Double‐digest restriction‐associated DNA sequencing‐based genotyping and its applications in sesame germplasm management Article Swipe
Pradeep Ruperao
,
Prasad Bajaj
,
Rashmi Yadav
,
Mahalingam Angamuthu
,
S. Rajkumar
,
Vandana Rai
,
Kapil Tiwari
,
Abhishek Rathore
,
Kuldeep Singh
,
Gyanendra Pratap Singh
,
U. B. Angadi
,
Sean Mayes
,
Parimalan Rangan
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/tpg2.20447
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/tpg2.20447
Sesame ( Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR‐National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics‐assisted double‐digest restriction‐associated DNA sequencing (ddRAD‐seq) approach. A total of 64,910 filtered single‐nucleotide polymorphisms (SNPs) were utilized to assess the genome‐scale diversity. Applications of this genome‐scale information (reduced representation using restriction enzymes) are demonstrated through the development of a molecular core collection (CC) representing maximal SNP diversity. This information is also applied in developing a mid‐density panel (MDP) comprising 2515 hyper‐variable SNPs, representing almost equally the genic and non‐genic regions. The sesame CC comprising 384 accessions, a representative set of accessions with maximal diversity, was identified using multiple criteria such as k‐mer (subsequence of length “k” in a sequence read) diversity, observed heterozygosity, CoreHunter3, GenoCore, and genetic differentiation. The coreset constituted around 15% of the total accessions studied, and this small subset had captured >60% SNP diversity of the entire population. In the coreset, the admixture analysis shows reduced genetic complexity, increased nucleotide diversity (π), and is geographically distributed without any repetitiveness in the CC germplasm. Within the CC, India‐originated accessions exhibit higher diversity (as expected based on the center of diversity concept), than those accessions that were procured from various other countries. The identified CC set and the MDP will be a valuable resource for genomics‐assisted accelerated sesame improvement program.
Related Topics
Concepts
Germplasm
Genetic diversity
Biology
Single-nucleotide polymorphism
Genetics
SNP genotyping
Genotyping
Restriction enzyme
Genome
Sesamum
Loss of heterozygosity
Population
Biotechnology
Genotype
Botany
Horticulture
Gene
Allele
Sociology
Demography
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/tpg2.20447
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/tpg2.20447
- OA Status
- gold
- Cited By
- 6
- References
- 67
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4394874259
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4394874259Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1002/tpg2.20447Digital Object Identifier
- Title
-
Double‐digest restriction‐associated DNA sequencing‐based genotyping and its applications in sesame germplasm managementWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-04-17Full publication date if available
- Authors
-
Pradeep Ruperao, Prasad Bajaj, Rashmi Yadav, Mahalingam Angamuthu, S. Rajkumar, Vandana Rai, Kapil Tiwari, Abhishek Rathore, Kuldeep Singh, Gyanendra Pratap Singh, U. B. Angadi, Sean Mayes, Parimalan RanganList of authors in order
- Landing page
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https://doi.org/10.1002/tpg2.20447Publisher landing page
- PDF URL
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/tpg2.20447Direct link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/tpg2.20447Direct OA link when available
- Concepts
-
Germplasm, Genetic diversity, Biology, Single-nucleotide polymorphism, Genetics, SNP genotyping, Genotyping, Restriction enzyme, Genome, Sesamum, Loss of heterozygosity, Population, Biotechnology, Genotype, Botany, Horticulture, Gene, Allele, Sociology, DemographyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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6Total citation count in OpenAlex
- Citations by year (recent)
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2025: 4, 2024: 2Per-year citation counts (last 5 years)
- References (count)
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67Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.2515 | 110 |
| abstract_inverted_index.This | 98 |
| abstract_inverted_index.also | 101 |
| abstract_inverted_index.core | 91 |
| abstract_inverted_index.crop | 10, 20 |
| abstract_inverted_index.from | 230 |
| abstract_inverted_index.such | 140 |
| abstract_inverted_index.than | 224 |
| abstract_inverted_index.that | 227 |
| abstract_inverted_index.this | 29, 75, 170 |
| abstract_inverted_index.were | 48, 66, 228 |
| abstract_inverted_index.will | 241 |
| abstract_inverted_index.with | 132 |
| abstract_inverted_index.(MDP) | 108 |
| abstract_inverted_index.(π), | 195 |
| abstract_inverted_index.Plant | 44 |
| abstract_inverted_index.SNPs, | 112 |
| abstract_inverted_index.based | 217 |
| abstract_inverted_index.being | 34 |
| abstract_inverted_index.food. | 27 |
| abstract_inverted_index.genic | 117 |
| abstract_inverted_index.other | 232 |
| abstract_inverted_index.panel | 107 |
| abstract_inverted_index.read) | 150 |
| abstract_inverted_index.shows | 188 |
| abstract_inverted_index.small | 171 |
| abstract_inverted_index.those | 225 |
| abstract_inverted_index.total | 59, 166 |
| abstract_inverted_index.using | 50, 80, 137 |
| abstract_inverted_index.(SNPs) | 65 |
