Genetic mapping of legume orthologs reveals high conservation of synteny between lentil species and the sequenced genomes of Medicago and chickpea

Abstract

Lentil (Lens culinaris Medik.) is a global food crop with increasing importance for food security in south Asia and other regions. Lens ervoides, a wild relative of cultivated lentil, is an important source of agronomic trait variation. Lens is a member of the galegoid clade of the Papilionoideae family, which includes other important dietary legumes such as chickpea (Cicer arietinum) and pea (Pisum sativum), and the sequenced model legume Medicago truncatula. Understanding the genetic structure of Lens spp. in relation to more fully sequenced legumes would allow leveraging of genomic resources. A set of 1107 TOG-based amplicons were identified in L. ervoides and a subset thereof used to design SNP markers for mapping. A map of L. ervoides consisting of 377 SNP markers spread across seven linkage groups was developed using a GoldenGate genotyping array and single SNP marker assays. Comparison with maps of M. truncatula and L. culinaris documented considerable shared synteny and led to the identification of a few major translocations and a major inversion that distinguish Lens from M. truncatula, as well as a translocation that distinguishes L. culinaris from L. ervoides. The identification of chromosome-level differences among Lens spp. will aid in the understanding of introgression of genes from L. ervoides into cultivated L. culinaris, furthering genetic research and breeding applications in lentil.

SNP-Based Linkage Mapping for Validation of QTLs for Resistance to Ascochyta Blight in Lentil

“…In the present study, comparative analysis was performed between the M. truncatula genome and the gene sequences associated with markers assigned on the consensus map. As previously reported (Sharpe et al, 2013; Gujaria-Verma et al, 2014; Kaur et al, 2014), direct and simple correspondences are observed between M. truncatula pseudomolecules and lentil LGs, although some evolutionary translocations and non-colinear relationships were also detected.…”

“…A number of genetic linkage maps have recently been developed for lentil, through the use of SSR and SNP marker technologies (Sharpe et al, 2013; Gujaria-Verma et al, 2014; Kaur et al, 2014). The cumulative lengths of maps from this study were marginally higher than those from previous studies (Sharpe et al, 2013; Kaur et al, 2014), possibly due to the effects of a higher number of map-assigned markers, or the genetic constitution of mapping populations (potentially influencing rates of recombination).…”

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

“…Gene discovery in lentil can also benefit from studying other legume crops. Lens is closely related to Medicago L. and Cicer L., and conserved synteny has been demonstrated among these three genera (Gujaria‐Verma et al., 2014). Shared chromosomal organization can facilitate gene searches in lentil; having the exome sequence data available for a diverse set of lines makes it possible to search for useful variants based on knowledge from other species.…”

QTLs for iron concentration in seeds of the cultivated lentil (Lens culinaris Medic.) via genotyping by sequencing

“…The total length of the linkage map was 497.1 cM in the current study. In previous lentil mapping studies, lengths of the linkage maps varied from 751 cM to 4060.6 cM (Eujayl et al, 1998;Rubeena et al, 2003;Duran et al, 2004;Hamwieh et al, 2005;Tanyolac et al, 2010;Gupta et al, 2012;De la Puente et al, 2013;Sharpe et al, 2013;Gujaria-Verma, 2014;Ates et al, 2016). The length of the map reported here was shorter than in these previous studies, but the value was close to the findings (751 cM) published by Hamwieh et al (2005).…”