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

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

Classifying lentil testa (seedcoat) phenotypes using unsupervised learning

NSERC/CRSNGLentils have different seed coat colours and patterns. Accurate classification of lentils by testa patterns helps plant scientists understand the genetics of seed coats in lentils. Computers can be used for this analysi

Generation and validation of genetic markers for the selection of carioca dry bean genotypes with the slow-darkening seed coat trait

Slow darkening (SD) is a trait that helps to maintain a brighter seed coat appearance in certain market classes of dry beans. The aim of this study was to generate new fluorescence-based markers and validate previously identified microsatellite markers for linkage to the SD trait in lines of the carioca market class. Four segregating populations were generated by Embrapa, the Brazilian Agricultural Research Corporation, from crosses between the SD cultivar BRSMG Madrepe´rola and the regular-darkening cultivars BRS Estilo, BRS Cometa, BRS Nota´vel and BRS Sublime. These populations were screened with the simple-sequence markers Pvsd- 1158 and PVM02TC116 and with a TaqManTM marker designed for the single-nucleotide polymorphism (SNP) PvbHLHp12804. A KASP marker was also designed for the PvbHLHp12804 marker for testing on advanced carioca lines developed by the University of Saskatchewan. In the carioca lines developed by Embrapa, PVM02TC116 proved unsuitable for marker-assisted selection (MAS). Both the Pvsd-1158 and PvbHLHp12804 markers were found to be tightly linked to the gene responsible for the SD trait, with genetic distances calculated at 2.8 cM for Pvsd-1158 and 2.0 and 3.1 cM for PvbbHLHp12804, respectively. These markers presented more than 97% of selection efficiency. The genotypic scoring using the PvbHLHp12804 KASP marker was perfectly correlated with the phenotype in all lines of the University of Saskatchewan. The results of this study validates the use of Pvsd-1158 as a gel-based marker for SD in carioca beans. The new fluorescence-based SNP PvbHLHp12804 markers exhibited very tight linkage to SD in carioca and pinto bean lines. These markers will be ideal for MAS for the SD trait in these market classes

Understanding photothermal interactions will help expand production range and increase genetic diversity of lentil (Lens culinaris Medik.)

Lentil is a staple in many diets around the world and growing in popularity as a quick-cooking, nutritious, plant-based source of protein in the human diet. Lentil varieties are usually grown close to where they were bred. Future climate change scenarios will result in increased temperatures and shifts in lentil crop production areas, necessitating expanded breeding efforts. We show how we can use a daylength and temperature model to identify varieties most likely to succeed in these new environments, expand genetic diversity, and give plant breeders additional knowledge and tools to help mitigate these changes for lentil producers.This research was conducted as part of the ‘Application of Genomics to Innovation in the Lentil Economy (AGILE)' project funded by Genome Canada and managed by Genome Prairie. We are grateful for the matching financial support from the Saskatchewan Pulse Growers, Western Grains Research Foundation, the Government of Saskatchewan, and the University of Saskatchewan. We acknowledge the support from our international partners: University of Basilicata (UNIBAS) in Italy; Institute for Sustainable Agriculture (IAS) in Spain; Center for Agriculture Research in the Dry Areas (ICARDA) in Morocco, India and Bangladesh; Local Initiatives for Biodiversity, Research and Development (LI-BIRD) in Nepal; and United States Department of Agriculture (USDA CRIS Project 5348-21000-017-00D) in the USA, for conducting field experiments in their respective countries

A genome-wide identification and comparative analysis of the lentil MLO genes

Revista electrónica on linePowdery mildew is a widespread fungal plant disease that can cause significant losses in many crops. Some MLO genes (Mildew resistance locus O) have proved to confer a durable resistance to powdery mildew in several species. Resistance granted by the MLO gene family members has prompted an increasing interest in characterizing these genes and implementing their use in plant breeding. Lentil (Lens culinaris Medik.) is a widely grown food legume almost exclusively consumed as dry seed with an average world production of 4.5 million tons. Powdery mildew causes severe losses on certain lentil cultivars under particular environmental conditions. Data mining of the lentil CDC Redberry draft genome allowed to identify up to 15 gene sequences with homology to known MLO genes, designated as LcMLOs. Further characterization of these gene sequences and their deduced protein sequences demonstrated conformity with key MLO protein characteristics such as the presence of transmembrane and calmodulin binding domains, as well as that of other conserved motifs. Phylogenetic and other comparative analyses revealed that LcMLO1 and LcMLO3 are the most likely gene orthologs related to powdery mildew response in other species, sharing a high similarity with other known resistance genes of dicot species, such as pea PsMLO1 and Medicago truncatula MtMLO1 and MtMLO3. Sets of primers were designed as tools to PCR amplify the genomic sequences of LcMLO1 and LcMLO3, also to screen lentil germplasm in search of resistance mutants. Primers were used to obtain the complete sequences of these two genes in all of the six wild lentil relatives. Respective to each gene, all Lens sequences shared a high similarity. Likewise, we used these primers to screen a working collection of 58 cultivated and 23 wild lentil accessions in search of length polymorphisms present in these two genes. All these data widen the insights on this gene family and can be useful for breeding programs in lentil and close related species.S

