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The  Lathyrus cicera  transcriptome was analysed in response to rust ( Uromyces pisi ) infection to develop novel molecular breeding tools with potential for genetic mapping of resistance in this robust orphan legume species. One RNA-seq library each was generated from control and rust-inoculated leaves from two  L. cicera  genotypes with contrasting quantitative resistance,  de novo  assembled into contigs and sequence polymorphisms were identified.  In toto , 19,224 SNPs differentiate the susceptible from the partially resistant genotype’s transcriptome. In addition, we developed and tested 341 expressed E-SSR markers from the contigs, of which 60.7% varied between the two  L. cicera  genotypes. A first  L. cicera  linkage map was created using part of the developed markers in a RIL population from the cross of the two genotypes. This map contains 307 markers, covered 724.2 cM and is organised in 7 major and 2 minor linkage groups, with an average mapping interval of 2.4 cM. The genic markers also enabled us to compare their position in  L. cicera  map with the physical position of the same markers mapped on  Medicago truncatula  genome, highlighting a high macrosyntenic conservation between both species. This study provides a large new set of genic polymorphic molecular markers with potential for mapping rust resistances. It represents the first step towards genomics-assisted precision breeding in  L. cicera .

First genetic linkage map of Lathyrus cicera based on RNA sequencing-derived markers: Key tool for genetic mapping of disease resistance