Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut
Abstract Groundnut (Arachis hypogaea L.), also known as peanut, is an allotetraploid legume crop composed of two different progenitor sub‐genomes. This crop is an important source for food, feed, and confectioneries. Leveraging translational genomics research has expedited the precision and speed in...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2025-06-01
|
| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.70019 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850121358911995904 |
|---|---|
| author | Manish K. Pandey Vinay Sharma Aamir W. Khan Pushpesh Joshi Sunil S. Gangurde Prasad Bajaj Pasupuleti Janila Annapurna Chitikineni Ramesh Bhat Babu N. Motagi Chandramohan Sangh Thankappan Radhakrishnan Sandip K. Bera Gregor Gorjanc Krishna Reddy Gujjula Nathan Hall Claudio D. Carrasco Kandalam Arjun Srinivas Chandram Rajeev K. Varshney |
| author_facet | Manish K. Pandey Vinay Sharma Aamir W. Khan Pushpesh Joshi Sunil S. Gangurde Prasad Bajaj Pasupuleti Janila Annapurna Chitikineni Ramesh Bhat Babu N. Motagi Chandramohan Sangh Thankappan Radhakrishnan Sandip K. Bera Gregor Gorjanc Krishna Reddy Gujjula Nathan Hall Claudio D. Carrasco Kandalam Arjun Srinivas Chandram Rajeev K. Varshney |
| author_sort | Manish K. Pandey |
| collection | DOAJ |
| description | Abstract Groundnut (Arachis hypogaea L.), also known as peanut, is an allotetraploid legume crop composed of two different progenitor sub‐genomes. This crop is an important source for food, feed, and confectioneries. Leveraging translational genomics research has expedited the precision and speed in making selections of progenies in several crops through either marker‐assisted selection or genomic selection, including groundnut. The availability of foundational genomic resources such as reference genomes for diploid progenitors and cultivated tetraploids, offered substantial opportunities for genomic interventions, including the development of genotyping assays. Here, a cost‐effective and high‐throughput genotyping assay has been developed with 5,081 single nucleotide polymorphisms (SNPs) referred to as “mid‐density assay.” This multi‐purpose assay includes 5,000 highly informative SNPs selected based on higher polymorphism information content (PIC) from our previously developed high‐density “Axiom_Arachis” array containing 58,233 SNPs. Additionally 82 SNPs associated with five resilience and quality traits were included for marker‐assisted selection. To test the utility of the mid‐density genotyping (MDG) assay, 2,573 genotypes from distinct sets of breeding populations were genotyped with the 5,081 SNPs. PIC of the SNPs in the MDG ranged from 0.34 to 0.37 among diverse sets. The first three principal components collectively explained 82.08% of the variance among these genotypes. The mid‐density assay demonstrated a proficient ability to distinguish between the genotypes, offering a high level of genome‐wide nucleotide diversity. This assay holds promise for possible deployment in the identification of varietal seed mixtures, genetic purity within gene bank germplasms and seed systems, foreground and background selection in backcross breeding programs, genomic selection, and sparse trait mapping studies in groundnut. |
| format | Article |
| id | doaj-art-95692d1a5d9b4fa29f3a851225eef618 |
| institution | OA Journals |
| issn | 1940-3372 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj-art-95692d1a5d9b4fa29f3a851225eef6182025-08-20T02:35:07ZengWileyThe Plant Genome1940-33722025-06-01182n/an/a10.1002/tpg2.70019Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnutManish K. Pandey0Vinay Sharma1Aamir W. Khan2Pushpesh Joshi3Sunil S. Gangurde4Prasad Bajaj5Pasupuleti Janila6Annapurna Chitikineni7Ramesh Bhat8Babu N. Motagi9Chandramohan Sangh10Thankappan Radhakrishnan11Sandip K. Bera12Gregor Gorjanc13Krishna Reddy Gujjula14Nathan Hall15Claudio D. Carrasco16Kandalam Arjun17Srinivas Chandram18Rajeev K. Varshney19Center for Excellence in Genomics and Systems Biology (CEGSB) and Center for Pre ‐Breeding Research (CPBR)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndiaCenter for Excellence in Genomics and Systems Biology (CEGSB) and Center for Pre ‐Breeding Research (CPBR)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndiaCenter for Excellence in Genomics and Systems Biology (CEGSB) and Center for Pre ‐Breeding Research (CPBR)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndiaCenter for Excellence in Genomics and Systems Biology (CEGSB) and Center for Pre ‐Breeding Research (CPBR)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndiaCenter for Excellence in Genomics and Systems Biology (CEGSB) and Center for Pre ‐Breeding Research (CPBR)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndiaCenter for Excellence in Genomics and Systems Biology (CEGSB) and Center for Pre ‐Breeding Research (CPBR)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndiaCenter for Excellence in Genomics and Systems Biology (CEGSB) and Center for Pre ‐Breeding Research (CPBR)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndiaCenter for Excellence in Genomics and Systems Biology (CEGSB) and Center for Pre ‐Breeding Research (CPBR)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndiaDepartment of BiotechnologyUniversity of Agricultural SciencesDharwadIndiaDepartment