Genome analysis and genetic mapping of restorer loci in raphanus

Genetic variation exists in Raphanus that could be of use to Brassica breeders. Of particular interest is the Ogura system of cytoplasmic male sterility (CMS) which has been worked on extensively in a Brassica napus background. Problems have been experienced in B. napusrestorer lines due to the inheritance of a large segment of Raphanus chromosome containing the fertility restoring locus. This restorer introgression is located on the Brassica C genome making it only of use for B. napus and not for B. rapa or B. juncea. This thesis describes the development of the materials necessary for the introgression into the Brassica A genome of a defined segment of Raphanus chromosome containing a restorer locus. Defined genetic stocks of Raphanus were developed that contained specific loci controlling restoration of Ogura CMS. This material was used to develop populations segregating for specific restorer loci. Extensive RFLP maps of three Raphanus populations were developed and aligned, resulting in a robust consensus map of the entire Raphanus genome. Three restorer loci were accurately mapped on three separate linkage groups. The segment of Raphanus that is implicated in the restoration of Ogura CMS in a B. napus restorer line developed by INRA was identified and it did not correspond to any of the regions containing the three mapped restorer loci, suggesting the presence of more restorer loci in Raphanus. Comparative mapping between the Raphanus genome map and previously generated Brassica A genome RFLP maps demonstrated large regions of collinearity between segments of chromosomes of the two species. Preliminary examination of the two genome maps suggest they contain essentially the same overall genetic content but with large segments of the genomes rearranged with respect to each other. Likely sites of Raphanus restorer introgression into the Brassica A genome were predicted. Trigenomic tetraploids were developed in which pairing and recombination between homoeologous segments of Raphanus and Brassica A chromosomes should result. Progeny of these individuals will allow an assessment of the pattern and extent of recombination that occurs between the chromosomes of the Raphanus and Brassica A genomes and should lead to the development of 'B. napus' lines carrying Ogura CMS restorer alleles from Raphanus

Walking on the wild side - expanding genetic diversity for future lentil breeding

Vandenberg, Albert et al.-- Trabajo presentado en la International Conference on Pulses for Health, Nutrition and Sustainable Agriculture in Drylands, celebrada en Marrakesh del 18 al 20 de abril de 2016.Systematic use of genetic variability through judicious use of diverse germplasm maximizes genetic gain per generation, and therefore, maximizes economic value of the crop. Sometime, however, the required genetic variation is simply not to be found in the cultivated germplasm. Under these circumstances, breeders may consider the use of wild relatives. The genus Lens consists of the cultivated L. culinaris plus six wild species. Wild relatives of lentil represent a rich source of resistance to both biotic and abiotic stresses, yet very little is known about them. The lentil research and breeding group at the University of Saskatchewan has been studying cultivated lentil and its wild relatives for the past two decades and has generated a wealth of cultivated x wild genetic resources, some of which have already shown utility in the breeding program. In the past few years we have worked with several international partners (Spain, Turkey, Morocco, Bangladesh, and Ethiopia) to phenotype promising individuals from three inter-specific populations (two L. culinaris x L. ervodies and one L. culinaris x L. orientalis) under several biotic and abiotic stresses. Over the next few years we plan to phenotypically and genotypically characterize the genetic variability available within the primary and secondary gene pools of genus Lens to determine the genetic basis of domestication and adaptation characteristics. Tools will also be generated for tracking introgressions from wild genomes into the cultivated one. The goal is to develop breeder-friendly resources for tracking key domestication genes, response to photoperiod, temperature and light quality, and generate resources and tools to allow breeders to better use exotic germplasm and wild relatives while reducing any negative impacts. It is anticipated that results of our work will contribute to lentil genetic improvement, conservation of biodiversity, and global food security.N

Use of crop wild relatives in lentil breeding - Sharing the benefits

Bett, K. E. et al.-- Trabajo presentado en la V Meeting Asociación Española de Leguminosas, AEL (Eucarpia International Symposium on Protein Crops), celebrada en Pontevedra del 4 al 7 de mayo de 2015.Use of crop wild relatives is regaining status as an important genetic strategy for future global food and nutritional security in the face of genetic erosion from loss of diversity and environmental shifts caused by climate change and loss of natural habitat. Since 2001, we have been using wild species for long term genetic improvement of lentil. The wild species are known to carry genes for tolerance to multiple biotic and abiotic stresses. We have been testing interspecies hybrids from crosses between Lens culinaris and L. ervoides or L. orientalis. Results of these trials will be shared.N