| abstract_inverted_index.64,910 | 61 |
| abstract_inverted_index.Bureau | 42 |
| abstract_inverted_index.Sesame | 1 |
| abstract_inverted_index.Within | 207 |
| abstract_inverted_index.almost | 114 |
| abstract_inverted_index.around | 162 |
| abstract_inverted_index.assess | 69 |
| abstract_inverted_index.center | 220 |
| abstract_inverted_index.entire | 180 |
| abstract_inverted_index.family | 14 |
| abstract_inverted_index.higher | 213 |
| abstract_inverted_index.length | 145 |
| abstract_inverted_index.sesame | 32, 122, 249 |
| abstract_inverted_index.study, | 30 |
| abstract_inverted_index.subset | 172 |
| abstract_inverted_index.>60% | 175 |
| abstract_inverted_index.Genetic | 45 |
| abstract_inverted_index.Sesamum | 3 |
| abstract_inverted_index.ancient | 8 |
| abstract_inverted_index.applied | 102 |
| abstract_inverted_index.coreset | 160 |
| abstract_inverted_index.equally | 115 |
| abstract_inverted_index.exhibit | 212 |
| abstract_inverted_index.genetic | 157, 190 |
| abstract_inverted_index.indicum | 4 |
| abstract_inverted_index.k‐mer | 142 |
| abstract_inverted_index.maximal | 95, 133 |
| abstract_inverted_index.oilseed | 9 |
| abstract_inverted_index.reduced | 189 |
| abstract_inverted_index.through | 85 |
| abstract_inverted_index.various | 231 |
| abstract_inverted_index.without | 200 |
| abstract_inverted_index.“k” | 146 |
| abstract_inverted_index.(NBPGR), | 47 |
| abstract_inverted_index.(reduced | 78 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.Genebank | 39 |
| abstract_inverted_index.National | 38 |
| abstract_inverted_index.analysis | 187 |
| abstract_inverted_index.captured | 174 |
| abstract_inverted_index.coreset, | 184 |
| abstract_inverted_index.criteria | 139 |
| abstract_inverted_index.enzymes) | 82 |
| abstract_inverted_index.expected | 216 |
| abstract_inverted_index.filtered | 62 |
| abstract_inverted_index.globally | 18 |
| abstract_inverted_index.multiple | 138 |
| abstract_inverted_index.observed | 152 |
| abstract_inverted_index.procured | 229 |
| abstract_inverted_index.program. | 251 |
| abstract_inverted_index.regions. | 120 |
| abstract_inverted_index.resource | 245 |
| abstract_inverted_index.sequence | 149 |
| abstract_inverted_index.studied, | 168 |
| abstract_inverted_index.utilized | 67 |
| abstract_inverted_index.valuable | 244 |
| abstract_inverted_index.GenoCore, | 155 |
| abstract_inverted_index.Resources | 46 |
| abstract_inverted_index.admixture | 186 |
| abstract_inverted_index.approach. | 57 |
| abstract_inverted_index.belonging | 11 |
| abstract_inverted_index.concept), | 223 |
| abstract_inverted_index.conserved | 35 |
| abstract_inverted_index.diversity | 177, 194, 214, 222 |
| abstract_inverted_index.genotyped | 49 |
| abstract_inverted_index.increased | 192 |
| abstract_inverted_index.molecular | 90 |
| abstract_inverted_index.accessions | 131, 167, 211, 226 |
| abstract_inverted_index.collection | 92 |
| abstract_inverted_index.comprising | 109, 124 |
| abstract_inverted_index.countries. | 233 |
| abstract_inverted_index.cultivated | 19 |
| abstract_inverted_index.developing | 104 |
| abstract_inverted_index.diversity, | 134, 151 |
| abstract_inverted_index.diversity. | 72, 97 |
| abstract_inverted_index.germplasm. | 206 |
| abstract_inverted_index.identified | 136, 235 |
| abstract_inverted_index.nucleotide | 193 |
| abstract_inverted_index.sequencing | 55 |
| abstract_inverted_index.Pedaliaceae | 15 |
| abstract_inverted_index.accelerated | 248 |
| abstract_inverted_index.accessions, | 33, 126 |
| abstract_inverted_index.complexity, | 191 |
| abstract_inverted_index.constituted | 161 |
| abstract_inverted_index.development | 87 |
| abstract_inverted_index.distributed | 199 |
| abstract_inverted_index.improvement | 250 |
| abstract_inverted_index.information | 77, 99 |
| abstract_inverted_index.non‐genic | 119 |
| abstract_inverted_index.population. | 181 |
| abstract_inverted_index.restriction | 81 |
| abstract_inverted_index.(subsequence | 143 |
| abstract_inverted_index.Applications | 73 |
| abstract_inverted_index.CoreHunter3, | 154 |
| abstract_inverted_index.demonstrated | 84 |
| abstract_inverted_index.representing | 94, 113 |
| abstract_inverted_index.(ddRAD‐seq) | 56 |
| abstract_inverted_index.mid‐density | 106 |
| abstract_inverted_index.polymorphisms | 64 |
| abstract_inverted_index.genome‐scale | 71, 76 |
| abstract_inverted_index.geographically | 198 |
| abstract_inverted_index.repetitiveness | 202 |
| abstract_inverted_index.representation | 79 |
| abstract_inverted_index.representative | 128 |
| abstract_inverted_index.ICAR‐National | 41 |
| abstract_inverted_index.double‐digest | 52 |
| abstract_inverted_index.heterozygosity, | 153 |
| abstract_inverted_index.differentiation. | 158 |
| abstract_inverted_index.hyper‐variable | 111 |
| abstract_inverted_index.India‐originated | 210 |
| abstract_inverted_index.genomics‐assisted | 51, 247 |
| abstract_inverted_index.single‐nucleotide | 63 |
| abstract_inverted_index.restriction‐associated | 53 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 94 |
| corresponding_author_ids | https://openalex.org/A5078049334 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 13 |
| corresponding_institution_ids | https://openalex.org/I165143802, https://openalex.org/I4210097415, https://openalex.org/I4210138055 |
| citation_normalized_percentile.value | 0.94055203 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |