ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Breeding
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1616424
Genetic dissection of root traits in a rice 'global MAGIC' population for candidate traits to breed for reduced methane emission
Provisionally accepted
Ripon Kumar Roy1,2,3Gopal Misra1Shaina Sharma1,4Bandana Pahi1,3Seyed Mahdi Hosseiniyan Khatibi1Kurniawan Rudi Trijatmiko1Sung Ryul Kim1
Jose E. Hernandez3
Amelia Henry1
Nese Sreenivasulu1
Maria Genaleen Diaz3
Eureka Teresa M Ocampo3
Pallavi Sinha1,4
Ajay Kohli1*- 1International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
- 2Bangladesh Rice Research Institute, Gazipur, Bangladesh
- 3University of the Philippines Los Baños, Los Baños, Philippines
- 4International Rice Research Institute, South Asia Hub, Patancheru, India
Select one of your emails
You have multiple emails registered with Frontiers:
Notify me on publication
Please enter your email address:
If you already have an account, please login
You don't have a Frontiers account ? You can register here
Rice cultivation is critical for global food security. The largely practiced method of rice cultivation by transplantation under flooded fields contributes significantly to methane (CH4) emissions, posing challenges to climate-smart agriculture. This study uses a multi-parent advanced generation inter-cross (MAGIC) population of 250 rice genotypes to understand the genetic basis of root traits that may govern CH4 mitigation. Phenotyping under controlled greenhouse conditions revealed significant variation in root diameter (0.122–0.481 mm) and porosity (5.344–56.793 g), and strong correlations between root diameter and porosity traits (r = 0.40–0.50, p < 0.001). Association studies revealed key candidate genes including Os05g0411200 (thermosensitive chloroplast development), Os10g0177300 (chalcone synthase), and Os04g0405300 (alcohol dehydrogenase), which regulate aerenchyma formation and auxin homeostasis. Protein-protein interaction networks linked these genes to flavonoid biosynthesis (KEGG map00941) and N-glycan pathways, earlier identified as critical for root architecture. Haplotype-phenotype analysis revealed 8 superior haplotypes across 7 genes for average root porosity, base root porosity, root diameter, and tip root porosity. These findings provide the foundation for breeding high-yielding rice varieties with reduced methane emissions, addressing the challenges of food security and climate change.
Keywords: root diameter, Root porosity, genome-wide association analysis, Superior Haplotype, protein-protein interaction, Methane emission
Received: 22 Apr 2025; Accepted: 04 Jun 2025.
Copyright: © 2025 Roy, Misra, Sharma, Pahi, Hosseiniyan Khatibi, Trijatmiko, Kim, Hernandez, Henry, Sreenivasulu, Diaz, Ocampo, Sinha and Kohli. 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: Ajay Kohli, International Rice Research Institute (IRRI), Los Baños, 1226, Laguna, Philippines
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.