Abstract
Lentil is nutritionally important crop for human diet and enriched with quality protein, complex carbohydrates, fibers, essential minerals, and vitamins. However, genetic improvement of lentil is hampered largely due to unattributed and unexploited genetic and genomic resources. To administer genomic resources in lentil, we have identified 9949 EST-SSR loci from lentil RNA Seq data and validated 50 of them using 234 genotypes representing various Lens species and 34 accessions of 12 different legumes. Out of 50 EST-SSRs, 46 were polymorphic with polymorphic information content (PIC) ranging from 0.16–0.74. The transferability of these markers exhibited varied levels from 45.1 to 71.3% across the cultivated/wild species of lentil and from 10.8 to 54.3% across the twelve legume genera. On the basis of total identified EST-SSRs, mononucleotide (51%) repeat proportion was high followed by trinucleotide (30%) and dinucleotide (14%) repeat. Population structure and cluster analysis classified all the studied genotypes into 4 groups. However, principal coordinate analysis (PCA) was able to group genotypes based on their area of collection. Annotation of all the 46 polymorphic marker sequences revealed that most of the markers linked to genes involved in metabolism of plants. Further, polymorphic markers were also used for linkage mapping in F3 population where 4 markers were found to be linked with a map distance of 72.5 cM. The newly developed markers represent an impressive tool for characterization of germplasm, genetic linkage mapping, phylogenetic studies, as well as to determine disparity in taxonomic status of subspecies of the genus Lens.
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Abbreviations
- PIC:
-
Polymorphic information content
- EST-SSRs:
-
Expressed sequence tag-simple sequence repeats
- ICARDA:
-
International Center for Agricultural Research in the Dry Areas
- NGS:
-
Next generation sequencing
- RNA-Seq:
-
RNA sequencing
- UPGMA:
-
Unweighted pair group method for arithmetic average
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Acknowledgements
The authors acknowledge sincerely the Director and Joint Director (Res), ICAR-Indian Agricultural Research Institute (IARI), New Delhi, Head, Division of Genetics and Incharge, National Phytotron Facility, IARI, New Delhi, for their valuable support in conducting the research. We also thank Dr. Ashutosh Sarkar, coordinator of ICARDA for providing seeds of various Lens species.
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The financial support was from DBT, New Delhi vide Project No. BT/PR3584/AGR/2/828/2011.
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DS, MP, KG, and RKY conceived and designed the experiments. CKS, KUT, PT, RSST, SK, KT, and AK performed molecular analysis and data analysis. DS, CKS, MP, and JT drafted the manuscript. All authors read and approved the final manuscript.
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Key message
•Fifty SSRs were validated in cultivars, landraces, and wild accessions.
•Cross transferability within 34 accessions of 12 different legumes were studied.
•Genic SSRs present in lentil are rich in trinucleotide repeats which maintain the frame shift of host gene.
•Four newly developed SSRs were linked to aluminum tolerance in F3.
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Fig S1
UPGMA tree derived from dissimilarity index of 18 conserved EST-SSR markers for 234 diverse genotypes. (JPG 555 kb)
Fig S2
UPGMA tree derived from dissimilarity index of 9 unique EST-SSR markers for 234 diverse genotypes. (JPG 488 kb)
Table S1
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Singh, D., Singh, C.K., Tribuvan, K.U. et al. Development, Characterization, and Cross Species/Genera Transferability of Novel EST-SSR Markers in Lentil, with Their Molecular Applications. Plant Mol Biol Rep 38, 114–129 (2020). https://doi.org/10.1007/s11105-019-01184-z
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DOI: https://doi.org/10.1007/s11105-019-01184-z