Multiomics of a rice population identifies genes and genomic regions that bestow low glycemic index and high protein content

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cg.authorship.typesCGIAR and advanced research instituteen_US
cg.contributor.affiliationInternational Rice Research Instituteen_US
cg.contributor.affiliationMax Planck Institute of Molecular Plant Physiologyen_US
cg.contributor.affiliationUniversity of Californiaen_US
cg.contributor.donorUS Foundation for Food and Agriculture Researchen_US
cg.contributor.donorEuropean Regional Development Funden_US
cg.contributor.donorDepartment of Agriculture and Farmers Welfare, Government of Indiaen_US
cg.contributor.donorCGIAR Trust Funden_US
cg.contributor.initiativeAccelerated Breedingen_US
cg.coverage.regionAfricaen_US
cg.coverage.regionAsiaen_US
cg.coverage.regionAmericasen_US
cg.coverage.regionAustralia and New Zealanden_US
cg.coverage.regionCaribbeanen_US
cg.coverage.regionEuropeen_US
cg.creator.identifierSaurabh Badoni: 0000-0001-6969-5662en_US
cg.creator.identifierSung-Ryul Kim: 0000-0003-1223-2442en_US
cg.creator.identifierRhowell Jr. Tiozon: 0000-0002-2177-8730en_US
cg.creator.identifierReuben James Buenafe: 0000-0002-0023-3678en_US
cg.creator.identifierInez Slamet-Loedin: 0000-0001-9145-3571en_US
cg.creator.identifierNese Sreenivasulu: 0000-0002-3998-038Xen_US
cg.howPublishedFormally Publisheden_US
cg.identifier.doihttps://doi.org/10.1073/pnas.2410598121en_US
cg.isijournalISI Journalen_US
cg.issn0027-8424en_US
cg.issue36en_US
cg.journalProceedings of the National Academy of Sciences of the United States of Americaen_US
cg.reviewStatusPeer Reviewen_US
cg.subject.actionAreaGenetic Innovationen_US
cg.subject.impactAreaNutrition, health and food securityen_US
cg.volume121en_US
dc.contributor.authorBadoni, Saurabhen_US
dc.contributor.authorPasion-Uy, Erstelle A.en_US
dc.contributor.authorKor, Sakshien_US
dc.contributor.authorKim, Sung-Ryulen_US
dc.contributor.authorTiozon, Rhowell N.en_US
dc.contributor.authorMisra, Gopalen_US
dc.contributor.authorBuenafe, Reuben James Q.en_US
dc.contributor.authorLabarga, Luster Mayen_US
dc.contributor.authorRamos-Castrosanto, Ana Roseen_US
dc.contributor.authorPratap, Vipinen_US
dc.contributor.authorSlamet-Loedin, Inezen_US
dc.contributor.authorSteimker, Julia vonen_US
dc.contributor.authorAlseekh, Salehen_US
dc.contributor.authorKohli, Ajayen_US
dc.contributor.authorKhush, Gurudev S.en_US
dc.contributor.authorSreenivasulu, Neseen_US
dc.date.accessioned2024-12-20T15:56:31Zen_US
dc.date.available2024-12-20T15:56:31Zen_US
dc.identifier.urihttps://hdl.handle.net/10568/168150en_US
dc.titleMultiomics of a rice population identifies genes and genomic regions that bestow low glycemic index and high protein contenten_US
dcterms.abstractTo counter the rising incidence of diabetes and to meet the daily protein needs, we created low glycemic index (GI) rice varieties with protein content (PC) surpassing 14%. In the development of recombinant inbred lines using Samba Mahsuri and IR36 amylose extender (IR36ae) as parental lines, we identified quantitative trait loci and genes associated with low GI, high amylose content (AC), and high PC. By integrating genetic techniques with classification models, this comprehensive approach identified candidate genes on chromosome 2 (qGI2.1/qAC2.1 spanning the region from 18.62 Mb to 19.95 Mb), exerting influence on low GI and high amylose. Notably, the phenotypic variant with high value was associated with the recessive allele of the starch branching enzyme 2b (sbeIIb). The genome-edited sbeIIb line confirmed low GI phenotype in milled rice grains. Further, combinations of alleles created by the highly significant SNPs from the targeted associations and epistatically interacting genes showed ultralow GI phenotypes with high amylose and high protein. Metabolomics analysis of rice with varying AC, PC, and GI revealed that the superior lines of high AC and PC, and low GI were preferentially enriched in glycolytic and amino acid metabolisms, whereas the inferior lines of low AC and PC and high GI were enriched with fatty acid metabolism. The high amylose high protein recombinant inbred line (HAHP_101) was enriched in essential amino acids like lysine. Such lines may be highly relevant for food product development to address diabetes and malnutrition.en_US
dcterms.accessRightsOpen Accessen_US
dcterms.audienceCGIARen_US
dcterms.audienceAcademicsen_US
dcterms.audienceDonorsen_US
dcterms.audienceScientistsen_US
dcterms.audienceGeneral Publicen_US
dcterms.available2024-08-27en_US
dcterms.bibliographicCitationBadoni, Saurabh, Erstelle A. Pasion-Uy, Sakshi Kor, Sung-Ryul Kim, Rhowell N. Tiozon Jr, Gopal Misra, Reuben James Q. Buenafe et al. "Multiomics of a rice population identifies genes and genomic regions that bestow low glycemic index and high protein content." Proceedings of the National Academy of Sciences 121, no. 36 (2024): e2410598121.en_US
dcterms.extent9 p.en_US
dcterms.issued2024-08-27en_US
dcterms.languageenen_US
dcterms.licenseCC-BY-4.0en_US
dcterms.publisherProceedings of the National Academy of Sciencesen_US
dcterms.subjectinbred linesen_US
dcterms.subjectvarietiesen_US
dcterms.subjectstarchen_US
dcterms.subjectproteinsen_US
dcterms.subjectriceen_US
dcterms.subjectgenomicsen_US
dcterms.typeJournal Articleen_US

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