Massive Analysis Of cDNA Ends (MACE): Simultaneous Genotyping & Transcriptomics (=TranSNiPtomics) Reveals Gene Expression and Polymorphic Molecular Markers For Barley Yellow Dwarf Virus (BYDV) Resistance

Massive Analysis of cDNA Ends (MACE) is a reduced-complexity sequencing strategy for the simultaneous analysis of gene expression and genic polymorphisms. Here MACE was used to examine the resistance mechanism to Barley Yellow Dwarf Virus (BYDV) which was introgressed from the wild species Hordeum bulbosum (barleys secondary genepool) to barley chromosome 3HL. A BC₂F₄ mapping population was used to establish a molecular-marker map to for the yet unknown resistance gene coined Ryd4^Hb. Besides quantitative gene expression data in response to the virus, MACE in combination with bulked segregant analysis revealed more than 200 resistance-specific markers most of which are located within the segment introgressed from H. bulbosum at the tip of 3HL . Three MACE markers were located at a distance of 0.1 to  0.5 cM to Ryd4^Hb and will be useful for marker assisted selection in breeding programs and for the isolation of the resistance gene itself.  The same bulks were analysed by RNAseq which produced approx. 3 times more markers, however at a more than 10 times higher sequencing depth. These results demonstrate the cost-efficiency of MACE for the utilization of wild germplasm for crop improvement.