ORIGINAL RESEARCH article

Front. Plant Sci.

Sec. Plant Abiotic Stress

Volume 16 - 2025 | doi: 10.3389/fpls.2025.1501878

This article is part of the Research TopicManaging Metal Toxicity in Plants and Soil: Strategies for Stress Mitigation and RemediationView all 10 articles

Genome wide association analysis of grain iron and zinc in rice grown under agroclimatic sites with contrasting soil iron status

Provisionally accepted
  • 1Indian Agricultural Research Institute (ICAR), New Delhi, India
  • 2The ICAR Research Complex for North Eastern Hill Region (ICAR RC NEH), Umiam, Meghalaya, India
  • 3Acharya Narendra Deva University of Agriculture and Technology, Ayodhya, Uttar Pradesh, India
  • 4Corteva Agriscience (India), Hyderabad, Andhra Pradesh, India

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

Iron (Fe) content in soil can influence rice cultivation, inciting responses ranging from deficiency to toxicity. Fe toxicity is a major constraint, particularly in areas where acidic soils predominate. Grain Fe content along with Zn is a major contemporary breeding objectives in rice in order to tackle micronutrient deficiency. There is no information available on the influence of soil Fe levels, normal and excess, can influence grain micronutrient contents, particularly in rice genotypes that are tolerant to excess soil Fe. In this study, a subset of 170 rice germplasm lines from the 3K panel were evaluated for grain Fe and Zn concentrations in brown rice across three different locations. Additionally, the response of these lines to Fe toxicity was assessed at one location. Significant phenotypic variation for both traits was observed. Fe toxicity led to increased grain Fe content but decreased Fe uptake efficiency (IAE), suggesting an adaptive mechanism to limit excess Fe absorption in the rhizosphere. Five significant single nucleotide polymorphisms (SNPs) associated with grain Fe (qGFe1.1 ADT , qGFe2.1 BPN-S , qGFe8.1 ADT , qGFe12.1 ADT , and qGFe12.2 BPN-N ) were identified on chromosomes 1, 2, 8, and 12, while one SNP associated with grain Zn (qGZn12.1 BPN-N ) was detected on chromosome 12. These SNPs co-localized with major genes and QTLs involved in heavy-metal homeostasis and transport, including OsMT2D and Os12g0435000. Superior haplotypes for two candidate genes were identified, with analysis revealing their frequencies and allelic effects in different subgroups. Two marker-trait associations (MTAs), qGFe12.1 ADT and qGZn12.1 BPN-N , were validated in an F2:3 population using linked SSR markers. These validated MTAs provide valuable genetic resources for biofortification breeding programs aimed at increasing Fe and Zn concentrations in rice grains, addressing micronutrient deficiencies among rice-dependent populations.

Keywords: Grain iron, iron toxicity, biofortification, GWAS, haplotype analysis

Received: 25 Sep 2024; Accepted: 29 May 2025.

Copyright: Ā© 2025 Shekhawat, Kumar, Singh, BHOWMICK, Shekharappa, YADAV, S, Ellur, Bollinedi, Singh and vinod. 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: KK vinod, Indian Agricultural Research Institute (ICAR), New Delhi, India

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