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

Carmen Santos,Peter Winter,Björn Rotter,Mara Lisa Alves,Nuno Felipe Almeida,Diego Rubiales,Ralf Horres,Susana Trindade Leitão,Maria Carlota Vaz Patto,Nicolas Krezdorn,Thaïs Aznar-Fernández

doi:10.1038/s41438-018-0047-9

Abstract

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.

Highlights

Introduction Lathyrus ciceraL., the chickling pea, is an annual legume belonging to the tribe Fabeae[1,2]
We investigate the transcriptomes of control and rust-inoculated leaves from two L. cicera genotypes, with contrasting quantitative resistance to rust, to achieve several aims, such as the following: (i) to develop novel expressed simple sequence repeat (E-SSR) and single-nucleotide polymorphism (SNP)-based molecular markers for future mapping and diversity studies in L. cicera, (ii) to examine the differential expression of allelic variants in the two contrasting genotypes after rust inoculation and, based on the SNP information within candidate alleles, (iii) to develop appropriate assays for future quantitative trait loci (QTL)/expression QTL analysis for rust resistance in L. cicera
Detected 297 potential polymorphic E-SSRs and 19,223 SNPs in more than 5,000 transcripts and tested exemplarily whether these could be converted into molecular markers for later use in molecular breeding and their usefulness in the development of the first L. cicera linkage map

Summary

Introduction

L., the chickling pea, is an annual legume belonging to the tribe Fabeae[1,2]. It is mainly grown as feedstock, both as fodder and grain[3]. L. cicera adapts well to harsh environments. It is resistant to drought, waterlogging[5] and to several important legume pathogens. Sources for resistance to rust[6], powdery mildew[7], bacterial blight[8] and crenate broomrape[9] have been identified. L. cicera is a good option for cropping systems in marginal lands and can function as a source of resistance genes for transfer to related species such as pea[10]

Methods

Results

Discussion

Conclusion