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High-Throughput Association Mapping in Brassica napus L.: Methods and Applications

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Plant Genotyping

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2638))

Abstract

Oil seed rape (Braasica napus L.) is ranked second among oil seed crops cultivated globally for edible oil for human, and seed cake for animal consumption. Recent genetic and genomics advancements highlighted the diversity that exists within B. napus, which is largely discovered using the most promising genetic markers called single nucleotide polymorphism (SNP). Their calling rate is also enhanced to ~100 folds after the continuous advancements in the next generation sequencing (NGS) technologies. As the high throughput of NGS resulted in multi-Giga bases data, the detailed quality control (QC) prior to downstream analyses is a pre-requisite. It mainly involved the removal of false positives, missing proportions, filtering of low-quality SNPs, and adjustments of minor-allele frequency and heterozygosity. After marker-trait association, for conformation of target SNPs, validations of SNPs can be performed using various methods, especially allele-specific PCR assay-based methods have been utilized for SNP genotyping of genes targeting agronomic traits and somaclonal variations occurred during transgenic studies. In the present study, the authors mainly argue on the genotypic progress, and pipelines/methods that are being used for detection, calling, filtering, and validation of SNPs. Also, insight is provided into the application of SNPs in linkage and association mapping, including QTL mapping and genome-wide association studies targeting mainly developmental traits related to the root system and plant architecture, flowering time, silique, and oil quality. Briefly, the present study provides the recent information and recommendations on the SNP genotyping methods and its applications, which can be useful for marker-assisted breeding in B. napus and other crops.

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Acknowledgments

The funding for RAG was supported by the National Natural Science Foundation of China (31950410560).

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Authors and Affiliations

  1. Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China

    Rafaqat Ali Gill, Md Mostofa Uddin Helal, Ming Hu, Chaobo Tong & Shengyi Liu

  2. Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China

    Minqiang Tang

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  1. Rafaqat Ali Gill
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Correspondence to Rafaqat Ali Gill .

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  1. College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia

    Yuri Shavrukov

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Gill, R.A., Helal, M.M.U., Tang, M., Hu, M., Tong, C., Liu, S. (2023). High-Throughput Association Mapping in Brassica napus L.: Methods and Applications. In: Shavrukov, Y. (eds) Plant Genotyping. Methods in Molecular Biology, vol 2638. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3024-2_6

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  • DOI: https://doi.org/10.1007/978-1-0716-3024-2_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3023-5

  • Online ISBN: 978-1-0716-3024-2

  • eBook Packages: Springer Protocols

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