TranSNiPtomics Of Drought-Tolerance Signalling In Chickpea: Measuring The Expression Of The Drought-Responsive Allelome With Massive Analysis Of cDNA Ends (MACE)

Identification of favorite or adverse alleles is highly beneficial for molecular breeding. At GenXPro, we developed an allele-finding pipeline based on reduced complexity sequencing coupled with proprietary up- and down-stream techniques and in-house bioinformatics, that is coined MACE (Massive Analysis of cDNA Ends). In MACE, gene expression levels are measured by sequencing and counting a single tag originating from the 3’ end of mRNAs, a region with high density of sequence polymorphisms. By using unique molecule identifiers (TrueQuant technique, GenXPro-GmbH), PCR copies are eliminated from the dataset to reduce false positive SNPs and biased expression values. When compared to regular RNAseq, the focus onto this 3’-UT region increases the coverage by 10-20 fold and allows to reliably identify SNPs at comparably lower sequencing costs. Exemplarily, MACE analysis of separately bulked drought-sensitive and -tolerant RILS from a cross between the drought-sensitive ICC1882 and -tolerant ICC4959 chickpea lines revealed beneficial and detrimental alleles (as identified by SNPs in the 3’ Ends) as well as their expression-levels.  Allele-specific SNPs in the 3’-UTRs were identified together with gene expression levels, and new candidate genes for drought-tolerance  discovered.