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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Breeding
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1541656

Genome-Wide Association Scan and Candidate Gene Analysis for Seed Coat Color in Sesame (Sesamum indicum L.)

Provisionally accepted
Mohammed Elsafy Mohammed Elsafy 1*Wafa Badawi Wafa Badawi 2Ahmed Ibrahim Ahmed Ibrahim 2Elamin Hafiz Baillo Elamin Hafiz Baillo 2Prabin Bajgain Prabin Bajgain 3Tilal Sayed Abdelhalim Tilal Sayed Abdelhalim 2Mahbubjon Rahmatov Mahbubjon Rahmatov 1*
  • 1 Department of Plant Breeding, Faculty of Landscape Architecture, Horticulture and Crop Production Science, Swedish University of Agricultural Sciences, Alnarp, Sweden
  • 2 Agricultural Research Corporation (ARC), Wad Madani, Al Jazirah, Sudan
  • 3 Department of Agronomy and Plant Genetics, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, St. Paul, Minnesota, United States

The final, formatted version of the article will be published soon.

    Introduction: Seed coat color in sesame is a crucial trait for breeding programs as it is closely associated with important characteristics such as oil content, protein levels, and disease resistance, which directly influence seed quality and market value.Methods: This study investigates the genetic basis of seed coat color in 200 Sudanese sesame genotypes grown for two consecutive years through comprehensive phenotyping, genomic diversity analysis, genome-wide association studies (GWAS), and candidate gene discovery.Results and discussion: Phenotypic analysis across two growing seasons revealed high heritability and significant correlations among color parameters (L*, a*, and b*), indicating strong genetic control over seed coat color. The genomic analysis identified distinct clusters among sesame accessions, with rapid linkage disequilibrium decay suggesting a high level of recombination. GWAS identified significant SNPs associated with seed coat color traits, revealing key genomic regions on chromosomes 3, 6, 9, 12, and 13. Candidate gene analysis highlighted several genes, including DOF zinc finger proteins and WRKY transcription factors, which may play essential roles in pigment biosynthesis pathways. These findings provide valuable insights for breeding programs to enhance desirable seed coat color traits in sesame.

    Keywords: biosynthesis, Encoding proteins, GWAS, Pigmentation, Sudan

    Received: 08 Dec 2024; Accepted: 02 Jan 2025.

    Copyright: © 2025 Elsafy, Badawi, Ibrahim, Hafiz Baillo, Bajgain, Abdelhalim and Rahmatov. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Mohammed Elsafy, Department of Plant Breeding, Faculty of Landscape Architecture, Horticulture and Crop Production Science, Swedish University of Agricultural Sciences, Alnarp, 23053, Sweden
    Mahbubjon Rahmatov, Department of Plant Breeding, Faculty of Landscape Architecture, Horticulture and Crop Production Science, Swedish University of Agricultural Sciences, Alnarp, 23053, Sweden

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.