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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Abiotic Stress
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1426321

Genome-wide association study (GWAS) and genotypic variation for the major tocopherol content in rice grain

Provisionally accepted
Sara Kazemzadeh Sara Kazemzadeh 1Naser Farrokhi Naser Farrokhi 1*Asadollah Ahmadikhah Asadollah Ahmadikhah 1*Kourosh Tabar Heydar Kourosh Tabar Heydar 2Abdolali Gilani Abdolali Gilani 3Hossein Askari Hossein Askari 1Pär K. Ingvarsson Pär K. Ingvarsson 4*
  • 1 Shahid Beheshti University, Tehran, Tehran, Iran
  • 2 Chemistry and Chemical Engineering Research Center of Iran, Teheran, Iran
  • 3 Agricultural and Natural Resources Research Institute of Khuzestan, Ahwaz, Iran
  • 4 Swedish University of Agricultural Sciences, Uppsala, Sweden

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

    Rice tocopherols, vitamin E compounds with antioxidant activity, play essential roles in human health. Even though the key genes involved in vitamin E biosynthetic pathways have been identified in plants, the genetic architecture of vitamin E content in rice grain remains unclear. A genome-wide association study (GWAS) on 179 genotypically diverse rice accessions with 34,323 SNP markers was conducted to detect QTLs that define total and α-tocopherol contents in rice grains. Total and α-tocopherol contents had a strong positive correlation and varied greatly across the accessions, ranging from 0.230-31.76 and 0.011-30.83 (μg/g), respectively. A total of 13 QTLs were identified, which were spread across five of the rice chromosomes. Among the 13 QTLs, 11 were considered major with phenotypic variation explained (PVE) greater than 10%. Twelve transcription factor (TF) genes, one microprotein (miP), and a transposon were found to be associated with the QTLs with putative roles in controlling tocopherol contents. Moreover, intracellular transport proteins, ABC transporters, nonaspanins, and SNARE, were identified as associated genes on chromosomes 1 and 8. In the vicinity of seven QTLs, protein kinases were identified as key signaling factors. Haplotype analysis revealed the QTLs qAlph1. 1, qTot1.1, qAlph2.1, qAlph6.1, qTot6.1, and qTot8.3 to have significant haplogroups. Quantitative RT-PCR validated the expression direction and magnitude of WRKY39 (Os02g0265200), PIP5Ks (Os08g0450800), and MADS59 (Os06g0347700) in defining the major tocopherol contents. This study provides insights for ongoing biofortification efforts to breed and/or engineer vitamin E and antioxidant levels in rice and other cereals.

    Keywords: kinases, MicroProtein, quantitative trait loci (QTLs), transcription factor, transporter

    Received: 08 May 2024; Accepted: 03 Sep 2024.

    Copyright: © 2024 Kazemzadeh, Farrokhi, Ahmadikhah, Tabar Heydar, Gilani, Askari and Ingvarsson. 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:
    Naser Farrokhi, Shahid Beheshti University, Tehran, 1983963113, Tehran, Iran
    Asadollah Ahmadikhah, Shahid Beheshti University, Tehran, 1983963113, Tehran, Iran
    Pär K. Ingvarsson, Swedish University of Agricultural Sciences, Uppsala, Sweden

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