ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Genetics, Epigenetics and Chromosome Biology
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1658653
Exploring Functional InDels and Genetic Diversity: Agro-Morphometric and Molecular Insights into the Western and Eastern Gene Pools of Carrot (Daucus carota L.)
Provisionally accepted
Trupthi Mudihal1
Sarvamagnala Cholin1*Chaitra Kulkarni2
K.M. Shivaprasad3Prakash Kumar4William Rolling5
Philipp W. Simon5,6*- 1University of Horticultural Sciences Bagalkot, Bagalkot, India
- 2Kittur Rani Channamma College of Horticulture, Arabhavi, India
- 3Indian Council of Forestry Research and Education, Dehradun, India
- 4Indian Statistical Institute Delhi Centre, New Delhi, India
- 5University of Wisconsin-Madison, Madison, United States
- 6USDA-ARS Midwest Area, Peoria, United States
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The carrot (Daucus carota L.) is a globally cultivated root vegetable with significant genetic diversity. This first study generated and validated carrot InDels to unravel the genetic divergence between Eastern and Western gene pools, integrating agro-morphometric traits with functional InDel markers. Eastern accessions exhibited larger plants, bigger roots with diverse colors, while Western accessions were more uniform orange color and compact in architecture. From RNA-seq data, 271 agarose-resolvable functional InDels (>15bp length difference) were identified, of which 48 validated markers showed high polymorphism (84.21%) across two gene pools supporting secondary domestication changes. Located in coding and UTR regions, these InDels likely regulate gene expression and may have contributed to significant genetic modifications among carrot gene pools. Genetic diversity in the Western gene pool indicated more intense selection and domestication. Population structure and phylogenetic analysis revealed clear gene pool differentiation (Fst = 0.181) with potential gene flow (Nm = 1.716). Functional annotation of linked InDels to key biological processes, highlighted their role in domestication. Key InDels (DcFInDel32, DcFInDel28, and DcFInDel55) were associated with multiple traits, underscoring their utility in marker-assisted selection (MAS). These findings provide insights for developing improved carrot cultivars with high yield and quality adapted to diverse climates.
Keywords: carrot, Gene Pool, Indels, Agro-morphometric, genetic diversity, Coding region, population structure
Received: 02 Jul 2025; Accepted: 22 Sep 2025.
Copyright: © 2025 Mudihal, Cholin, Kulkarni, Shivaprasad, Kumar, Rolling and Simon. 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:
Sarvamagnala Cholin, sarucholin@gmail.com
Philipp W. Simon, philipp.simon@ars.usda.gov
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.