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Regional association and transcriptome analysis revealed candidate genes controlling plant height in Brassica napus

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Abstract

Plant height is a key morphological trait in rapeseed, which not only plays an important role in determining plant architecture, but is also an important characteristic related to yield. Presently, the improvement of plant architecture is a major challenge in rapeseed breeding. This work was carried out to identify genetic loci related to plant height in rapeseed. In this study, a genome-wide association study (GWAS) of plant height was performed using a Brassica 60 K Illumina Infinium SNP array and 203 Brassica napus accessions. Eleven haplotypes containing important candidate genes were detected and significantly associated with plant height on chromosomes A02, A03, A05, A07, A08, C03, C06, and C09. Moreover, regional association analysis of 50 resequenced rapeseed inbred lines was used to further analyze these eleven haplotypes and revealed nucleotide variation in the BnFBR12-A08 and BnCCR1-C03 gene regions related to the phenotypic variation in plant height. Furthermore, coexpression network analysis showed that BnFBR12-A08 and BnCCR1-C03 were directly connected with hormone genes and transcription factors and formed a potential network regulating the plant height of rapeseed. Our results will aid in the development of haplotype functional markers to further improve plant height in rapeseed.

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Abbreviations

GWAS :

Genome-wide association study

QTL :

Quantitative trait loci

SNP :

Single nucleotide polymorphism

MAF :

Minor allele frequency

FDR :

False discovery rate

PCA :

Principal component analysis

WGCNA :

Weighted correlation network analysis

PCCs :

Pearson correlation coefficients

H 2 :

Broad-sense heritability

GO :

Gene ontology

FBR12 :

FUMONISIN B1-RESISTANT12

CCR1 :

CINNAMOYL COA REDUCTASE 1

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Acknowledgements

We thank other lab members for their help in this article revision and drawing. We are grateful to the editors and reviewers for their constructive comments on the manuscript.

Funding

This study was funded by the National Nature Science Foundation of China (grant No. 32072100).

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  1. Rui Ren and Wei Liu 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

    Rui Ren, Wei Liu, Min Yao, Yuan Jia, Luyao Huang, Wenqian Li, Xin He, Mei Guan, Zhongsong Liu, Chunyun Guan, Xinghua Xiong & Lunwen Qian

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

    Wei Hua

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Contributions

Lunwen Qian and Xinghua Xiong conceived the research idea and plans. Rui Ren and Wei Liu prepared the manuscript. Rui Ren, Yuan Jia, and Min Yao performed data mining and bioinformatics. Luyao Huang and Wenqian Li carried out reagents and the field experiments. Xin He, Mei Guan, Zhongsong Liu, Chunyun Guan, Wei Hua, Xinghua Xiong, and Lunwen Qian read and commented the manuscript. All authors read and approved the final manuscript.

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Correspondence to Xinghua Xiong or Lunwen Qian.

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11032_2022_1337_MOESM1_ESM.pptx

Supplementary file 1 Figure S1 Correlation coefficients and frequency distributions for plant height in 50 resequencing Chinese semi-winter rapeseed accessions. Figure S2 Six haplotype region carrying candidate genes significant association with plant height on chromosome A02, A03, A05 and A07 in 203 Chinese semi-winter rapeseed accessions, respectively. Red triangles represent genes related to plant height. The heatmap spans the SNP markers in LD with the most strongly associated SNPs. Figure S3 Five haplotype region carrying candidate genes significant association with plant height on chromosome A08, C03, C06 and C09 in 203 Chinese semi-winter rapeseed accessions, respectively. Red triangles represent genes related to plant height. The heatmap spans the SNP markers in LD with the most strongly associated SNPs. Figure S4 Different haplotype genes’ expression of BnFBR12-A08 and BnCCR1-C03 by Quantitative real-time PCR. ***p ≤ 0.001. Figure S5 Coexpression network analysis. The red nodes represent candidate genes BnCCR1-C03 and BnFBR12-A08. The triangle node and rhombus node represent genes directly linked to these two candidate genes. Figure S6 Gene Ontology (GO) enrichment analysis in blue module (a) and yellow module (b). Each class top 10 gene ontology (GO) terms had lined out in bubble chart. The bubble size represents the number genes of the category. The bubble color represents the size of the P value. Figure S7 Coexpression network of BnFBR12-A08 in Brassica napus. Red nodes represent BnFBR12-A08 gene. These genes from the coexpression network are divided into the following categories: Abscisic acid pathway (Lime nodes), Auxin pathway (Cyan nodes), Cytokinin pathway (Pink nodes), Gibberellin pathway (Lavender nodes) and Transcription factor (Dimgray nodes). (PPTX 6723 KB)

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Ren, R., Liu, W., Yao, M. et al. Regional association and transcriptome analysis revealed candidate genes controlling plant height in Brassica napus. Mol Breeding 42, 69 (2022). https://doi.org/10.1007/s11032-022-01337-1

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