Development of a cost-effective high-throughput mid-density 5K genotyping assay for germplasm characterization and breeding in groundnut
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 s...
| Main Authors: | , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Wiley
2025
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/179538 |
| _version_ | 1855525932167593984 |
|---|---|
| author | Pandey, Manish K. Sharma, Vinay Khan, Aamir W. Pushpesh, Joshi Gangurde, Sunil S. Bajaj, Prasad Pasupuleti, Janila Chitikineni, Annapurna Bhat, Ramesh Motagi, Babu N. Sangh, Chandramohan Radhakrishnan, Thankappan Bera, Sandip K. Gorjanc, Gregor Gujjula, Krishna Reddy Hall, Nathan Carrasco, Claudio D. Kandalam, Arjun Chandram, Srinivas Varshney. Rajeev K. |
| author_browse | Bajaj, Prasad Bera, Sandip K. Bhat, Ramesh Carrasco, Claudio D. Chandram, Srinivas Chitikineni, Annapurna Gangurde, Sunil S. Gorjanc, Gregor Gujjula, Krishna Reddy Hall, Nathan Kandalam, Arjun Khan, Aamir W. Motagi, Babu N. Pandey, Manish K. Pasupuleti, Janila Pushpesh, Joshi Radhakrishnan, Thankappan Sangh, Chandramohan Sharma, Vinay Varshney. Rajeev K. |
| author_facet | Pandey, Manish K. Sharma, Vinay Khan, Aamir W. Pushpesh, Joshi Gangurde, Sunil S. Bajaj, Prasad Pasupuleti, Janila Chitikineni, Annapurna Bhat, Ramesh Motagi, Babu N. Sangh, Chandramohan Radhakrishnan, Thankappan Bera, Sandip K. Gorjanc, Gregor Gujjula, Krishna Reddy Hall, Nathan Carrasco, Claudio D. Kandalam, Arjun Chandram, Srinivas Varshney. Rajeev K. |
| author_sort | Pandey, Manish K. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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 | Journal Article |
| id | CGSpace179538 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1795382026-01-09T02:07:37Z Development of a cost-effective high-throughput mid-density 5K genotyping assay for germplasm characterization and breeding in groundnut Pandey, Manish K. Sharma, Vinay Khan, Aamir W. Pushpesh, Joshi Gangurde, Sunil S. Bajaj, Prasad Pasupuleti, Janila Chitikineni, Annapurna Bhat, Ramesh Motagi, Babu N. Sangh, Chandramohan Radhakrishnan, Thankappan Bera, Sandip K. Gorjanc, Gregor Gujjula, Krishna Reddy Hall, Nathan Carrasco, Claudio D. Kandalam, Arjun Chandram, Srinivas Varshney. Rajeev K. groundnuts legumes genomics genotypes plant breeding 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. 2025-03-31 2026-01-08T19:03:13Z 2026-01-08T19:03:13Z Journal Article https://hdl.handle.net/10568/179538 en Open Access application/pdf Wiley Pandey, Manish K. ; Sharma, Vinay; Khan, Aamir W.; Pushpesh, Joshi; Gangurde, Sunil S.; Bajaj, Prasad; Pasupuleti, Janila; Chitikineni, Annapurna; Bhat, Ramesh; Motagi, Babu N.; Sangh, Chandramohan; Radhakrishnan, Thankappan; Bera, Sandip K.; Gorjanc, Gregor; Gujjula, Krishna Reddy; Hall, Nathan; Carrasco, Claudio D.; Kandalam, Arjun; Chandram, Srinivas; & Varshney. Rajeev K. 2025. Development of a cost-effective high-throughput mid-density 5K genotyping assay for germplasm characterization and breeding in groundnut. The Plant Genome, 18, e70019. https://doi.org/10.1002/tpg2.70019 |
| spellingShingle | groundnuts legumes genomics genotypes plant breeding Pandey, Manish K. Sharma, Vinay Khan, Aamir W. Pushpesh, Joshi Gangurde, Sunil S. Bajaj, Prasad Pasupuleti, Janila Chitikineni, Annapurna Bhat, Ramesh Motagi, Babu N. Sangh, Chandramohan Radhakrishnan, Thankappan Bera, Sandip K. Gorjanc, Gregor Gujjula, Krishna Reddy Hall, Nathan Carrasco, Claudio D. Kandalam, Arjun Chandram, Srinivas Varshney. Rajeev K. Development of a cost-effective high-throughput mid-density 5K genotyping assay for germplasm characterization and breeding in groundnut |
| 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 |
| topic | groundnuts legumes genomics genotypes plant breeding |
| url | https://hdl.handle.net/10568/179538 |
| work_keys_str_mv | AT pandeymanishk developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT sharmavinay developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT khanaamirw developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT pushpeshjoshi developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT gangurdesunils developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT bajajprasad developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT pasupuletijanila developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT chitikineniannapurna developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT bhatramesh developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT motagibabun developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT sanghchandramohan developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT radhakrishnanthankappan developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT berasandipk developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT gorjancgregor developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT gujjulakrishnareddy developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT hallnathan developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT carrascoclaudiod developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT kandalamarjun developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT chandramsrinivas developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut AT varshneyrajeevk developmentofacosteffectivehighthroughputmiddensity5kgenotypingassayforgermplasmcharacterizationandbreedingingroundnut |