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| Status |
Public on Mar 02, 2022 |
| Title |
Identification of the potential genes regulating seed germination speed in maize |
| Organism |
Zea mays |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: To identify the potential genes that regulate seed germination speed in maize, we performed a time-series transcriptome analysis with two inbred maize lines (72-3 fast germination, F9721 slow germination) during the seed germination and compared the differentially expressed genes (DEGs) in transcriptome with genes identified by GWAS
Methods: Methods: mRNA profiles of two maize inbred lines 72-3 and F9721 showing divergent seed germination at six stages during germination were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed at the gene level. Hisat2 was used to align clean reads to maize B73 reference genome, and HTSeq was used to count transcript abundance. DESeq2 models were used to compare DEGs at each germination stage within or between samples
Results: Comparative transcriptome study identified 12 hours after imbibition (HAI) as the critical stage responsible for the variation of germination speed. The DEGs between 72-3 and F9721 were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, oxidoreductase activity pathways, hormone signal transduction, and amino acid transporter activity pathways
Conclusions: Combined with evidence from gene expression data, GWAS, and gene synteny with other model species, we finally anchored three genes as the likely candidate genes regulating germination speed in maize
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| Overall design |
RNAseq for two inbred maize lines with divergent seed germination speed and compare the DEGs at critical germination stage with candidate genes identified using GWAS
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| Contributor(s) |
Zhang H, Zang J, Liu J |
| Citation(s) |
35214886 |
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| Submission date |
Jan 08, 2022 |
| Last update date |
Mar 03, 2022 |
| Contact name |
Zhang Huairen |
| E-mail(s) |
samhuairen@gmail.com
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| Phone |
8618911398324
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| Organization name |
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
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| Street address |
No. 1 West Beichen Road
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platforms (1) |
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| Samples (30)
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| Relations |
| BioProject |
PRJNA795680 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE193292_RAW.tar |
4.5 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE193292_RNAseq_seed_germination_TPM.txt.gz |
5.1 Mb |
(ftp)(http) |
TXT |
| GSE193292_RNAseq_seed_germination_raw_counts.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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