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Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines

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Abstract

Key message

Seventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with co-localization by the other map** methods; The functions of three candidate genes were validated using mutants; nine target proteins and five networks were filtered by joint analysis of GWAS and WGCNA.

Abstract

Seed dormancy (SD) and pre-harvest sprouting (PHS) affect yield, as well as grain and hybrid quality in seed production. Therefore, identification of genetic and regulatory pathways underlying PHS and SD is key to gene function analysis, allelic variation mining and genetic improvement. In this study, 78,360 SNPs by SLAF-seq of 230 maize chromosome segment introgression lines (ILs), PHS under five environments were used to conduct GWAS (genome wide association study) (a threshold of 1/n), and seventeen unreported PHS QTLs were obtained, including eleven QTLs with PVE > 10% and three QTLs under multiple environments. Two QTL loci were co-located between the other two genetic map** methods. Using differential gene expression analyses at two stages of grain development, gene functional analysis of Arabidopsis mutants, and gene functional analysis in the QTL region, seventeen PHS QTL-linked candidate genes were identified, and their five molecular regulatory networks constructed. Based on the Arabidopsis T-DNA mutations, three candidate genes were shown to regulate for SD and PHS. Meanwhile, using RNA-seq of grain development, the weighted correlation network analysis (WGCNA) was performed, deducing five regulatory pathways and target genes that regulate PHS and SD. Based on the conjoint analysis of GWAS and WGCNA, four pathways, nine target proteins and target genes were revealed, most of which regulate cell wall metabolism, cell proliferation and seed dehydration tolerance. This has important theoretical and practical significance for elucidating the genetic basis of maize PHS and SD, as well as mining of genetic resources and genetic improvement of traits.

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Data availability

All raw data generated of 36 samples used in this study were deposited in Bioproject in National Genomics Data Center (NGDC) database with the accession number PRJCA017883 subPRO026577.

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Acknowledgements

This work was supported by State Key Laboratory of North China Crop Improvement and Regulation (NCCIR2020ZZ-6), Natural Science Foundation of Heibei Province of China (C2021204078), and Hebei Key R&D Plan “Special project on scientific and technological innovation of modern seed industry” (21326328D). We thank Prof. Jianbing Yan of Huazhong Agricultural University for providing seeds of the 368 natural maize populations.

Funding

This study was funded by the State Key Laboratory of North China Crop Improvement and Regulation (NCCIR2020ZZ-6), Natural Science Foundation of Heibei Province of China (C2021204078), and Hebei Key R&D Plan “Special project on scientific and technological innovation of modern seed industry” (21326328D).

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Author notes

  1. **aolin Ma and Liqing Feng had the same contribution in this work.

Authors and Affiliations

  1. State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China

    **aolin Ma, Liqing Feng, Anyan Tao, Tinashe Zenda, Yuan He, Daxiao Zhang, Huijun Duan & Yongsheng Tao

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  1. **aolin Ma
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  2. Liqing Feng
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  8. Yongsheng Tao
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Contributions

YT and HD designed the experiment. XM, AT, LF, YH, and DZ collected the phenotypes and performed the data analysis. YT and HD wrote the manuscript. XM, AT, LF, TZ, YH, and DZ edited the manuscript. All authors have read and approved the manuscript.

Corresponding authors

Correspondence to Huijun Duan or Yongsheng Tao.

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The authors declare that the research was conducted in the absence of any commercial or financial relationship that could be construed as a potential conflict of interest.

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This study does not include human or animal subjects.

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Communicated by Thomas Lubberstedt.

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Ma, X., Feng, L., Tao, A. et al. Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines. Theor Appl Genet 136, 259 (2023). https://doi.org/10.1007/s00122-023-04495-8

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