African rice (Oryza glaberrima Steud.), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.
Bibliographical noteKAUST Repository Item: Exported on 2023-08-07
Acknowledgements: This work was supported by Institut de Recherche pour le Développement (IRD) institutional funding, a grant (IRIGIN project) from the France Genomique French National infrastructure and funded as part of ‘‘Investissement d’avenir’’ (ANR-10-INBS-09) and the French Ministère de l’Enseignement Supérieur et de la Recherche provided a PhD grant for FN. The authors acknowledge Ndomassi Tando and the ISO 9001 certified IRD itrop HPC (member of the South Green Platform) at IRD Montpellier for providing HPC resources that have contributed to the research results reported within this paper. Authors thank Stéphane D. Nicolas (INRAE), Pascal Gantet (UM), and Jean-Christophe Glaszmann (CIRAD) for helpful discussions and suggestions for our research project. We thank Dr. James Tregear, IRD, for his careful reading and language editing of the manuscript. We also thank the reviewers for their valuable comments on the earlier version of the manuscript. This work was supported by Institut de Recherche pour le Développement (IRD) institutional funding, a grant (IRIGIN project) from the France Genomique French National infrastructure and funded as part of ‘‘Investissement d’avenir’’ (ANR-10-INBS-09) and the French Ministry of Higher Education and Research (MESR) provided a PhD grant for FN.
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