Genomic relationships among different Timor hybrid (Coffea L.) accessions as revealed by SNP identification and RNA-seq analysis

Abstract

The Timor hybrid (TH), a natural hybrid between C. arabica and C. canephora, is the main source of resistance to coffee leaf rust disease that has been used as progenitor during development of most of the modern Coffea arabica L. varieties. In this work a comparison of the introgression level of three accessions of the TH was conducted using massive RNAseq data analysis. To investigate the number of unigenes possibly impacted by introgression, the characterization and quantification of genome-derived SNPs were carried out on almost 20,000 unigenes. Overall results confirmed the CIFC1343 as the most introgressed accession of the TH when compared to either CIFC832-1 or CIFC832-2. Although less introgressed, the CIFC832-2 seems to be an interesting alternative for coffee breeders because it carries additional genome introgressions than observed for CIFC832-1. Our findings illustrate an alternative approach that use RNAseq data for SNP identification and interpretation in a polyploid species. © Springer International Publishing Switzerland 2014.