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

Sunil S Gangurde; Janila Pasupuleti; Sejal Parmar; Murali T Variath; Deekshitha Bomireddy; Surendra S Manohar; Rajeev K Varshney; Prashant Singam; Baozhu Guo; Manish K Pandey

doi:10.3389/fgene.2023.1128182

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

Front Genet. 2023 Mar 16:14:1128182. doi: 10.3389/fgene.2023.1128182. eCollection 2023.

Authors

Sunil S Gangurde^{1

2

3}, Janila Pasupuleti¹, Sejal Parmar^{1

2}, Murali T Variath¹, Deekshitha Bomireddy¹, Surendra S Manohar¹, Rajeev K Varshney^{1

4}, Prashant Singam², Baozhu Guo³, Manish K Pandey^{1

2}

Affiliations

¹ Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
² Department of Genetics, Osmania University, Hyderabad, India.
³ USDA-ARS, Crops Genetics and Breeding Research Unit, Tifton, GA, United States.
⁴ State Agricultural Biotechnology Centre, Centre for Crop & Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.

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 six QTLs for SHP, with three consistent QTLs on chromosomes A05, A08, and B10. Similarly, for HSW, seven QTLs located on chromosomes A01, A02, 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, fibre protein, lipid transfer protein, senescence-associated protein, and disease-resistant NBS-LRR proteins were identified in the QTL regions associated with shelling percentage. The associated markers for 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.

Keywords: Axiom_Arachis array; candidate gene discovery; diagnostic markers; high-density genotyping; peanut.

Grants and funding

The funding was received from Indian Council of Agricultural Research (ICAR) through ICAR-ICRISAT project, Department of Biotechnology (DBT), Government of India, MARS-Wrigley and Bill and Melinda Gates Foundation (BMGF), United States.