Genetic mapping identifies genomic regions and candidate genes for seed weight and shelling percentage in groundnut

Authors: GANGURDE, SUNIL - University Of Georgia; PASUPULETI, JANILA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; PARMAR, SEJAL - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; VARIATH, MURALI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; BOMIREDDY, DEEKSHITHA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; MANOHAR, SURENDRA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; VARSHNEY, RAJEEV - Murdoch University; PRASHANT, SINGAM - Osmania University; Guo, Baozhu; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/20/2023
Publication Date: 3/16/2023
Citation: Gangurde, S., Pasupuleti, J., Parmar, S., Variath, M.T., Bomireddy, D., Manohar, S.S., Varshney, R.K., Prashant, S., Guo, B., Pandey, M.K. 2023. Genetic mapping identifies genomic regions and candidate genes for seed weight and shelling percentage in groundnut. Frontiers in Genetics. 14:1128182. https://doi.org/10.3389/fgene.2023.1128182.
DOI: https://doi.org/10.3389/fgene.2023.1128182

Interpretive Summary: Improvement of peanut yield and quality traits are two crucial points for peanut breeding programs. The yield is influenced by the seed/pod weights, shelling percentage and seed/pod size. Therefore, this study was to identify the genomic regions associated with 100-seed weight (HSW) and shelling percentage (SHP) using a recombinant inbred line (RIL) mapping population with 352 RILs, which was phenotyped for three years and genotyped with peanut 58K SNP array. A genetic map was generated with 4199 SNP loci and a map distance of 2708.36 cM. Quantitative trait loci and markers were identified for both HSW and SHP. BIG SEED locus and spermidine synthase candidate genes associated with seed weight were identified in the QTL region on chromosome B09. Laccase, fiber protein, lipid transfer protein, senescence-associated protein, and disease-resistant NBS-LRR proteins were identified in the QTL regions linked to shelling percentage. Molecular markers had been used to separate the small- and large-seeded RILs.

Technical Abstract: Seed size is not only a yield-related trait but also an important measure to determine the commercial value of groundnut in the international market. For instance, small size is preferred in oil production, whereas large-sized seeds are preferred in confectioneries. In order to identify the genomic regions associated with 100-seed weight (HSW) and shelling percentage (SHP), the recombinant inbred line (RIL) population (Chico × ICGV 02251) of 352 individuals was phenotyped for three seasons and genotyped with an Axiom_Arachis array containing 58K SNPs. A genetic map with 4199 SNP loci was constructed, spanning a map distance of 2708.36 cM. QTL analysis identified five QTLs for SHP, with three consistent QTLs on chromosomes A05, B06, and B10. Similarly, for HSW, seven QTLs located on chromosomes A01, A04, A10, B05, B06, and B09 were identified. BIG SEED locus and spermidine synthase candidate genes associated with seed weight were identified in the QTL region on chromosome B09. Laccase, fiber protein, lipid transfer protein, senescence-associated protein, and disease-resistant NBS-LRR proteins identified in the QTL regions are associated with shelling percentage. The major-effect QTLs for both traits successfully distinguished between the small- and large-seeded RILs. QTLs identified for HSW and SHP can be used for developing potential selectable markers to improve the cultivars with desired seed size and shelling percentage to meet the demands of confectionery industries.