Abstract
Key message
We report here the discovery of high-confidence MQTL regions and of putative candidate genes associated with seed weight in B. napus using a highly dense consensus genetic map and by comparing various large-scale multiomics datasets.
Abstract
Seed weight (SW) is a direct determinant of seed yield in Brassica napus and is controlled by many loci. To unravel the main genomic regions associated with this complex trait, we used 13 available genetic maps to construct a consensus and highly dense map, comprising 40,401 polymorphic markers and 9191 genetic bins, harboring a cumulative length of 3047.8 cM. Then, we performed a meta-analysis using 639 projected SW quantitative trait loci (QTLs) obtained from studies conducted since 1999, enabling the identification of 57 meta-QTLS (MQTLs). The confidence intervals of our MQTLs were 9.8 and 4.3 times lower than the average CIs of the original QTLs for the A and C subgenomes, respectively, resulting in the detection of some key genes and several putative novel candidate genes associated with SW. By comparing the genes identified in MQTL intervals with multiomics datasets and coexpression analyses of common genes, we defined a more reliable and shorter list of putative candidate genes potentially involved in the regulation of seed maturation and SW. As an example, we provide a list of promising genes with high expression levels in seeds and embryos (e.g., BnaA03g04230D, BnaC03g08840D, BnaA10g29580D and BnaA03g27410D) that can be more finely studied through functional genetics experiments or that may be useful for MQTL-assisted breeding for SW. The high-density genetic consensus map and the single nucleotide polymorphism (SNP) physical map generated from the latest B. napus cv. Darmor-bzh v10 assembly will be a valuable resource for further mapping and map-based cloning of other important traits.
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All analyzed data during this study are included within the article or in its associated supplementary information files.
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Acknowledgements
Thanks to Professor Kun Lu for his help in extracting RNA-Sequencing data from the https://brassica.biodb.org/ database. We are grateful to the reviewers and editors for their constructive review and comments for this manuscript.
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This research was supported by the National Key Research and Development Program of China (2022YFD1200400), the National Natural Science Foundation of China (31971902, 32001509).
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The project was conceived, coordinated and supervised by LL and MRG. SB collected, analyzed and interpreted all of the data and wrote the manuscript. MRG constructed physical map. HDR performed meta-analysis, GWAS collinearity and drew graphs. MG and HDR constructed consensus map. SF and PH gathered, analyzed the QTLs data. ASN analyzed the gene dataset. All authors read, revised and approved the final manuscript.
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Bilgrami, S., Darzi Ramandi, H., Farokhzadeh, S. et al. Meta-analysis of seed weight QTLome using a consensus and highly dense genetic map in Brassica napus L.. Theor Appl Genet 136, 161 (2023). https://doi.org/10.1007/s00122-023-04401-2
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DOI: https://doi.org/10.1007/s00122-023-04401-2