Abstract
Embryogenic callus induction (ECI) is an initial step in plant cell totipotency that is essential for somatic cell regeneration. Identifying genes associated with embryogenic callus (EC) formation is critical to understand the molecular mechanism of totipotency and crop biotechnology breeding. In this study, we used a population of 177 maize (Zea mays L.) inbred lines as an association panel to investigate the percentage of embryogenic callus induction (%ECI) from their immature embryos in two independent seasons. Whole-genome resequencing of this population produced 3,786,431 high-quality single nucleotide polymorphisms (SNPs), after which a genome-wide association study (GWAS) was performed for the ECI trait. The results showed that %ECIs varied greatly from 0.00 to 98.15% among the tested inbred lines, with a broad-sense heritability of 0.71. Using the FarmCPU method, we detected 104 candidate genes within the linkage disequilibrium (LD) blocks of 57 significant SNPs (P < 0.000001). Among these genes, ZmCLE4B and Ereb83 harbored significant sense mutations, and inbred lines with different alleles of these genes showed significant differences in ECI (P < 0.00001). Expression analyses of these two genes in five EC-induction stages in two ECI-contradictory inbred lines revealed that different alleles of the genes behave divergently in response to callus induction culture. Additionally, using an intermate population, we noted that ZmCLE4B plants with different homozygous alleles were phenotypically different (P < 0.01). Taken together, the current results suggest that ZmCLE4B is likely a major factor in ECI.
Key message
A total of 104 candidate genes for embryogenic callus induction (ECI) were identified, and molecular evidence showed that the ZmCLE4B gene is likely a major factor in ECI.
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Data availability
The phenotypic data analyzed in the study is included in the supplemental files, and the resequencing data used in the GWAS is available from the corresponding author upon reasonable request.
Code availability
Not applicable.
Abbreviations
- EC:
-
Embryogenic callus
- ECI:
-
Embryogenic callus induction
- %ECI:
-
Percentage of embryogenic callus induction
- NEC:
-
Nonembryogenic callus
- SNP:
-
Single nucleotide polymorphism
- GWAS:
-
Genome-wide association study
- LD:
-
Linkage disequilibrium
- CGAS:
-
Candidate gene association study
- PCA:
-
Principal component analysis
- BLUP:
-
Best linear unbiased prediction
- FarmCPU:
-
Fixed and random model circulating probability unification
- GLM:
-
General linear model
- qPCR:
-
Quantitative real-time PCR
- RIL:
-
Recombinant inbred lines
- QTL:
-
Quantitative trait loci
- SSR:
-
Simple sequence repeat
- RFLP:
-
Restriction fragment length polymorphism
- RNAi:
-
RNA interference
- miRNA:
-
MicroRNA
- siRNA: CLE:
-
CLAVATA3/Embryo surrounding region-related
- WUS:
-
WUSCHEL
- STM:
-
Shoot meristemless
- CLV1:
-
CLAVATA1
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Acknowledgements
We are grateful to Prof. Haichun Jing and his laboratory at the Chinese Academy of Sciences (Beijing, China) for kindly providing the maize association panel and its genotypes for use in this study (unpublished data).
Funding
This work was supported by the National Natural Science Foundation of China (Grant No. 31901067) and the Agricultural Science and Technology Innovation Program of Jilin Province (Grant No. C92070501).
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LD conceived the idea, performed the experiments, analyzed the data and wrote the manuscript. SH assisted with the experiments. SH and YZ provided support for the bioinformatics analysis. DH revised the manuscript. All the authors have read and approved this manuscript.
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Dai, L., Han, S., Zhang, Y. et al. Genetic architecture of embryogenic callus induction in maize from the perspective of population genomics. Plant Cell Tiss Organ Cult 150, 345–359 (2022). https://doi.org/10.1007/s11240-022-02284-7
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DOI: https://doi.org/10.1007/s11240-022-02284-7