Genetic dissection of root traits in a rice ‘global MAGIC’ population for candidate traits to breed for reduced methane emission
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 int...
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| Language: | English |
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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1616424/full |
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| author | Ripon Kumar Roy Ripon Kumar Roy Ripon Kumar Roy Gopal Misra Shaina Sharma Shaina Sharma Bandana Pahi Bandana Pahi Seyed Mahdi Hosseiniyan Khatibi Kurniawan Rudi Trijatmiko Sung Ryul Kim Jose E. Hernandez Amelia Henry Nese Sreenivasulu Maria Genaleen Q. Diaz Eureka Teresa M. Ocampo Pallavi Sinha Pallavi Sinha Ajay Kohli |
| author_facet | Ripon Kumar Roy Ripon Kumar Roy Ripon Kumar Roy Gopal Misra Shaina Sharma Shaina Sharma Bandana Pahi Bandana Pahi Seyed Mahdi Hosseiniyan Khatibi Kurniawan Rudi Trijatmiko Sung Ryul Kim Jose E. Hernandez Amelia Henry Nese Sreenivasulu Maria Genaleen Q. Diaz Eureka Teresa M. Ocampo Pallavi Sinha Pallavi Sinha Ajay Kohli |
| author_sort | Ripon Kumar Roy |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-88f3b22e90bc4f0898cdca85d4a3df9f |
| institution | Matheson Library |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-88f3b22e90bc4f0898cdca85d4a3df9f2025-07-09T05:37:10ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-07-011610.3389/fpls.2025.16164241616424Genetic dissection of root traits in a rice ‘global MAGIC’ population for candidate traits to breed for reduced methane emissionRipon Kumar Roy0Ripon Kumar Roy1Ripon Kumar Roy2Gopal Misra3Shaina Sharma4Shaina Sharma5Bandana Pahi6Bandana Pahi7Seyed Mahdi Hosseiniyan Khatibi8Kurniawan Rudi Trijatmiko9Sung Ryul Kim10Jose E. Hernandez11Amelia Henry12Nese Sreenivasulu13Maria Genaleen Q. Diaz14Eureka Teresa M. Ocampo15Pallavi Sinha16Pallavi Sinha17Ajay Kohli18Rice Breeding Innovations, International Rice Research Institute (IRRI), Los Baños, PhilippinesRice Breeding Innovations, Bangladesh Rice Research Institute (BRRI), Gazipur, BangladeshInstitute of Biological Sciences, University of Philippines, Los Baños, PhilippinesRice Breeding Innovations, International Rice Research Institute (IRRI), Los Baños, PhilippinesRice Breeding Innovations, International Rice Research Institute (IRRI), Los Baños, PhilippinesRice Breeding Innovations, International Rice Research Institute, South Asia Hub, Telangana, IndiaRice Breeding Innovations, International Rice Research Institute (IRRI), Los Baños, PhilippinesRice Breeding Innovations, International Rice Research Institute, South Asia Hub, Telangana, IndiaRice Breeding Innovations, International Rice Research Institute (IRRI), Los Baños, PhilippinesRice Breeding Innovations, International Rice Research Institute (IRRI), Los Baños, PhilippinesRice Breeding Innovations, International Rice Research Institute (IRRI), Los Baños, PhilippinesInstitute of Crop Sciences, University of Philippines Los Baños, Los Baños, PhilippinesRice Breeding Innovations, International Rice Research Institute (IRRI), Los Baños, PhilippinesRice Breeding Innovations, International Rice Research Institute (IRRI), Los Baños, PhilippinesInstitute of Biological Sciences, University of Philippines, Los Baños, PhilippinesInstitute of Crop Sciences, University of Philippines Los Baños, Los Baños, PhilippinesRice Breeding Innovations, International Rice Research Institute (IRRI), Los Baños, PhilippinesRice Breeding Innovations, International Rice Research Institute, South Asia Hub, Telangana, IndiaRice Breeding Innovations, International Rice Research Institute (IRRI), Los Baños, PhilippinesRice 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.https://www.frontiersin.org/articles/10.3389/fpls.2025.1616424/fullroot diameterroot porositygenome-wide association analysissuperior haplotypeprotein-protein interactionmethane emission |
| spellingShingle | Ripon Kumar Roy Ripon Kumar Roy Ripon Kumar Roy Gopal Misra Shaina Sharma Shaina Sharma Bandana Pahi Bandana Pahi Seyed Mahdi Hosseiniyan Khatibi Kurniawan Rudi Trijatmiko Sung Ryul Kim Jose E. Hernandez Amelia Henry Nese Sreenivasulu Maria Genaleen Q. Diaz Eureka Teresa M. Ocampo Pallavi Sinha Pallavi Sinha Ajay Kohli Genetic dissection of root traits in a rice ‘global MAGIC’ population for candidate traits to breed for reduced methane emission Frontiers in Plant Science root diameter root porosity genome-wide association analysis superior haplotype protein-protein interaction methane emission |
| title | Genetic dissection of root traits in a rice ‘global MAGIC’ population for candidate traits to breed for reduced methane emission |
| title_full | Genetic dissection of root traits in a rice ‘global MAGIC’ population for candidate traits to breed for reduced methane emission |
| title_fullStr | Genetic dissection of root traits in a rice ‘global MAGIC’ population for candidate traits to breed for reduced methane emission |
| title_full_unstemmed | Genetic dissection of root traits in a rice ‘global MAGIC’ population for candidate traits to breed for reduced methane emission |
| title_short | Genetic dissection of root traits in a rice ‘global MAGIC’ population for candidate traits to breed for reduced methane emission |
| title_sort | genetic dissection of root traits in a rice global magic population for candidate traits to breed for reduced methane emission |
| topic | root diameter root porosity genome-wide association analysis superior haplotype protein-protein interaction methane emission |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1616424/full |
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