transcript quantification of wheat homeologs

Triticum aestivum (Bread wheat) has a hexaploid AABBDD genome. The duplicated gene copies, called homeologs, from A, B and D subgenomes may have biased expression levels influencing the phenotype. Though there are different methods for transcripts quantification of homeolog genes, it remains unclear which method performs better given the same RNA-seq data set. To test this, RNA-seq data was collected from two bread wheat-related species, tetra Chinese Spring and Aegilops tauschii, which have tetraploid AABB and diploid DD genomes, respectively.