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Regional association analysis coupled with transcriptome analyses reveal candidate genes affecting seed oil accumulation in Brassica napus

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Regional association analysis of 50 re-sequenced Chinese semi-winter rapeseed accessions in combination with co-expression analysis reveal candidate genes affecting oil accumulation in Brassica napus.

Abstract

One of the breeding goals in rapeseed production is to enhance the seed oil content to cater to the increased demand for vegetable oils due to a growing global population. To investigate the genetic basis of variation in seed oil content, we used 60 K Brassica Infinium SNP array along with phenotype data of 203 Chinese semi-winter rapeseed accessions to perform a genome-wide analysis of haplotype blocks associated with the oil content. Nine haplotype regions harbouring lipid synthesis/transport-, carbohydrate metabolism- and photosynthesis-related genes were identified as significantly associated with the oil content and were mapped to chromosomes A02, A04, A05, A07, C03, C04, C05, C08 and C09, respectively. Regional association analysis of 50 re-sequenced Chinese semi-winter rapeseed accessions combined with transcriptome datasets from 13 accessions was further performed on these nine haplotype regions. This revealed natural variation in the BnTGD3-A02 and BnSSE1-A05 gene regions correlated with the phenotypic variation of the oil content within the A02 and A04 chromosome haplotype regions, respectively. Moreover, co-expression network analysis revealed that BnTGD3-A02 and BnSSE1-A05 were directly linked with fatty acid beta-oxidation-related gene BnKAT2-C04, thus forming a molecular network involved in the potential regulation of seed oil accumulation. The results of this study could be used to combine favourable haplotype alleles for further improvement of the seed oil content in rapeseed.

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Funding

This study was funded by the National Natural Science Foundation of China (grant no. 31801399), the National Basic Research and Development Programme (2015CB150206) and the National Key Research and Development Project (grant no. 2017YFD0101703).

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Author notes

  1. Min Yao and Mei Guan have contributed equally to this work.

Authors and Affiliations

  1. Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China

    Min Yao, Mei Guan, Qian Yang, Luyao Huang, Xinghua Xiong, Xin He, Chunyun Guan, Wei Hua & Lunwen Qian

  2. College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China

    Wei Qian

  3. Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, 430062, China

    Wei Hua

  4. Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany

    Rod J. Snowdon

  5. Molecular Biology, Department of Pathology, MTI-LRH, Peshawar, 25000, Pakistan

    Habib U. Jan

  6. Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia

    Kai P. Voss-Fels

  7. The Roslin Institute University of Edinburgh Easter Bush Research Centre Midlothian, Midlothian, EH25 9RG, UK

    Christian R. Werner

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  1. Min Yao
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  2. Mei Guan
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  3. Qian Yang
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  9. Xin He
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Contributions

CG, WH and LQ conceived and designed the experiments. MG and MY wrote the manuscript. MY, CW, KV and QY performed the statistical analyses. LH, XX and XH completed field phenotypic data collection. RS, HJ and WQ reviewed the manuscript and made significant contributions in revision. All authors have read and approved the final manuscript.

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Correspondence to Wei Hua or Lunwen Qian.

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Communicated by Albrecht E. Melchinger.

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Yao, M., Guan, M., Yang, Q. et al. Regional association analysis coupled with transcriptome analyses reveal candidate genes affecting seed oil accumulation in Brassica napus. Theor Appl Genet 134, 1545–1555 (2021). https://doi.org/10.1007/s00122-021-03788-0

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