Glume Transcriptome Profiling in Wild vs. Domesticated Tetraploid Wheat

Plant and animal domestication is considered a major event in the development of agriculture and subsequent emergence of ancient civilizations. Reduced glume toughness has been a major component of wheat domestication. We performed comparative transcriptome profiling (RNAseq analysis) of wheat glumes, from wild emmer wheat (W), the progenitor of domesticated wheat, and domesticated tetraploid wheat, including landraces (L) and cultivars (C). We aligned 147.7 million pair-end reads to the A and B genomes, using the whole chromosome survey sequences of wheat (IWGSC; http://www.wheatgenome.org) and identified 194,893 transcripts, of which 73,150 were expressed in common in the three wheat groups. Differentially expressed genes (DEGs) were identified (FDR adjusted p-value<0.05 and log₂foldchange (FC)≥1): 1,745 between W vs. C; 1357 between W vs. L, and 1277 between C vs. L. In total, 37%, 40% and 34% DEGs, respectively, were uniquely expressed in only one of the groups and mostly had relatively low expression level. Annotation and gene ontology analyses revealed putative gene function for only 30-34% of the DEGs in all comparisons. Among the highly expressed DEGs in W we have identified genes that are involved in cell wall biosynthesis (cellulose synthase), lignin (phenylalanine ammonia lyase, flavonol 4-sulfotransferase, 4-coumarate: CoA ligase), pectin (pectin lyse) and wax (CER1) and may contribute to the much higher mechanical strength of wild wheat glumes. In summary, our glume transcriptome analysis provides valuable information on genes that may have been involved in wheat evolution under domestication.