ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Breeding
This article is part of the Research TopicAdvancing Climate-Resilient Crop Plants: Integrating Molecular and Physiological StrategiesView all 6 articles
Pleiotropic SNPs and genes linked to enhanced seed longevity and vigor for climate resilient pearl millet production
Provisionally accepted
Netyam Kannababu
Sandeep Nanjundappa
RENUKA MALIPATILBharathi ChunduriArutla SrikanthRonda VenkateswarluJinu JacobVijayakumar M Malathi
Tara Satyavathi Chellapilla*
Nepolean Thirunavukkarasu*- ICAR - Indian Institute of Millets Research, Hyderabad, India
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Seed longevity and vigor are critical factors for sustainable crop production, particularly in environments prone to stress, where consistent germination and seedling establishment are crucial. This study investigates the genetic architecture underlying seed longevity and vigor traits in pearl millet (Pennisetum glaucum [L.] R. Br.) through genome-wide association studies (GWAS). The GWAS panel comprising 201 inbred lines representing B and R lines was phenotyped under both control and accelerated aging (AA) conditions for 27 seed longevity and seedling vigor traits and their relative measures. Phenotypic analysis revealed significant changes in seed traits following AA in germination percentages, seedling vigour indices and mean germination times. A 4K mid-density SNP panel was used for genotyping, producing 2,015 high-confidence SNPs after stringent filtering for GWAS. The Bayesian information and linkage disequilibrium iteratively nested keyway (BLINK) and Multi-locus mixed model (MLMM) models identified 413 significant marker-trait associations (MTAs), with 185 MTAs common to both models. A pleiotropic SNP, PMSnpB394 on chromosome 2, was linked to 14 seed longevity traits. Key genes associated with these traits include hormone signaling (Auxin response factor, DOG1), stress response (LEA_2, 10 kDa heat shock protein), metabolism (Glyceraldehyde-3-phosphate dehydrogenase, Beta-galactosidase) and seed coat structure (Peroxidase, 3-Ketoacyl-CoA synthase). These MTAs and candidate genes provide valuable insights into the molecular mechanisms underlying seed longevity and vigor and serve as promising targets for marker-assisted selection and breeding strategies aimed at developing climate-resilient cultivars in the rainfed ecologies.
Keywords: pearl millet, accelerated aging, Genome-Wide Association Study, Marker-traitassociation, Climate resilience
Received: 01 Oct 2025; Accepted: 07 Jan 2026.
Copyright: © 2026 Kannababu, Nanjundappa, MALIPATIL, Chunduri, Srikanth, Venkateswarlu, Jacob, Malathi, Chellapilla and Thirunavukkarasu. 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:
Tara Satyavathi Chellapilla
Nepolean Thirunavukkarasu
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