Lu, Q and Umer, M J and Liu, H and Li, H and Wang, R and Huang, L and Yu, Q and Varshney, R K and Pandey, M K and Hong, Y and Chen, X (2025) Functional analysis of a GWAS pleiotropic hotspot suggests an auxin biosynthesis gene (AhPDS1), regulating pod development in peanut (Arachis hypogaea L.). The Plant Journal, 124 (5). pp. 1-17. ISSN 0960-7412
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Abstract
Peanut productivity and quality improvement rely on understanding the genetic factors influencing pod and seed size. This study aims to identify genetic factors and regulatory mechanisms influencing pod and seed size in peanuts. Herein, a genome-wide association study (GWAS) was conducted using 390 accessions from 15 peanut growing regions to analyze pod and seed traits across multiple planting seasons. A significant phenotypic variation was observed, with broad-sense heritability ranging from 53.6 to 85.4%. Strong correlations between pod and seed traits further suggest potential for co-selection in breeding efforts. A pleiotropic hotspot on chromosome B06 was strongly associated with six pod and seed traits. A peanut pod size regulator AhPDS1 (PODSIZE-1, Ahy_B06g085516) homolog of Arabidopsis thaliana YUCCA4 (AtYUC4, AT5G11320), involved in auxin biosynthesis, was selected as a candidate regulating pod and seed size. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) confirmed higher AhPDS1 expression in large pod as compared with the small pod genotypes. Subcellular localization showed AhPDS1 to be predominantly cytoplasmic, and GUS reporter assays indicated widespread expression in roots, stems, leaves, flowers, and pods, suggesting a broad functional role. Further overexpression of AhPDS1 in Arabidopsis and rice enhanced pod, seed, and grain sizes via the indole-3-pyruvic acid pathway in transgene lines. These findings highlight AhPDS1 as a potential target for peanut molecular breeding, offering opportunities to enhance pod size via auxin biosynthesis and support sustainable crop improvement.
| Item Type: | Article |
|---|---|
| Divisions: | Global Research Program - Accelerated Crop Improvement |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | peanut, GWAS, AhPDS1, auxin biosynthesis, molecular breeding |
| Subjects: | Mandate crops > Groundnut Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 26 Feb 2026 11:16 |
| Last Modified: | 26 Feb 2026 11:16 |
| URI: | http://oar.icrisat.org/id/eprint/13499 |
| Official URL: | https://onlinelibrary.wiley.com/doi/epdf/10.1111/t... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | This work was supported by the National Natural Science Foundation of China (32172051 and 32301869), the National Key R&D Program of China (2023YFD1202800), China Agriculture Research System of MOF and MARA (CARS-13), the Open Competition Program of Top Ten Critical Priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan in Guangdong Province (2022SDZG05), Guangdong Provincial Key Research and Development Program-Modern Seed Industry (2022B0202060004), Guangdong Science and Technology Plan Project (2023B1212060038), Guangdong Basic and Applied Basic Research Foundation (2023A1515010098), the Special Support Program of Guangdong Province (2021TX06N789), Guangzhou Basic and Applied Basic Research Foundation (202201010281 and 2023A04J0776), Special Fund for High Level Academy of Agriculture Science (R2020PY-JX004, R2020PY-JG005, R2021PY-QY003, R2022YJ-YB3025 and R2023PY-JG007), the Foundation of Director of Crop Research Institute of Guangdong Academy of Agriculture Sciences (202101, 202201 and 202306), the Project of Collaborative Innovation Center of GDAAS (XTXM202203). |
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