Development, Characterization, and Cross Species/Genera Transferability of Novel EST-SSR Markers in Lentil, with Their Molecular Applications

Development, Characterization, and Cross Species/Genera Transferability of Novel EST-SSR Markers in Lentil, with Their Molecular Applications

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 genomi...

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Bibliographic Details
Published in:Plant molecular biology reporter Vol. 38; no. 1; pp. 114 - 129
Main Authors: Singh, Dharmendra, Singh, Chandan Kumar, Tribuvan, Kishor U, Tyagi, Punit, Taunk, Jyoti, Tomar, Ram Sewak Singh, Kumari, Shanti, Tripathi, Kuldeep, Kumar, Ashok, Gaikwad, Kishor, Yadav, Rajendra Kumar, Pal, Madan
Format: Journal Article
Language:English
Published: New York Springer US 01-03-2020
Springer Nature B.V
Subjects:
Annotations
Bioinformatics
Biomarkers
Biomedical and Life Sciences
Carbohydrates
Cluster analysis
Expressed sequence tags
Fibers
Gene mapping
Gene sequencing
Genera
Genetic resources
Genotypes
Germplasm
Legumes
Leguminous plants
Life Sciences
Mapping
Metabolomics
Minerals
Original Paper
Phylogeny
Plant Breeding/Biotechnology
Plant Sciences
Population structure
Proteomics
Ribonucleic acid
RNA
Species
Vitamins
Lentil
Cross-genera transferability
Genetic diversity
Unigene sequences
RNA-Seq
EST-SSR
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Summary: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 F 3 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 .
ISSN:0735-9640
1572-9818
DOI:10.1007/s11105-019-01184-z