Genetic dissection of root traits in a rice ‘global MAGIC’ population for candidate traits to breed for reduced methane emission

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dc.creatorRoy, Ripon Kumar
dc.creatorMisra, Gopal
dc.creatorSharma, Shaina
dc.creatorPahi, Bandana
dc.creatorHosseiniyan Khatibi, Seyed Mahdi
dc.creatorTrijatmiko, Kurniawan Rudi
dc.creatorKim, Sung Ryul
dc.creatorHernandez, Jose E.
dc.creatorHenry, Amelia
dc.creatorSreenivasulu, Nese
dc.creatorDiaz, Maria Genaleen Q.
dc.creatorOcampo, Eureka Teresa M.
dc.creatorSinha, Pallavi
dc.creatorKohli, Ajay
dc.date2025-07-09
dc.date2025-08-11T02:03:54Z
dc.date2025-08-11T02:03:54Z
dc.date.accessioned2026-06-27T04:13:56Z
dc.descriptionRice 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.
dc.formatapplication/pdf
dc.identifierhttps://hdl.handle.net/10568/176056
dc.identifier.urihttp://hdl.handle.net/123456789/25928
dc.languageen
dc.publisherFrontiers Media
dc.rightsOpen Access
dc.sourceRoy RK, Misra G, Sharma S, Pahi B, Hosseiniyan Khatibi SM, Trijatmiko KR, Kim SR, Hernandez JE, Henry A, Sreenivasulu N, Diaz MGQ, Ocampo ETM, Sinha P and Kohli A (2025) Genetic dissection of root traits in a rice ‘global MAGIC’ population for candidate traits to breed for reduced methane emission. Front. Plant Sci. 16:1616424.
dc.subjectroots
dc.subjectgenome-wide association studies
dc.subjectgenetic improvement
dc.subjectmethane emission
dc.subjecthaplotypes
dc.subjectporosity
dc.subjectrice
dc.titleGenetic dissection of root traits in a rice ‘global MAGIC’ population for candidate traits to breed for reduced methane emission
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)