Nehru, G and Behera, P P and Mathew, A and Kiranmayee, B and Aparna, V and Purohit, A and Mukthambica, K and Pandey, M K and Janila, P (2025) Marker-Assisted Selection (MAS), Quality Control and METs in Groundnut Breeding Pipeline at ICRISAT to Enhance Genetic Gain. In: Advances in Arachis through Genomics and Biotechnology (AAGB-2025), 23-25 March 2025, Novotel, Goa, India.
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Groundnut, an oil and food legume crop is valued for its nutritional content, including protein and essential fatty acids. The EiB (Excellence in Breeding) low-density genotyping service is a shared KASPTM genotyping platform serving all CGIAR centers and their partner programs. The EiB low-density genotyping service is based on Kompetitive Allele Specific PCR (KASP) markers. Groundnut has 82 QC SNPs based on PIC (polymorphism information content) and 49 trait-specific SNPs on the EiB portal. ICRISAT groundnut breeding pipeline employs a 10-SNP panel selected based on parental polymorphism for confirming the hybridity of the F1s. During 2023-24, the program has confirmed the hybridity of 564 F1 plants. A 10-SNP panel is employed for MAS that include, two SNP markers, snpAH00116 and snpAH0002 to select FAD2A mutant alleles on A- and B- genomes, respectively. For the major QTL governing late leaf spot (LLS) resistance, snpAH0004, snpAH0005, snpAH0010, and snpAH0014, and for the major QTL governing rust resistance, snpAH0017, snpAH00135, snpAH00137 and snpAH0026 are employed in the breeding pipeline. A mid-density genotyping panel containing 2500 SNP markers distributed across 20 groundnut chromosomes is used to genotype all the lines (~200 per annum) advanced to Stage I multi-environment testing (MET). The SNPs for the mid-density panel have been identified using the whole genome re-sequencing of 263 cultivated accessions of groundnut reference. The mid-density genotype data is employed for line purity, and to determine gBLUPs that is used for parent selection for recycling, and Genomic Selection (GS). Cultivars tailored for specific adaptation to a target agro-climatic zone maximizes realized genetic potential. This requires identifying homogenous production units (HPUs) and testing within a HPU to minimize the G X E and select the lines best suited for a HPU. ICRISAT has adopted a multi-environment testing (MET) strategy guided by the characterization of environment. A set of 27 advanced breeding lines were evaluated across two HPUs during Rainy 2022, using an alpha lattice design with two replications. Best linear unbiased predictors (BLUP) based analysis revealed, ICGVs 211022, 211021 and 211008 were specifically adapted to HPU 2 comprising of Gujarat state, while ICGVs 211019 and 211020 thrived in HPU 6 comprising southern states of India. Interestingly, ICGVs 211029 and 211016 exhibited broad adaptability for both the HPUs. According to Smith-Hazel multi trait indices, positive selection gain was observed for seed yield and shelling percentage in HPU 2. Overall both HPUs exhibited a net positive selection gain. The index consistently identified ICGVs 211020 and 211022 as superior ideotypes in both HPUs, ensuring selection reliability and wider adaptability. These multi-trait selection indices help breeders sustain progress in key traits like pod yield, while preserving the genetic gains in secondary traits like shelling outturn. The consistent positive selection gain across the HPUs underscores the effectiveness of targeted breeding in improving yield.
| Item Type: | Conference or Workshop Item (Speech) |
|---|---|
| Divisions: | Global Research Program - Accelerated Crop Improvement |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | BLUP, HPUs, GEIs, KASP, MAS, QC, Smith-hazel index |
| Subjects: | Others > Plant Breeding Mandate crops > Groundnut Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 07 Jul 2025 03:52 |
| Last Modified: | 07 Jul 2025 03:52 |
| URI: | http://oar.icrisat.org/id/eprint/13208 |
| Acknowledgement: | UNSPECIFIED |
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