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Global wild annual Lens collection: a potential resource for lentil genetic base broadening and yield enhancement.

ABSTRACT: Crop wild relatives (CWRs) are invaluable gene sources for various traits of interest, yet these potential resources are themselves increasingly threatened by the impact of climate change as well as other anthropogenic and socio-economic factors. The prime goal of our research was to cover all aspects of wild Lens genetic resource management like species characterization, agro-morphological evaluation, diversity assessment, and development of representative sets for its enhanced utilization in lentil base broadening and yield improvement initiatives. We characterized and evaluated extensively, the global wild annual Lens taxa, originating from twenty seven counties under two agro-climatic conditions of India consecutively for three cropping seasons. Results on various qualitative and quantitative characters including two foliar diseases showed wide variations for almost all yield attributing traits including multiple disease resistance in the wild species, L. nigricans and L. ervoides accessions. The core set developed from the entire Lens taxa had maximum representation from Turkey and Syria, indicating rich diversity in accessions originating from these regions. Diversity analysis also indicated wide geographical variations across genepool as was reflected in the core set. Potential use of core set, as an initial starting material, for genetic base broadening of cultivated lentil was also suggested.

SUBMITTER: Singh M

PROVIDER: S-EPMC4177869 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Global wild annual Lens collection: a potential resource for lentil genetic base broadening and yield enhancement.

Singh Mohar M Bisht Ishwari Singh IS Kumar Sandeep S Dutta Manoranjan M Bansal Kailash Chander KC Karale Moreshwar M Sarker Ashutosh A Amri Ahmad A Kumar Shiv S Datta Swapan Kumar SK

PloS one 20140925 9

Crop wild relatives (CWRs) are invaluable gene sources for various traits of interest, yet these potential resources are themselves increasingly threatened by the impact of climate change as well as other anthropogenic and socio-economic factors. The prime goal of our research was to cover all aspects of wild Lens genetic resource management like species characterization, agro-morphological evaluation, diversity assessment, and development of representative sets for its enhanced utilization in l ...[more]

PMID: 25254552

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Project description:Intensive breeding of cultivated lentil has resulted in a relatively narrow genetic base, which limits the options to increase crop productivity through selection. Assessment of genetic diversity in the wild gene pool of lentil, as well as characterization of useful and novel alleles/genes that can be introgressed into elite germplasm, presents new opportunities and pathways for germplasm enhancement, followed by successful crop improvement. In the current study, a lentil collection consisting of 467 wild and cultivated accessions that originated from 10 diverse geographical regions was assessed, to understand genetic relationships among different lentil species/subspecies. A total of 422,101 high-confidence SNP markers were identified against the reference lentil genome (cv. CDC Redberry). Phylogenetic analysis clustered the germplasm collection into four groups, namely, Lens culinaris/Lens orientalis, Lens lamottei/Lens odemensis, Lens ervoides, and Lens nigricans. A weak correlation was observed between geographical origin and genetic relationship, except for some accessions of L. culinaris and L. ervoides. Genetic distance matrices revealed a comparable level of variation within the gene pools of L. culinaris (Nei's coefficient 0.01468-0.71163), L. ervoides (Nei's coefficient 0.01807-0.71877), and L. nigricans (Nei's coefficient 0.02188-1.2219). In order to understand any genic differences at species/subspecies level, allele frequencies were calculated from a subset of 263 lentil accessions. Among all cultivated and wild lentil species, L. nigricans exhibited the greatest allelic differentiation across the genome compared to all other species/subspecies. Major differences were observed on six genomic regions with the largest being on Chromosome 1 (c. 1 Mbp). These results indicate that L. nigricans is the most distantly related to L. culinaris and additional structural variations are likely to be identified from genome sequencing studies. This would provide further insights into evolutionary relationships between cultivated and wild lentil germplasm, for germplasm improvement and introgression.

Project description:BackgroundStemphylium blight (SB), caused by Stemphylium botryosum, is a devastating disease in lentil production. Although it is known that accessions of Lens ervoides possess superior SB resistance at much higher frequency than the cultivated lentil species, very little is known about the molecular basis regulating SB resistance in L. ervoides. Therefore, a comprehensive molecular study of SB resistance in L. ervoides was needed to exploit this wild resource available at genebanks for use by plant breeders in resistance breeding.ResultsMicroscopic and qPCR quantification of fungal growth revealed that 48, 96, and 144 h post-inoculation (hpi) were interesting time points for disease development in L. ervoides recombinant inbred lines (RILs) LR-66-637 (resistant to SB) and LR-66-577 (susceptible to SB). Results of transcriptome sequencing at 0, 48, 96 and 144 hpi showed that 8810 genes were disease-responsive genes after challenge by S. botryosum. Among them, 7526 genes displayed a similar expression trend in both RILs, and some of them were likely involved in non-host resistance. The remaining 1284 genes were differentially expressed genes (DEGs) between RILs. Of those, 712 DEGs upregulated in LR-66-637 were mostly enriched in 'carbohydrate metabolic process', 'cell wall organization or biogenesis', and 'polysaccharide metabolic process'. In contrast, there were another 572 DEGs that were upregulated in LR-66-577, and some of them were enriched in 'oxidation-reduction process', 'asparagine metabolic process' and 'asparagine biosynthetic process'. After comparing DEGs to genes identified in previously described quantitative trait loci (QTLs) for resistance to SB, nine genes were common and three of them showed differential gene expression between a resistant and a susceptible bulk consisting of five RILs each. Results showed that two genes encoding calcium-transporting ATPase and glutamate receptor3.2 were candidate resistance genes, whereas one gene with unknown function was a candidate susceptibility gene.ConclusionThis study provides new insights into the mechanisms of resistance and susceptibility in L. ervoides RILs responding to S. botryosum infection. Furthermore, we identified candidate resistance or susceptibility genes which warrant further gene function analyses, and which could be valuable for resistance breeding, if their role in resistance or susceptibility can be confirmed.

Dataset Information

Global wild annual Lens collection: a potential resource for lentil genetic base broadening and yield enhancement.

Publications

Global wild annual Lens collection: a potential resource for lentil genetic base broadening and yield enhancement.

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