Differential Gene Expression Analysis of Two Sorghum Bicolor Germplasm Accessions Representing Diverse Races

Diversity in cultivated Sorghum bicolor is represented by five diverse races with specific geographical adaptations. To understand underpinning genetic factors for these variations, we conducted an RNA-Seq experiment to study Differential Gene Expression (DGE) and Genome wide variants between two diverse sorghum accessions, viz., N13, an accession representing race durra and E36-1, an accession representing race caudatum. Total RNA from representative plants was extracted at nine growth stages, from germinating seed to mature dry grain. The total RNA samples were pooled across stages for each accession, processed and libraries were constructed in order to sequence mRNA using Illumina Genome Analyzer (Illumina GAIIx). A total of 5.1Gb (33.6 million reads) and 4.1Gb (27.5 million reads) high quality (at Q20) paired end data, respectively for N13 and E36-1, was generated with maximum 150bp read length. A transcriptome assembly was built using the reference annotations available through Phytozome v10 (Sorghum bicolor (BTx623)). Assembly generated 37K and 33K transcripts, respectively for N13 and E36-1. DGE analysis was carried out for the resulted assembly using Cuffdiff (version 2.2.1) with upper quartile FPKM normalization method. Out of all transcripts, we found 190 isoforms had significant expression, with 67 and 120 isoforms only in N13 and E36-1 samples, respectively. We propose to perform pathway analysis on the differentially expressed transcripts to generate expression profile heat-maps. For further genome-wide variant analysis, we will map the data against the reference genome and variations (SNPs and In-Dels) will be detected between the samples.