Abstract
In a rapidly changing climate, flowering time (FL) adaptation is important to maximize seed yield in flax (Linum usitatissimum L.). However, our understanding of the genetic mechanism underlying FL in this multipurpose crop remains limited. With the aim of dissecting the genetic architecture of FL in flax, a genome-wide association study (GWAS) was performed on 200 accessions of the flax core collection evaluated in four environments. Two single-locus and six multi-locus models were applied using 70,935 curated single nucleotide polymorphism (SNP) markers. A total of 40 quantitative trait nucleotides (QTNs) associated with 27 quantitative trait loci (QTL) were identified in at least two environments. The number of QTL with positive-effect alleles in accessions was significantly correlated with FL (r = 0.77 to 0.82), indicating principally additive gene actions. Nine QTL were significant in at least three of the four environments accounting for 3.06–14.71% of FL variation. These stable QTL spanned regions that harbored 27 Arabidopsis thaliana and Oryza sativa FL-related orthologous genes including FLOWERING LOCUS T (Lus10013532), FLOWERING LOCUS D (Lus10028817), transcriptional regulator SUPERMAN (Lus10021215), and gibberellin 2-beta-dioxygenase 2 (Lus10037816). In silico gene expression analysis of the 27 FL candidate gene orthologous suggested that they might play roles in the transition from vegetative to reproductive phase, flower development and fertilization. Our results provide new insights into the QTL architecture of flowering time in flax, identify potential candidate genes for further studies, and demonstrate the effectiveness of combining different GWAS models for the genetic dissection of complex traits.
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Acknowledgements
This work was funded by Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) project N°1161133, and supported by the Agriaquaculture Nutritional Genomic Center (CGNA) and the Gobierno Regional de La Araucania, Chile. CGNA acknowledges the collaboration of Agriculture and Agri-Food Canada (AAFC) and the Total Utilization Flax GENomics (TUFGEN) project formerly funded by Genome Canada and other stakeholders of the Canadian flax industry. Madeleine Levesque-Lemay is also acknowledged for her helpful assistance in manuscript preparation.
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BJSC and SC conceived and designed the study. GA and BJSC conducted the phenotyping of FL. SC performed curation of next-generation sequencing data. BJSC conducted GWA analyses. BJSC and GA prepared tables and figures. BJSC and SC drafted the manuscript. All authors reviewed and edited the manuscript.
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Soto-Cerda, B.J., Aravena, G. & Cloutier, S. Genetic dissection of flowering time in flax (Linum usitatissimum L.) through single- and multi-locus genome-wide association studies. Mol Genet Genomics 296, 877–891 (2021). https://doi.org/10.1007/s00438-021-01785-y
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DOI: https://doi.org/10.1007/s00438-021-01785-y