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Genome-wide association study and transcriptome analysis reveal natural variation of key genes regulation flowering time in rapeseed

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Abstract

Flowering time is a crucial determinant of both the yield and oil quality of rapeseed as well as a key indicator of plant maturity. We performed a genome-wide association study and transcriptome analysis to identify key genes/loci regulating flowering time in Brassica napus L. Forty-six haplotype regions harboring candidate genes were determined to be significantly associated with flowering time, and 28 of these haplotype regions overlapped with previously reported quantitative trait loci. A further investigation of these haplotype regions revealed nucleotide variations in the genes BnaFT-A02, BnaFRI-A10, and BnaFPA-A09 that correlated with phenotypic variations in flowering time. Furthermore, the co-expression network analysis indicated that BnaFT-A02 is directly linked to BnaFRI-A10 and BnaFPA-A09, in a subnetwork and also associated with 13 vernalization, 31 photoperiod, 33 autonomous pathway, and 10 gibberellin pathway genes, forming a potential network regulating flowering time in rapeseed. These results provide valuable haplotype markers for the breeding of early maturing rapeseed varieties.

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Data availability

All data supporting the findings of this study are included in the paper and its supplementary data or are available from the corresponding author on request.

Abbreviations

GWAS:

Genome-wide association study

DH:

Doubled haploid

QTL:

Quantitative trait loci

SNP:

Single nucleotide polymorphism

MAF:

Minor allele frequency

MLM:

Mixed linear model

FDR:

False discovery rate

PCA:

Principal component analysis

Q-Q plot:

Quantile-quantile plot

WGCNA:

Weighted gene co-expression network analysis

H 2 :

Broad-sense heritability

Hap:

Haplotype

GO:

Gene ontology

FT :

FLOWERING LOCUS T

FRI :

FRIGIDA

FPA :

FLOWERING LOCUS PA

FLC :

FLOWERING LOCUS C

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Acknowledgements

We thank TopEdit (www.topeditsci.com) for its linguistic assistance during the preparation of this manuscript.

Funding

This study was funded by the Hunan Province Science and Technology Innovation Leading Talent Project (grant No. S2023YZCXLJ0098), the Science Foundation for Distinguished Youth Scholars of Hunan Province (grant No. 2022JJ10027), and the National Natural Science Foundation of China (grant No. 32072100).

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  1. Xingru Xiang and Ping Qiu are contributed equally to this work.

Authors and Affiliations

  1. College of Agronomy, Hunan Agricultural University, Changsha, 410128, China

    Xingru Xiang, Ping Qiu, Zhichao Mei, Min Yao, Wei Liu, Dan He, Song Cao, Xin He, Xinghua Xiong, Zhongsong Liu & Lunwen Qian

  2. Yuelushan Laboratory, Changsha, 410128, China

    Xingru Xiang, Ping Qiu, Zhichao Mei, Min Yao, Wei Liu, Dan He, Song Cao, Xin He, Xinghua Xiong, Zhongsong Liu & Lunwen Qian

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  1. Xingru Xiang
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Contributions

Lunwen Qian conceived the research idea and plans. Xingru Xiang and Ping Qiu analyzed data and prepared the manuscript. Zhichao Mei, Min Yao and Wei Liu performed data mining and bioinformatics. Dan He and Song Cao carried out reagents and the field experiments. Xin He, Xinghua Xiong, Zhongsong Liu and Lunwen Qian revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Lunwen Qian.

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Xiang, X., Qiu, P., Mei, Z. et al. Genome-wide association study and transcriptome analysis reveal natural variation of key genes regulation flowering time in rapeseed. Mol Breeding 44, 40 (2024). https://doi.org/10.1007/s11032-024-01479-4

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