A Lens map was developed based on the segregational analysis of five kinds of molecular and morphological genetic markers in 113 F(2) plants obtained from a single hybrid of Lens culinaris ssp. culinaris x L. c. ssp. orientalis. A total of 200 markers were used on the F(2) population, including 71 RAPDs, 39 ISSRs, 83 AFLPs, two SSRs and five morphological loci. The AFLP technique generated more polymorphic markers than any of the others, although AFLP markers also showed the highest proportion (29.1%) of distorted segregation. At a LOD score of 3.0, 161 markers were grouped into ten linkage groups covering 2,172.4 cM, with an average distance between markers of 15.87 cM. There were six large groups with 12 or more markers each, and four small groups with two or three markers each. Thirty-nine markers were unlinked. A tendency for markers to cluster in the central regions of large linkage groups was observed. Likewise, clusters of AFLP, ISSR or RAPD markers were also observed in some linkage groups, although RAPD markers were more evenly spaced along the linkage groups. In addition, two SSR, three RAPD and one ISSR markers segregated as codominant. ISSR markers are valuable tools for Lens genetic mapping and they have a high potential in the generation of saturated Lens maps.

Lentil quantitative trait loci (QTL) related to plant structure (branches at first node, height of first node, total number of branches, plant height), growth habit (flowering time, pod dehiscence) and yield (number of seeds, seed weight, seed diameter) were located using a F2 population of 113 individuals derived from the intersubspecific cross of Lens culinaris ssp. culinaris and L. c. ssp. orientalis. Several traits were found to be significantly correlated. Using interval and composite interval mapping a total of 23 QTL for nine quantitative traits were located. No QTL was identified for the number of F3 seed produced. Six QTL were positioned respectively in linkage groups III and VI, and five QTL in linkage group I. Each remaining group included one or two QTL, except groups VII and IX where no QTL was found. The multiple QTL model explained more than 80% of the observed phenotypic variance with logarithm of the odds (LOD) scores above 10 for three of the quantitative traits analyzed (branches at first node, flowering time, and dehiscence). For the remaining traits the phenotypic variance explained was relatively low, between the 50% and 20%, and the LOD scores ranged between 4 and 8. The possible homology between some QTL and other previously described is discussed in relation to their chromosomal location.

Four different hybridization experiments were carried out to obtain interspecific hybrids with Spanish cultivars of lentil (Lens culinaris M.). In hybridization experiments I and II, undertaken with only pollination and pollination with the addition of gibberellic acid after fertilization, respectively, no lentil hybrids were recovered. A single interspecific hybrid with L. odemensis was obtained in experiment III using the embryo rescue protocol of Cohen et al. (1984), in this case, a crossing efficiency of 0.11% and a rescue efficiency of 2.5% were obtained. Hybridization experiment IV used a specific embryo rescue protocol developed in this study. In this experiment, ovule-embryos of 18 DAP were cultured on MS salts with 1% sucrose and 1 μM IAA + 0.8 μM KN; after two weeks, embryos were released from the ovular integuments and cultured on the same medium for another two weeks in upright position. Afterwards, the embryos were transferred to test tubes containing the same medium and one month later plantlets were obtained. Using the above protocol, out of a total of 1707 pollinations, 6 interspecific hybrids with L. odemensis, 2 with L. nigricans and one with L. ervoides were recovered, yielding on average a crossing efficiency of 0.53% and an average rescue efficiency of 8.26%. Taking into consideration only the interspecific crossing blocks in which hybrids were recovered, the crossing efficiency with L. odemensis was 9%, while with both L. nigircans and L. ervoides the crossing efficiencies were 3%. Rescue efficiencies based on hybrids recovered per number of ovules cultured ranged between 50-100%.

This chapter describes the history, taxonomy (morphological and molecular), centre of origin, spread of culture, and evolution of the cultivated forms of lentil. Lentils were domesticated, in the Near East or, more accurately, in the foothills of the mountains of southern Turkey and northern Syria. The raw materials were populations of orientalis, but primitive farmers could also have used some other species of the genus, whose similarity has been shown in this chapter, in mixed populations rather than in pure strands. But orientalis and odemensis forms are the most likely candidates to have been companion weeds of the cultigen. However, molecular marker analyses have indicated that the genetic variability within cultivated lentils is relatively low, which supports the idea that microsperma and macrosperma morphotypes are simple variants for quantitative traits resulting from disruptive selection. It is difficult to establish how much the wild relatives have contributed to the cultigen gene pool.

Usage of high-throughput sequencing approaches allow for the generation and characterization of reference transcriptome datasets that support gene-based marker discovery, which in turn can be used to build genetic maps among other purposes. We have obtained a transcriptome assembly including 49,453 genes for the lentil ( Lens culinaris Medik.) cultivar Alpo using RNAseq methodology. This transcriptome was used as reference to obtain 6,306 quality polymorphic markers (SNPs and short indels) analyzing genotype data from a RIL population at F 7 generation derived from the interspecific cross between L . culinaris cv. Alpo and L . odemensis accession ILWL235. L . odemensis is a wild species included in the secondary gene pool and can be used as a source for gene introgression in lentil breeding programs. Marker data were used to construct the first genetic interspecific map between these two species. This linkage map has been used to precisely identify regions of the CDC-Redberry lentil draft genome in which the candidate genes for some qualitative traits (seed coat spotting pattern, flower color, and stem pigmentation) could be located. The genome regions corresponding to a significant single quantitative trait locus (QTL) controlling “time to flowering” located in chromosome 6 and three QTLs regulating seed size and positioned in chromosomes 1 and 5 (two QTLs) were also identified. Significant QTLs for Ascochyta blight resistance in lentil were mapped to chromosome 6 in the genome region or close to it where QTLs for Ascochyta blight resistance have previously been reported.