Fig. 1: Grafting coupled with RNA-seq to identify transcripts that move from tissue of one genotype/species/ecotype/cultivar into tissue of another across the graft junction.

Grafting-based strategy for identification of mRNAs that move from shoot (scion) to root (stock), from genotype 2 to genotype 1, using a scion:stock = genotype 2:genotype 1 heterograft. The same strategy can be used to identify transcripts that move from shoot to root from genotype 1 to genotype 2 using a genotype 1:genotype 2 graft. Transcripts that move root to shoot can be identified by analysing mRNAs in shoot tissue. Natural grafts, such as those established between the parasitic dodder plant and its host plants, can be used in place of artificial grafts. A key challenge in all such approaches is how to assign transcripts to each genotype; methods for doing so are based on (1) SNP identification or on (2) the alignment to different reference genomes. For grafts from the same species, or similar genotypes, SNPs can be used to distinguish between genotypes and thus identify the source genotype of each transcript (1). For grafts between different species, mapping (2) each RNA-seq read to the genome assemblies can be an effective method for determining which transcripts are specific to one species.