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

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.

The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high‐density linkage maps in comparative mapping and synteny analysis

“…However, little is known about the underlying resistance mechanisms available against E. pisi in these species. In L. cicera, three quantitative trait loci (QTLs) for partial resistance against E. pisi, explaining 8.2 to 13% of the phenotypic variation, were recently identified (Santos, Martins, Rubiales, & Vaz Patto, 2020), suggesting that partial resistance to powdery mildew in L. cicera has an oligogenic genetic basis. Conversely, in L. sativus, nothing is known about the genetic basis of the detected partial resistance against E. pisi.…”

“…Furthermore, histological and molecular studies should reveal the role of MLO genes in Lathyrus' partial resistance to E. pisi or to other diseases. Indeed, some MLO transcripts were found to be downregulated in partially resistant L. sativus and L. cicera genotypes upon rust infection (Uromyces pisi) (Almeida et al, 2014;Santos et al, 2018), suggesting their involvement in the rust response of Lathyrus. Among higher plants, the MLO family members are proteins with 30 invariable amino-acids (Elliott et al, 2005) and seven conserved trans-membrane domains localized at the cell membrane that have been phylogenetically grouped into seven clades (I to VII) (Acevedo-Garcia, Kusch, & Panstruga, 2014;Rispail & Rubiales, 2016).…”

“…The first published L. cicera genetic linkage map was constructed for a recombinant inbred line (RIL) population segregating for powdery mildew (E. pisi) and rust (U. pisi) resistance (Vaz Patto et al, 2006;Vaz Patto, Fernández-Aparicio, Moral, & Rubiales, 2009), using simple sequence repeat (SSR) and SNP (single nucleotide polymorphism) molecular markers (Santos et al, 2018). This genetic map was recently improved by the incorporation of new markers obtained by Diversity Arrays Technology combined with next-generation sequencing (DArTseq), a high throughput marker genotyping platform that has been successfully used for the identification of QTLs for partial resistance to powdery mildew (Santos et al, 2020). In L. sativus, the first genetic linkage map was obtained with a F 2 population genotyped mainly with random amplified polymorphic DNA markers (Chowdhury & Slinkard, 1999).…”

“…The L. cicera parental genotypes shows contrasting responses against E. pisi. BGE023542 is partially resistant with a high infection type of 4 (compatible reaction with no visible necrosis) and a reduced disease severity of 9 to 18.5%, scored as the percentage of leaf area coverage by mycelia, and BGE008277 is susceptible (infection type = 4, disease severity = 39-48%) (Santos et al, 2020;Vaz Patto et al, 2007). Raipur-4 and LS87-124-4-1 are both partially resistant against E. pisi infection, both with infection type = 4 and low disease severity (5.5 and 7.5% for Raipur-4 and LS87-124-4-1, respectively) (D.C. Martins, personal communication, 2020).…”

Grass pea (Lathyrus sativus L.): orphan crop, nutraceutical or just plain food?

“…Functional categorization associated these genes with processes involved in biotic/ abiotic stress, cell wall metabolism, and hormone signalling (Almeida et al 2015). Very recently, the L. cicera transcriptome was investigated in response to rust (Uromyces pisi) and different types of molecular markers were developed to construct the first L. cicera linkage map with potential for genetic mapping of resistance in this robust species and its most closely related species L. sativus (Santos et al 2018).…”