annual crops are considerably more environmentally friendly, due to their rhizomatous root systems and efficient nutrient use due to high root to leaf densities.  In light of the above, there have been recent initiatives for the development of perennial grains for use as alternative crops on both current agricultural lands, in addition to less arable lands that do not currently support crop production.  Sorghum, a robust and morphologically diverse genus of herbaceous grasses, contains both perennials and annuals, and therefore, provides an excellent model system for the study of perenniality.  The cultivated annual grain S. bicolor is well characterized, and a high-quality genome sequence is available (BTx623).  Additionally, S. bicolor forms fertile hybrids with its wild perennial relative S. propinquum, making these two species a good model for studies aimed at elucidating the genetic underpinnings of traits associated with perenniality. Therefore, we have generated ~15 Gb of genomic sequence for S. propinquum accession PI653737 using Illumina HiSeq technology and assembled these data to the S. bicolor reference.  After quality filter/trimming, over 270 million reads uniquely aligned producing 20.33X coverage (17.12X mean depth) and covering 91.2% of the reference BTx623 genome.  Filtered SNP-calling produced over 2.6 million SNPs.  SNP distribution, particularly with respect to known QTL, and presence/absence variation in gene content will be discussed.