Diversity and Exome Variation in Saccharum Spp

Sugarcane cultivars have a narrow genetic basis mostly due to an under-utilization of genetic sources. The genetic variation of Saccharum spp., including 1186 accessions in the World Collection of Sugarcane and Related Grasses (WCSRG), maintained by USDA comprising 16 species collected from 45 different countries was assessed.  A wide range of phenotypic variance and a total gene diversity of 0.304 in a range of 0 to 0.5 were revealed. The WCSRG was grouped into three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in a second cluster, and mostly non-Saccharum spp. in a third cluster. To investigate the sequence variation, 12 phenotypically diverse accessions with chromosome number ranged from 48 to 115, representing nine different species were selected for exome sequencing through a hybridization-based target enrichment approach. In total 55,946 120-mer probes targeting approximately 14 thousand genes and spanning 6.7 Mb sequence regions were designed from gene sequences of sugarcane and sorghum to capture the exome region of the 12 accessions. Deep sequencing of captured fragments generated 411 million reads with 83% of the cleaned reads aligned to the sorghum genome. Approximately 115 thousands of SNPs (1/5,723 bases) were called and majority (96.7%) of them were synonymous and existed in the non-coding regions of the exome. The exome sequences of a diverse panel of accessions can generate a catalog of genetic variation of sugarcane to be used in association studies for complicated traits dissection, in plant breeding, and in polyploidy evolutionary sciences.