of BiotechnologyUniversity of Agricultural SciencesDharwadIndiaICAR‐Indian Institute of Groundnut Research (IIGR)Junagadh IndiaICAR‐Indian Institute of Groundnut Research (IIGR)Junagadh IndiaICAR‐Indian Institute of Groundnut Research (IIGR)Junagadh IndiaThe Roslin Institute and The Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUKThermo Fisher ScientificWalthamMassachusettsUSAThermo Fisher ScientificWalthamMassachusettsUSAThermo Fisher ScientificWalthamMassachusettsUSAThermo Fisher ScientificWalthamMassachusettsUSAThermo Fisher ScientificWalthamMassachusettsUSACenter for Excellence in Genomics and Systems Biology (CEGSB) and Center for Pre ‐Breeding Research (CPBR)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndiaAbstract Groundnut (Arachis hypogaea L.), also known as peanut, is an allotetraploid legume crop composed of two different progenitor sub‐genomes. This crop is an important source for food, feed, and confectioneries. Leveraging translational genomics research has expedited the precision and speed in making selections of progenies in several crops through either marker‐assisted selection or genomic selection, including groundnut. The availability of foundational genomic resources such as reference genomes for diploid progenitors and cultivated tetraploids, offered substantial opportunities for genomic interventions, including the development of genotyping assays. Here, a cost‐effective and high‐throughput genotyping assay has been developed with 5,081 single nucleotide polymorphisms (SNPs) referred to as “mid‐density assay.” This multi‐purpose assay includes 5,000 highly informative SNPs selected based on higher polymorphism information content (PIC) from our previously developed high‐density “Axiom_Arachis” array containing 58,233 SNPs. Additionally 82 SNPs associated with five resilience and quality traits were included for marker‐assisted selection. To test the utility of the mid‐density genotyping (MDG) assay, 2,573 genotypes from distinct sets of breeding populations were genotyped with the 5,081 SNPs. PIC of the SNPs in the MDG ranged from 0.34 to 0.37 among diverse sets. The first three principal components collectively explained 82.08% of the variance among these genotypes. The mid‐density assay demonstrated a proficient ability to distinguish between the genotypes, offering a high level of genome‐wide nucleotide diversity. This assay holds promise for possible deployment in the identification of varietal seed mixtures, genetic purity within gene bank germplasms and seed systems, foreground and background selection in backcross breeding programs, genomic selection, and sparse trait mapping studies in groundnut.https://doi.org/10.1002/tpg2.70019 |
| spellingShingle | Manish K. Pandey Vinay Sharma Aamir W. Khan Pushpesh Joshi Sunil S. Gangurde Prasad Bajaj Pasupuleti Janila Annapurna Chitikineni Ramesh Bhat Babu N. Motagi Chandramohan Sangh Thankappan Radhakrishnan Sandip K. Bera Gregor Gorjanc Krishna Reddy Gujjula Nathan Hall Claudio D. Carrasco Kandalam Arjun Srinivas Chandram Rajeev K. Varshney Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut The Plant Genome |
| title | Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut |
| title_full | Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut |
| title_fullStr | Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut |
| title_full_unstemmed | Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut |
| title_short | Development of a cost‐effective high‐throughput mid‐density 5K genotyping assay for germplasm characterization and breeding in groundnut |
| title_sort | development of a cost effective high throughput mid density 5k genotyping assay for germplasm characterization and breeding in groundnut |
| url | https://doi.org/10.1002/tpg2.70019 |
| work_keys_str_mv | AT manishkpandey developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT vinaysharma developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT aamirwkhan developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT pushpeshjoshi developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT sunilsgangurde developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT prasadbajaj developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT pasupuletijanila developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT annapurnachitikineni developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT rameshbhat developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT babunmotagi developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT chandramohansangh developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT thankappanradhakrishnan developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT sandipkbera developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT gregorgorjanc developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT krishnareddygujjula developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT nathanhall developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT claudiodcarrasco developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT kandalamarjun developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT srinivaschandram developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT rajeevkvarshney developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut |